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%%% BibTeX-file{
%%% author = "Nelson H. F. Beebe",
%%% version = "1.13",
%%% date = "21 May 2014",
%%% time = "14:43:44 MDT",
%%% filename = "jacm.bib",
%%% address = "University of Utah
%%% Department of Mathematics, 110 LCB
%%% 155 S 1400 E RM 233
%%% Salt Lake City, UT 84112-0090
%%% USA",
%%% telephone = "+1 801 581 5254",
%%% FAX = "+1 801 581 4148",
%%% checksum = "09730 9236 50795 478441",
%%% email = "beebe at math.utah.edu, beebe at acm.org,
%%% beebe at computer.org (Internet)",
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%%% keywords = "ACM Journal of Experimental Algorithmics;
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%%% docstring = "This is a COMPLETE bibliography of the
%%% ACM Journal of Experimental Algorithmics
%%% (CODEN none, ISSN 1084-6654). The journal
%%% appears once a year, and has no separate
%%% issue numbers.
%%%
%%% At version 1.13, the COMPLETE year coverage
%%% looked like this:
%%%
%%% 1996 ( 4) 2003 ( 6) 2010 ( 12)
%%% 1997 ( 5) 2004 ( 6) 2011 ( 18)
%%% 1998 ( 9) 2005 ( 15) 2012 ( 2)
%%% 1999 ( 8) 2006 ( 17) 2013 ( 12)
%%% 2000 ( 17) 2007 ( 0) 2014 ( 2)
%%% 2001 ( 10) 2008 ( 29)
%%% 2002 ( 12) 2009 ( 28)
%%%
%%% Article: 212
%%%
%%% Total entries: 212
%%%
%%% The author will be grateful for reports of
%%% any errors or omissions in this file; they
%%% will be corrected in future editions.
%%%
%%% Articles and letters or corrections that
%%% comment on them are cross-referenced in both
%%% directions, so that citation of one of them
%%% will automatically include the others.
%%%
%%% The ACM maintains Web pages for this journal at
%%%
%%% http://portal.acm.org/browse_dl.cfm?idx=J430
%%%
%%% That data has been automatically converted
%%% to BibTeX form, corrected for spelling and
%%% page number errors, and merged into this
%%% file.
%%%
%%% ACM copyrights explicitly permit abstracting
%%% with credit, so article abstracts, keywords,
%%% and subject classifications have been
%%% included in this bibliography wherever
%%% available. Article reviews have been
%%% omitted, until their copyright status has
%%% been clarified.
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%%%
%%% In this bibliography, entries are sorted in
%%% publication order, with the help of
%%% ``bibsort -byvolume''. The bibsort utility,
%%% and several related programs for
%%% bibliography maintenance, is available on
%%% ftp.math.utah.edu in /pub/tex/bib, and at
%%% other Internet sites which mirror it,
%%% including the Comprehensive TeX Archive
%%% Network (CTAN); the command `finger
%%% ctantug.org' will produce a list of
%%% CTAN hosts.
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%%% Acknowledgement abbreviations:
@String{ack-nhfb = "Nelson H. F. Beebe,
University of Utah,
Department of Mathematics, 110 LCB,
155 S 1400 E RM 233,
Salt Lake City, UT 84112-0090, USA,
Tel: +1 801 581 5254,
FAX: +1 801 581 4148,
e-mail: \path|beebe@math.utah.edu|,
\path|beebe@acm.org|,
\path|beebe@computer.org| (Internet),
URL: \path|http://www.math.utah.edu/~beebe/|"}
%%% ====================================================================
%%% Journal abbreviations:
@String{j-ACM-J-EXP-ALGORITHMICS = "ACM Journal of Experimental Algorithmics"}
%%% ====================================================================
%%% Bibliography entries, sorted in publication order.
@Article{Knuth:1996:II,
author = "Donald E. Knuth",
title = "Irredundant intervals",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "1",
pages = "1:1--1:??",
month = "????",
year = "1996",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/235141.235146",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:01:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "This expository note presents simplifications of a
theorem due to Gy{\H{o}}ri and an algorithm due to
Franzblau and Kleitman: Given a family $F$ of $m$
intervals on a linearly ordered set of n elements, we
can construct in $O(m + n)^2$ steps an irredundant
subfamily having maximum cardinality, as well as a
generating family having minimum cardinality. The
algorithm is of special interest because it solves a
problem analogous to finding a maximum independent set,
but on a class of objects that is more general than a
matroid. This note is also a complete, runnable
computer program, which can be used for experiments in
conjunction with the public-domain software of The
Stanford GraphBase.",
acknowledgement = ack-nhfb,
articleno = "1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Gittleman:1996:PSS,
author = "Arthur Gittleman",
title = "Predicting string search speed",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "1",
pages = "2:1--2:??",
month = "????",
year = "1996",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/235141.235147",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:01:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "String search is fundamental in many text processing
applications. Sunday recently gave several algorithms
to find the first occurrence of a pattern string as a
substring of a text, providing experimental data from
searches in a text of about 200K characters to support
his claim that his algorithms are faster than the
standard Boyer--Moore algorithm. We present a
methodology for the average-case analysis of the
performance of string search algorithms---for such
algorithms, a worst-case analysis does not yield much
useful information, since the performance of the
algorithm is directly affected by such characteristics
as the size of the character set, the character
frequencies, and the structure of the text. Knuth
described a finite automaton which can be used to save
information about character comparisons. Baeza-Yates,
Gonnet, and Regnier gave a probabilistic analysis of
the worst- and average-case behavior of a string search
algorithm based upon such an automaton. We construct
Knuth automata to model Sunday's algorithms and use the
methods of Baeza-Yates et al. to obtain an average-case
analysis which confirms Sunday's experimental data.",
acknowledgement = ack-nhfb,
articleno = "2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Bader:1996:PPA,
author = "David A. Bader and David R. Helman and Joseph
J{\'a}J{\'a}",
title = "Practical parallel algorithms for personalized
communication and integer sorting",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "1",
pages = "3:1--3:??",
month = "????",
year = "1996",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/235141.235148",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:01:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "A fundamental challenge for parallel computing is to
obtain high-level, architecture independent, algorithms
which efficiently execute on general-purpose parallel
machines. With the emergence of message passing
standards such as MPI, it has become easier to design
efficient and portable parallel algorithms by making
use of these communication primitives. While existing
primitives allow an assortment of collective
communication routines, they do not handle an important
communication event when most or all processors have
non-uniformly sized personalized messages to exchange
with each other. We focus in this paper on the
h-relation personalized communication whose efficient
implementation will allow high performance
implementations of a large class of algorithms. While
most previous h-relation algorithms use randomization,
this paper presents a new deterministic approach for
h-relation personalized communication with
asymptotically optimal complexity for h>p$^2$. As an
application, we present an efficient algorithm for
stable integer sorting. The algorithms presented in
this paper have been coded in Split-C and run on a
variety of platforms, including the Thinking Machines
CM-5, IBM SP-1 and SP-2, Cray Research T3D, Meiko
Scientific CS-2, and the Intel Paragon. Our
experimental results are consistent with the
theoretical analysis and illustrate the scalability and
efficiency of our algorithms across different
platforms. In fact, they seem to outperform all similar
algorithms known to the authors on these platforms.",
acknowledgement = ack-nhfb,
articleno = "3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{LaMarca:1996:ICP,
author = "Anthony LaMarca and Richard Ladner",
title = "The influence of caches on the performance of heaps",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "1",
pages = "4:1--4:??",
month = "????",
year = "1996",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/235141.235145",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:01:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "As memory access times grow larger relative to
processor cycle times, the cache performance of
algorithms has an increasingly large impact on overall
performance. Unfortunately, most commonly used
algorithms were not designed with cache performance in
mind. This paper investigates the cache performance of
implicit heaps. We present optimizations which
significantly reduce the cache misses that heaps incur
and improve their overall performance. We present an
analytical model called collective analysis that allows
cache performance to be predicted as a function of both
cache configuration and algorithm configuration. As
part of our investigation, we perform an approximate
analysis of the cache performance of both traditional
heaps and our improved heaps in our model. In addition
empirical data is given for five architectures to show
the impact our optimizations have on overall
performance. We also revisit a priority queue study
originally performed by Jones [25]. Due to the
increases in cache miss penalties, the relative
performance results we obtain on today's machines
differ greatly from the machines of only ten years ago.
We compare the performance of implicit heaps, skew
heaps and splay trees and discuss the difference
between our results and Jones's.",
acknowledgement = ack-nhfb,
articleno = "4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Buchsbaum:1997:AAS,
author = "Adam L. Buchsbaum and Raffaele Giancarlo",
title = "Algorithmic aspects in speech recognition: an
introduction",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "2",
pages = "1:1--1:??",
month = "????",
year = "1997",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/264216.264219",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:14 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Speech recognition is an area with a considerable
literature, but there is little discussion of the topic
within the computer science algorithms literature. Many
computer scientists, however, are interested in the
computational problems of speech recognition. This
paper presents the field of speech recognition and
describes some of its major open problems from an
algorithmic viewpoint. Our goal is to stimulate the
interest of algorithm designers and experimenters to
investigate the algorithmic problems of effective
automatic speech recognition.",
acknowledgement = ack-nhfb,
articleno = "1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "automata theory; graph searching",
}
@Article{Battiti:1997:RSH,
author = "Roberto Battiti and Marco Protasi",
title = "Reactive search, a history-sensitive heuristic for
{MAX}-{SAT}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "2",
pages = "2:1--2:??",
month = "????",
year = "1997",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/264216.264220",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:14 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The Reactive Search (RS) method proposes the
integration of a simple history-sensitive (machine
learning) scheme into local search for the on-line
determination of free parameters. In this paper a new
RS algorithm is proposed for the approximated solution
of the Maximum Satisfiability problem: a component
based on local search with temporary prohibitions (Tabu
Search) is complemented with a reactive scheme that
determines the appropriate value of the prohibition
parameter by monitoring the Hamming distance along the
search trajectory. The proposed algorithm (H-RTS) can
therefore be characterized as a dynamic version of Tabu
Search. In addition, the non-oblivious functions
recently introduced in the framework of approximation
algorithms are used to discover a better local optimum
in the initial part of the search. The algorithm is
developed in two phases. First the bias-diversification
properties of individual candidate components are
analyzed by extensive empirical evaluation, then a
reactive scheme is added to the winning component,
based on Tabu Search. The final tests on a benchmark of
random MAX-3-SAT and MAX-4-SAT problems demonstrate the
superiority of H-RTS with respect to alternative
heuristics.",
acknowledgement = ack-nhfb,
articleno = "2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Smith:1997:EHF,
author = "Bradley J. Smith and Gregory L. Heileman and Chaouki
Abdallah",
title = "The exponential hash function",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "2",
pages = "3:1--3:??",
month = "????",
year = "1997",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/264216.264221",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:14 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this paper an efficient open address hash function
called exponential hashing is developed. The motivation
for this hash function resulted from our ongoing
efforts to apply dynamical systems theory to the study
of hashing; however, the analysis conducted in this
paper is primarily based on traditional number theory.
Proofs of optimal table parameter choices are provided
for a number of hash functions. We also demonstrate
experimentally that exponential hashing essentially
matches the performance of a widely-used optimal double
hash function for uniform data distributions, and
performs significantly better for nonuniform data
distributions. We show that exponential hashing
exhibits a higher integer Lyapunov exponent and entropy
than double hashing for initial data probes, which
offers one explanation for its improved performance on
nonuniform data distributions.",
acknowledgement = ack-nhfb,
articleno = "3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "ADT; chaos; dynamic dictionary; dynamical systems
theory; exponential hashing; Lyapunov exponent; number
theory",
}
@Article{Purchase:1997:ESB,
author = "H. C. Purchase and R. F. Cohen and M. I. James",
title = "An experimental study of the basis for graph drawing
algorithms",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "2",
pages = "4:1--4:??",
month = "????",
year = "1997",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/264216.264222",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:14 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Designers of graph drawing algorithms and systems
claim to illuminate application data by producing
layouts that optimise measurable aesthetic qualities.
Examples of these aesthetics include symmetry (where
possible, a symmetrical view of the graph should be
displayed), minimise arc crossing(the number of arc
crossings in the display should be minimised), and
minimise bends (the total number of bends in polyline
arcs should be minimised).The aim of this paper is to
describe our work to validate these claims by
performing empirical studies of human understanding of
graphs drawn using various layout aesthetics. This work
is important since it helps indicate to algorithm and
system designers what are the aesthetic qualities most
important to aid understanding, and consequently to
build more effective systems.",
acknowledgement = ack-nhfb,
articleno = "4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "human-computer interaction",
}
@Article{Alberts:1997:ESD,
author = "David Alberts and Giuseppe Cattaneo and Giuseppe F.
Italiano",
title = "An empirical study of dynamic graph algorithms",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "2",
pages = "5:1--5:??",
month = "????",
year = "1997",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/264216.264223",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:14 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The contributions of this paper are both of
theoretical and of experimental nature. From the
experimental point of view, we conduct an empirical
study on some dynamic connectivity algorithms which
where developed recently. In particular, the following
implementations were tested and compared with simple
algorithms: simple sparsification by Eppstein et al.
and the recent randomized algorithm by Henzinger and
King. In our experiments, we considered both random and
non-random inputs. Moreover, we present a simplified
variant of the algorithm by Henzinger and King, which
for random inputs was always faster than the original
implementation. For non-random inputs, simple
sparsification was the fastest algorithm for small
sequences of updates; for medium and large sequences of
updates, the original algorithm by Henzinger and King
was faster. From the theoretical point of view, we
analyze the average case running time of simple
sparsification and prove that for dynamic random graphs
its logarithmic overhead vanishes.",
acknowledgement = ack-nhfb,
articleno = "5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Hemaspaandra:1998:PBA,
author = "Lane A. Hemaspaandra and Kulathur S. Rajasethupathy
and Prasanna Sethupathy and Marius Zimand",
title = "Power balance and apportionment algorithms for the
{United States Congress}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "3",
pages = "1:1--1:??",
month = "????",
year = "1998",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/297096.297106",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We measure the performance, in the task of
apportioning the Congress of the United States, of an
algorithm combining a heuristic-driven (simulated
annealing) search with an exact-computation dynamic
programming evaluation of the apportionments visited in
the search. We compare this with the actual algorithm
currently used in the United States to apportion
Congress, and with a number of other algorithms that
have been proposed. We conclude that on every set of
census data in this country's history, the
heuristic-driven apportionment provably yields far
fairer apportionments than those of any of the other
algorithm considered, including the algorithm currently
used by the United States for Congressional
apportionment.",
acknowledgement = ack-nhfb,
articleno = "1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "apportionment algorithms; power indices; simulated
annealing",
}
@Article{Cho:1998:WBL,
author = "Seonghun Cho and Sartaj Sahni",
title = "Weight-biased leftist trees and modified skip lists",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "3",
pages = "2:1--2:??",
month = "????",
year = "1998",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/297096.297111",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We propose the weight biased leftist tree as an
alternative to traditional leftist trees [CRAN72] for
the representation of mergeable priority queues. A
modified version of skip lists [PUGH90] that uses fixed
size nodes is also proposed. Experimental results show
our modified skip list structure is faster than the
original skip list structure for the representation of
dictionaries. Experimental results comparing weight
biased leftist trees and competing priority queue
structures are presented.",
acknowledgement = ack-nhfb,
articleno = "2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "dictionary; leftist trees; priority queues; skip
lists",
}
@Article{Yan:1998:LBE,
author = "Yong Yan and Xiaodong Zhang",
title = "Lock bypassing: an efficient algorithm for
concurrently accessing priority heaps",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "3",
pages = "3:1--3:??",
month = "????",
year = "1998",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/297096.297116",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The heap representation of priority queues is one of
the most widely used data structures in the design of
parallel algorithms. Efficiently exploiting the
parallelism of a priority heap has significant
influence on the efficiency of a wide range of
applications and parallel algorithms. In this paper, we
propose an aggressive priority heap operating
algorithm, called the lock bypassing algorithm (LB) on
shared memory systems. This algorithm minimizes
interference of concurrent enqueue and dequeue
operations on priority heaps while keeping the strict
priority property: a dequeue always returns the minimum
of a heap. The unique idea that distinguishes the LB
algorithm from previous concurrent algorithms on
priority heaps is the use of locking-on-demand and
lock-bypassing techniques to minimize locking
granularity and to maximize parallelism. The LB
algorithm allows an enqueue operation to bypass the
locks along its insertion path until it reaches a
possible place where it can perform the insertion.
Meanwhile a dequeue operation also makes its locking
range and locking period as small as possible by
carefully tuning its execution procedure. The LB
algorithm is shown to be correct in terms of deadlock
freedom and heap consistency. The performance of the LB
algorithm was evaluated analytically and experimentally
in comparison with previous algorithms. Analytical
results show that the LB algorithm reduces by half the
number of locks waited for in the worst case by
previous algorithms. The experimental results show that
the LB algorithm outperforms previously designed
algorithms by up to a factor of 2 in hold time.",
acknowledgement = ack-nhfb,
articleno = "3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "aggressive locking; parallel algorithm; performance
evaluation; priority heap; shared-memory system",
}
@Article{Helman:1998:NDP,
author = "David R. Helman and Joseph J{\'a}J{\'a} and David A.
Bader",
title = "A new deterministic parallel sorting algorithm with an
experimental evaluation",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "3",
pages = "4:1--4:??",
month = "????",
year = "1998",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/297096.297128",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We introduce a new deterministic parallel sorting
algorithm for distributed memory machines based on the
regular sampling approach. The algorithm uses only two
rounds of regular all-to-all personalized communication
in a scheme that yields very good load balancing with
virtually no overhead. Moreover, unlike previous
variations, our algorithm efficiently handles the
presence of duplicate values without the overhead of
tagging each element with a unique identifier. This
algorithm was implemented in SPLIT-C and run on a
variety of platforms, including the Thinking Machines
CM-5, the IBM SP-2-WN, and the Cray Research T3D. We
ran our code using widely different benchmarks to
examine the dependence of our algorithm on the input
distribution. Our experimental results illustrate the
efficiency and scalability of our algorithm across
different platforms. In fact, the performance compares
closely to that of our random sample sort algorithm,
which seems to outperform all similar algorithms known
to the authors on these platforms. Together, their
performance is nearly invariant over the set of input
distributions, unlike previous efficient algorithms.
However, unlike our randomized sorting algorithm, the
performance and memory requirements of our regular
sorting algorithm can be deterministically
guaranteed.",
acknowledgement = ack-nhfb,
articleno = "4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "generalized sorting; integer sorting; parallel
algorithms; parallel performance; sorting by regular
sampling",
}
@Article{Frigioni:1998:EAD,
author = "Daniele Frigioni and Mario Ioffreda and Umberto Nanni
and Giulio Pasqualone",
title = "Experimental analysis of dynamic algorithms for the
single",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "3",
pages = "5:1--5:??",
month = "????",
year = "1998",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/297096.297147",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this paper we propose the first experimental study
of the fully dynamic single-source shortest-paths
problem on directed graphs with positive real edge
weights. In particular, we perform an experimental
analysis of three different algorithms: Dijkstra's
algorithm, and the two output bounded algorithms
proposed by Ramalingam and Reps in [30] and by
Frigioni, Marchetti-Spaccamela and Nanni in [18],
respectively. The main goal of this paper is to provide
a first experimental evidence for: (a) the
effectiveness of dynamic algorithms for shortest paths
with respect to a traditional static approach to this
problem; (b) the validity of the theoretical model of
output boundedness to analyze dynamic graph algorithms.
Beside random generated graphs, useful to capture the
'asymptotic' behavior of the algorithms, we also
developed experiments by considering a widely used
graph from the real world, i.e., the Internet graph.",
acknowledgement = ack-nhfb,
articleno = "5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "dynamic algorithms; experimental analysis of
algorithms; shortest paths",
}
@Article{Magun:1998:GMA,
author = "Jakob Magun",
title = "Greeding matching algorithms, an experimental study",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "3",
pages = "6:1--6:??",
month = "????",
year = "1998",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/297096.297131",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We conduct an experimental study of several greedy
algorithms for finding large matchings in graphs.
Further we propose a new graph reduction, called
$k$-Block Reduction, and present two novel algorithms
using extra heuristics in the matching step and
$k$-Block Reduction for $k = 3$. Greedy matching
algorithms can be used for finding a good approximation
of the maximum matching in a graph $G$ if no exact
solution is required, or as a fast preprocessing step
to some other matching algorithm. The studied greedy
algorithms run in $O(m)$. They are easy to implement
and their correctness and their running time are simple
to prove. Our experiments show that a good greedy
algorithm looses on average at most one edge on random
graphs from $G(n,p)$ with up to 10,000 vertices.
Furthermore the experiments show for which edge
densities in random graphs the maximum matching problem
is difficult to solve.",
acknowledgement = ack-nhfb,
articleno = "6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Andersson:1998:IR,
author = "Arne Andersson and Stefan Nilsson",
title = "Implementing radixsort",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "3",
pages = "7:1--7:??",
month = "????",
year = "1998",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/297096.297136",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present and evaluate several optimization and
implementation techniques for string sorting. In
particular, we study a recently published radix sorting
algorithm, Forward radixsort, that has a provably good
worst-case behavior. Our experimental results indicate
that radix sorting is considerably faster (often more
than twice as fast) than comparison-based sorting
methods. This is true even for small input sequences.
We also show that it is possible to implement a
radixsort with good worst-case running time without
sacrificing average-case performance. Our
implementations are competitive with the best
previously published string sorting programs.",
acknowledgement = ack-nhfb,
articleno = "7",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "adaptive radixsort; algorithms; forward radixsort;
radix sorting; sorting; string sorting",
}
@Article{Cherkassky:1998:APC,
author = "Boris V. Cherkassky and Andrew V. Goldberg and Paul
Martin and Joao C. Setubal and Jorge Stolfi",
title = "Augment or push: a computational study of bipartite
matching and unit-capacity flow algorithms",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "3",
pages = "8:1--8:??",
month = "????",
year = "1998",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/297096.297140",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We conduct a computational study of unit capacity flow
and bipartite matching algorithms. Our goal is to
determine which variant of the push-relabel method is
most efficient in practice and to compare push-relabel
algorithms with augmenting path algorithms. We have
implemented and compared three push-relabel algorithms,
three augmenting-path algorithms (one of which is new),
and one augment-relabel algorithm. The depth-first
search augmenting path algorithm was thought to be a
good choice for the bipartite matching problem, but our
study shows that it is not robust (meaning that it is
not consistently fast on all or most inputs). For the
problems we study, our implementations of the FIFO and
lowest-level selection push-relabel algorithms have the
most robust asymptotic rate of growth and work best
overall. Augmenting path algorithms, although not as
robust, on some problem classes are faster by a
moderate constant factor. Our study includes several
new problem families and input graphs with as many as
$5 \times 105$ vertices.",
acknowledgement = ack-nhfb,
articleno = "8",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Radzik:1998:IDT,
author = "Tomasz Radzik",
title = "Implementation of dynamic trees with in-subtree
operations",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "3",
pages = "9:1--9:??",
month = "????",
year = "1998",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/297096.297144",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We describe an implementation of dynamic trees with
'in-subtree' operations. Our implementation follows
Sleator and Tarjan's framework of dynamic-tree
implementations based on splay trees. We consider the
following two examples of 'in-subtree' operations. (a)
For a given node v, find a node with the minimum key in
the subtree rooted at v. (b) For a given node v, find a
random node with key X in the subtree rooted at v
(value X is fixed throughout the whole computation).
The first operation may provide support for edge
deletions in the dynamic minimum spanning tree problem.
The second one may be useful in local search methods
for degree-constrained minimum spanning tree problems.
We conducted experiments with our dynamic-tree
implementation within these two contexts, and the
results suggest that this implementation may lead to
considerably faster codes than straightforward
approaches do.",
acknowledgement = ack-nhfb,
articleno = "9",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; design; dynamic minimum spanning tree;
dynamic trees; experimentation; performance; splay
trees",
}
@Article{Burke:1999:MAS,
author = "E. K. Burke and A. J. Smith",
title = "A memetic algorithm to schedule planned maintenance
for the national grid",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "4",
pages = "1:1--1:??",
month = "????",
year = "1999",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/347792.347801",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:52 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The combination of local search operators, problem
specific information and a genetic algorithm has
provided very good results in certain scheduling
problems, particularly in timetabling and maintenance
scheduling problems. The resulting algorithm from this
hybrid approach has been termed a Memetic Algorithm.
This paper investigates the use of such an algorithm
for the scheduling of transmission line maintenance for
a known problem that has been addressed in the
literature using a combination of a genetic algorithm
and greedy optimisers. This problem is concerned with
the scheduling of maintenance for an electricity
transmission network where every transmission line must
be maintained once within a specified time period. The
objective is to avoid situations where sections of the
network are disconnected, and to minimise the
overloading of lines which are in service. In this
paper we look at scheduling maintenance for the South
Wales region of the national transmission network. We
present and discuss, in some detail, a memetic
algorithm that incorporates local search operators
including tabu search and simulated annealing. A
comparison is made both with the results from previous
work, and against a selection of optimising techniques.
The approach presented in this paper shows a
significant improvement over previously published
results on previously tackled problems. We also present
results on another problem which has not been tackled
in the literature but which is closer to the real world
maintenance scheduling problems faced by such companies
as The National Grid Company plc using the South Wales
region.",
acknowledgement = ack-nhfb,
articleno = "1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "heuristics; hill climbing; maintenance scheduling;
memetic algorithms; simulated annealing; tabu search",
}
@Article{Kim:1999:NSP,
author = "Sun Kim",
title = "A new string-pattern matching algorithm using
partitioning and hashing efficiently",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "4",
pages = "2:1--2:??",
month = "????",
year = "1999",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/347792.347803",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:52 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this paper, we present a new string-pattern
matching algorithm that partitions the text into
segments of the input pattern length and searches for
pattern occurrences using a simple hashing scheme.
Unlike the well known Boyer--Moore style algorithm, our
algorithm does not compute variable shift length, thus
providing a conceptually simpler way to search for
patterns. Empirical evaluation shows that our algorithm
runs significantly faster than Sunday's and Horspool's
extensions of the Boyer--Moore algorithm. The notion of
the non-occurrence heuristic used in our algorithm,
together with a text partitioning scheme, leads to a
simplified scheme for searching for pattern
occurrences, thus yielding better run time
performance.",
acknowledgement = ack-nhfb,
articleno = "2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Eiron:1999:MMC,
author = "N. Eiron and M. Rodeh and I. Steinwarts",
title = "Matrix multiplication: a case study of enhanced data
cache utilization",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "4",
pages = "3:1--3:??",
month = "????",
year = "1999",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/347792.347806",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:52 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Modern machines present two challenges to algorithm
engineers and compiler writers: They have superscalar,
super-pipelined structure, and they have elaborate
memory subsystems specifically designed to reduce
latency and increase bandwidth. Matrix multiplication
is a classical benchmark for experimenting with
techniques used to exploit machine architecture and to
overcome the limitations of contemporary memory
subsystems. This research aims at advancing the state
of the art of algorithm engineering by balancing
instruction level parallelism, two levels of data
tiling, copying to provably avoid any cache conflicts,
and prefetching in parallel to computational
operations, in order to fully exploit the memory
bandwidth. Measurements on IBM's RS/6000 43P
workstation show that the resultant matrix
multiplication algorithm outperforms IBM's ESSL by
6.8-31.8\%, is less sensitive to the size of the input
data, and scales better. In this paper we introduce a
cache aware algorithm for matrix multiplication. We
also suggest generic guidelines that may be applied to
compute intensive algorithm to efficiently utilize the
data cache. We believe that some of our concepts may be
embodied in compilers.",
acknowledgement = ack-nhfb,
articleno = "3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; BLAS; blocking; cache; matrix
multiplication; performance; prefetching",
}
@Article{Erlebach:1999:EIO,
author = "T. Erlebach and K. Jansen",
title = "Efficient implementation of an optimal greedy
algorithm for wavelength assignment in directed tree
networks",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "4",
pages = "4:1--4:??",
month = "????",
year = "1999",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/347792.347808",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:52 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In all-optical networks with wavelength-division
multiplexing several connections can share a physical
link if the signals are transmitted on different
wavelengths. As the number of available wavelengths is
limited in practice, it is important to find wavelength
assignments minimizing the number of different
wavelengths used. This path coloring problem is
NP-hard, and the best known polynomial-time
approximation algorithm for directed tree networks
achieves approximation ratio $5 / 3$, which is optimal
in the class of greedy algorithms for this problem. It
is shown how the algorithm can be modified in order to
improve its running-time to $O({\rm Tec}(N,L))$ for
sets of paths with maximum load $L$ in trees with $N$
nodes, where ${\rm Tec}(n, k)$ is the time for
edge-coloring a $k$-regular bipartite graph with n
nodes. An implementation of this efficient version of
the algorithm in C++ using the LEDA class library is
described, and experimental results regarding the
running-times and the number of wavelengths used are
reported. An additional heuristic that reduces the
number of wavelengths used in the average case while
maintaining the worst-case bound of $5 L / 3$ is
described.",
acknowledgement = ack-nhfb,
articleno = "4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; bipartite edge coloring; directed tree
networks; experimentation; path coloring",
}
@Article{Huson:1999:HTR,
author = "D. Huson and S. Nettles and K. Rice and T. Warnow and
S. Yooseph",
title = "Hybrid tree reconstruction methods",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "4",
pages = "5:1--5:??",
month = "????",
year = "1999",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/347792.347812",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:52 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "A major computational problem in biology is the
reconstruction of evolutionary trees for species sets,
and accuracy is measured by comparing the topologies of
the reconstructed tree and the model tree. One of the
major debates in the field is whether large
evolutionary trees can be even approximately accurately
reconstructed from biomolecular sequences of
realistically bounded lengths (up to about 2000
nucleotides) using standard techniques (polynomial-time
distance methods, and heuristics for NP-hard
optimization problems). Using both analytical and
experimental techniques, we show that on large trees,
the two most popular methods in systematic biology,
Neighbor-Joining and Maximum Parsimony heuristics, as
well as two promising methods introduced by theoretical
computer scientists, are all likely to have significant
errors in the topology reconstruction of the model
tree. We also present a new general technique for
combining outputs of different methods (thus producing
hybrid methods), and show experimentally how one such
hybrid method has better performance than its
constituent parts.",
acknowledgement = ack-nhfb,
articleno = "5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Jacob:1999:CSR,
author = "R. Jacob and M. Marathe and K. Nagel",
title = "A computational study of routing algorithms for
realistic transportation networks",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "4",
pages = "6:1--6:??",
month = "????",
year = "1999",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/347792.347814",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:52 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We carry out an experimental analysis of a number of
shortest-path (routing) algorithms investigated in the
context of the TRANSIMS (TRansportation ANalysis and
SIMulation System) project. The main focus of the paper
is to study how various heuristic as well as exact
solutions and associated data structures affect the
computational performance of the software developed for
realistic transportation networks. For this purpose we
have used a road network representing, with high degree
of resolution, the Dallas Fort-Worth urban area. We
discuss and experimentally analyze various one-to-one
shortest-path algorithms. These include classical exact
algorithms studied in the literature as well as
heuristic solutions that are designed to take into
account the geometric structure of the input instances.
Computational results are provided to compare
empirically the efficiency of various algorithms. Our
studies indicate that a modified Dijkstra's algorithm
is computationally fast and an excellent candidate for
use in various transportation planning applications as
well as ITS related technologies.",
acknowledgement = ack-nhfb,
articleno = "6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "design and analysis of algorithms; experimental
analysis; network design; shortest-paths algorithms;
transportation planning",
}
@Article{Muller-Hannemann:1999:IWM,
author = "M. M{\"u}ller-Hannemann and A. Schwartz",
title = "Implementing weighted $b$-matching algorithms: towards
a flexible software design",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "4",
pages = "7:1--7:??",
month = "????",
year = "1999",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/347792.347815",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:52 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present a case study on the design of an
implementation of a fundamental combinatorial
optimization problem: weighted b-matching. Although
this problem is well-understood in theory and efficient
algorithms are known, only little experience with
implementations is available. This study was motivated
by the practical need for an efficient b-matching
solver as a subroutine in our approach to a mesh
refinement problem in computer-aided design (CAD).The
intent of this paper is to demonstrate the importance
of flexibility and adaptability in the design of
complex algorithms, but also to discuss how such goals
can be achieved for matching algorithms by the use of
design patterns. Starting from the basis of the famous
blossom algorithm we explain how to exploit in
different ways the flexibility of our software design
which allows an incremental improvement of efficiency
by exchanging subalgorithms and data structures. In a
comparison with a code by Miller and Pekny we also
demonstrate that our implementation is even without
fine-tuning very competitive. Our code is significantly
faster, with improvement factors ranging between 15 and
466 on TSPLIB instances.",
acknowledgement = ack-nhfb,
articleno = "7",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; b-matching; blossom algorithm; design
patterns; experimentation; object-oriented design;
software design",
}
@Article{Schwerdt:1999:CWT,
author = "J. Schwerdt and M. Smid and J. Majhi and R. Janardan",
title = "Computing the width of a three-dimensional point set:
an experimental study",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "4",
pages = "8:1--8:??",
month = "????",
year = "1999",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/347792.347816",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:02:52 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We describe a robust, exact, and efficient
implementation of an algorithm that computes the width
of a three-dimensional point set. The algorithm is
based on efficient solutions to problems that are at
the heart of computational geometry: three-dimensional
convex hulls, point location in planar graphs, and
computing intersections between line segments. The
latter two problems have to be solved for planar graphs
and segments on the unit sphere, rather than in the
two-dimensional plane. The implementation is based on
LEDA, and the geometric objects are represented using
exact rational arithmetic.",
acknowledgement = ack-nhfb,
articleno = "8",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "computational geometry; implementation; layered
manufacturing; spherical geometry",
}
@Article{Eppstein:2000:FHC,
author = "David Eppstein",
title = "Fast hierarchical clustering and other applications of
dynamic closest pairs",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "1:1--1:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.351829",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We develop data structures for dynamic closest pair
problems with arbitrary distance functions, that do not
necessarily come from any geometric structure on the
objects. Based on a technique previously used by the
author for Euclidean closest pairs, we show how to
insert and delete objects from an n-object set,
maintaining the closest pair, in $O(n \log^2 n)$ time
per update and $O(n)$ space. With quadratic space, we
can instead use a quadtree-like structure to achieve an
optimal time bound, $O(n)$ per update. We apply these
data structures to hierarchical clustering, greedy
matching, and TSP heuristics, and discuss other
potential applications in machine learning, Gr{\"o}bner
bases, and local improvement algorithms for partition
and placement problems. Experiments show our new
methods to be faster in practice than previously used
heuristics.",
acknowledgement = ack-nhfb,
articleno = "1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "conga line data structure; matching; nearest-neighbor
heuristic; quadtree; TSP",
}
@Article{Chong:2000:CBD,
author = "Kyn-Rak Chong and Sartaj Sahni",
title = "Correspondence-based data structures for double-ended
priority queues",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "2:1--2:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.351828",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We describe three general methods--total, dual, and
leaf correspondence--that may be used to derive
efficient double-ended priority queues from
single-ended priority queues. These methods are
illustrated by developing double-ended priority queues
based on the classical heap. Experimental results
indicate that the leaf-correspondence method generally
leads to a faster double-ended priority queue than
either total or dual correspondence. On randomly
generated test sets, however, the splay tree
outperforms the tested correspondence-based
double-ended priority queues.",
acknowledgement = ack-nhfb,
articleno = "2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "correspondence-based data structures; double-ended
priority queues; heaps; leftist trees; runtime
efficiency; splay trees",
}
@Article{Xiao:2000:IMP,
author = "Li Xiao and Xiaodong Zhang and Stefan A. Kubricht",
title = "Improving memory performance of sorting algorithms",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "3:1--3:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384245",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Memory hierarchy considerations during sorting
algorithm design and implementation play an important
role in significantly improving execution performance.
Existing algorithms mainly attempt to reduce capacity
misses on direct-mapped caches. To reduce other types
of cache misses that occur in the more common
set-associative caches and the TLB, we restructure the
mergesort and quicksort algorithms further by
integrating tiling, padding, and buffering techniques
and by repartitioning the data set. Our study shows
that substantial performance improvements can be
obtained using our new methods.",
acknowledgement = ack-nhfb,
articleno = "3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "caches; memory performance; mergesort; quicksort;
TLB",
}
@Article{Navarro:2000:FFS,
author = "Gonzalo Navarro and Mathieu Raffinot",
title = "Fast and flexible string matching by combining
bit-parallelism and suffix automata",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "4:1--4:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384246",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The most important features of a string matching
algorithm are its efficiency and its flexibility.
Efficiency has traditionally received more attention,
while flexibility in the search pattern is becoming a
more and more important issue. Most classical string
matching algorithms are aimed at quickly finding an
exact pattern in a text, being Knuth--Morris--Pratt
(KMP) and the Boyer--Moore (BM) family the most famous
ones. A recent development uses deterministic 'suffix
automata' to design new optimal string matching
algorithms, e.g. BDM and TurboBDM. Flexibility has been
addressed quite separately by the use of
'bit-parallelism', which simulates automata in their
nondeterministic form by using bits and exploiting the
intrinsic parallelism inside the computer word, e.g.
the Shift-Or algorithm. Those algorithms are extended
to handle classes of characters and errors in the
pattern and/or in the text, their drawback being their
inability to skip text characters. In this paper we
merge bit-parallelism and suffix automata, so that a
nondeterministic suffix automaton is simulated using
bit-parallelism. The resulting algorithm, called BNDM,
obtains the best from both worlds. It is much simpler
to implement than BDM and nearly as simple as Shift-Or.
It inherits from Shift-Or the ability to handle
flexible patterns and from BDM the ability to skip
characters. BNDM is 30\%-40\% faster than BDM and up to
7 times faster than Shift-Or. When compared to the
fastest existing algorithms on exact patterns (which
belong to the BM family), BNDM is from 20\% slower to 3
times faster, depending on the alphabet size. With
respect to flexible pattern searching, BNDM is by far
the fastest technique to deal with classes of
characters and is competitive to search allowing
errors. In particular, BNDM seems very adequate for
computational biology applications, since it is the
fastest algorithm to search on DNA sequences and
flexible searching is an important problem in that
area. As a theoretical development related to flexible
pattern matching, we introduce a new automaton to
recognize suffixes of patterns with classes of
characters. To the best of our knowledge, this
automaton has not been studied before.",
acknowledgement = ack-nhfb,
articleno = "4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Caldwell:2000:DIM,
author = "Andrew E. Caldwell and Andrew B. Kahng and Igor L.
Markov",
title = "Design and implementation of move-based heuristics for
{VLSI} hypergraph partitioning",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "5:1--5:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384247",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We summarize the techniques of implementing move-based
hypergraph partitioning heuristics and evaluating their
performance in the context of VLSI design applications.
Our first contribution is a detailed software
architecture, consisting of seven reusable components,
that allows flexible, efficient and accurate assessment
of the practical implications of new move-based
algorithms and partitioning formulations. Our second
contribution is an assessment of the modern context for
hypergraph partitioning research for VLSI design
applications. In particular, we discuss the current
level of sophistication in implementation know-how and
experimental evaluation, and we note how requirements
for real-world partitioners --- if used as motivation
for research --- should affect the evaluation of
prospective contributions. Two 'implicit decisions' in
the implementation of the Fiduccia-Mattheyses heuristic
are used to illustrate the difficulty of achieving
meaningful experimental evaluation of new algorithmic
ideas.",
acknowledgement = ack-nhfb,
articleno = "5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; balanced min-cut hypergraph partitioning;
experimentation; measurement; performance; VLSI CAD",
}
@Article{Levine:2000:FRC,
author = "Matthew S. Levine",
title = "Finding the right cutting planes for the {TSP}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "6:1--6:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384248",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Given an instance of the Traveling Salesman Problem
(TSP), a reasonable way to get a lower bound on the
optimal answer is to solve a linear programming
relaxation of an integer programming formulation of the
problem. These linear programs typically have an
exponential number of constraints, but in theory they
can be solved efficiently with the ellipsoid method as
long as we have an algorithm that can take a solution
and either declare it feasible or find a violated
constraint. In practice, it is often the case that many
constraints are violated, which raises the question of
how to choose among them so as to improve performance.
For the simplest TSP formulation it is possible to
efficiently find all the violated constraints, which
gives us a good chance to try to answer this question
empirically. Looking at random two dimensional
Euclidean instances and the large instances from
TSPLIB, we ran experiments to evaluate several
strategies for picking among the violated constraints.
We found some information about which constraints to
prefer, which resulted in modest gains, but were unable
to get large improvements in performance.",
acknowledgement = ack-nhfb,
articleno = "6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; combinatorial optimization; cutting plane;
experimentation; minimum cut; performance; traveling
salesman problem",
}
@Article{Sanders:2000:FPQ,
author = "Peter Sanders",
title = "Fast priority queues for cached memory",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "7:1--7:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384249",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The cache hierarchy prevalent in todays high
performance processors has to be taken into account in
order to design algorithms that perform well in
practice. This paper advocates the adaption of external
memory algorithms to this purpose. This idea and the
practical issues involved are exemplified by
engineering a fast priority queue suited to external
memory and cached memory that is based on k-way
merging. It improves previous external memory
algorithms by constant factors crucial for transferring
it to cached memory. Running in the cache hierarchy of
a workstation the algorithm is at least two times
faster than an optimized implementation of binary heaps
and 4-ary heaps for large inputs.",
acknowledgement = ack-nhfb,
articleno = "7",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "cache; cache efficiency; data structure; external
memory; heap; implementation; multi way merging;
priority queue; secondary storage",
}
@Article{Muller-Hannemann:2000:IWM,
author = "Matthias M{\"u}ller-Hannemann and Alexander Schwartz",
title = "Implementing weighted $b$-matching algorithms:
insights from a computational study",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "8:1--8:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384250",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present an experimental study of an implementation
of weighted perfect b-matching based on the primal-dual
blossom algorithm. Although this problem is
well-understood in theory and efficient algorithms are
known, only little experience with implementations is
available. In this paper several algorithmic variants
are compared on synthetic and application problem data
of very sparse graphs. This study was motivated by the
practical need for an efficient b-matching solver for
the latter application, namely as a subroutine in our
approach to a mesh refinement problem in computer-aided
design (CAD).Linear regression and operation counting
is used to analyze code variants. The experiments
confirm that a fractional jump-start speeds up the
algorithm, they indicate that a variant based on
pairing heaps is slightly superior to a k-heap variant,
and that scaling of large b-values is not necessary,
whereas a delayed blossom shrinking heuristic
significantly improves running times only for graphs
with average degree two. The fastest variant of our
implementation appears to be highly superior to a code
by Miller and Pekny (1995).",
acknowledgement = ack-nhfb,
articleno = "8",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "b-matching; blossom algorithm; operation counting",
}
@Article{Shibuya:2000:CSP,
author = "Tetsuo Shibuya",
title = "Computing the $n \times m$ shortest path efficiently",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "9:1--9:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384251",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Computation of all the shortest paths between multiple
sources and multiple destinations on various networks
is required in many problems, such as the traveling
salesperson problem (TSP) and the vehicle routing
problem (VRP). This paper proposes new algorithms that
compute the set of shortest paths efficiently by using
the A* algorithm. The efficiency and properties of
these algorithms are examined by using the results of
experiments on an actual road network.",
acknowledgement = ack-nhfb,
articleno = "9",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "*{$<$} m shortest paths; algorithm; algorithms; A{$<$}
experimentation; GIS; n \times /sup{$>$} sup>",
}
@Article{Vishkin:2000:ELR,
author = "Dascal Vishkin and Uzi Vishkin",
title = "Experiments with list ranking for explicit
multi-threaded {(XMT)} instruction parallelism",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "10:1--10:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384252",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Algorithms for the problem of list ranking are
empirically studied with respect to the Explicit
Multi-Threaded (XMT) platform for instruction-level
parallelism (ILP). The main goal of this study is to
understand the differences between XMT and more
traditional parallel computing implementation
platforms/models as they pertain to the well studied
list ranking problem. The main two findings are: (i)
good speedups for much smaller inputs are possible and
(ii) in part, the first finding is based on a new
variant of a 1984 algorithm, called the No-Cut
algorithm. The paper incorporates analytic
(non-asymptotic) performance analysis into experimental
performance analysis for relatively small inputs. This
provides an interesting example where experimental
research and theoretical analysis complement one
another. Explicit Multi-Threading (XMT) is a
fine-grained computation framework introduced in our
SPAA'98 paper. Building on some key ideas of parallel
computing, XMT covers the spectrum from algorithms
through architecture to implementation; the main
implementation related innovation in XMT was through
the incorporation of low-overhead hardware and software
mechanisms (for more effective fine-grained
parallelism). The reader is referred to that paper for
detail on these mechanisms. The XMT platform aims at
faster single-task completion time by way of ILP.",
acknowledgement = ack-nhfb,
articleno = "10",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Werneck:2000:FMC,
author = "Renato Werneck and Jo{\~a}o Setubal and Arlindo da
Conceic{\~a}o",
title = "Finding minimum congestion spanning trees",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "11:1--11:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384253",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Given a weighted graph $G = (V, E)$, a positive
integer $k$, and a penalty function $w_p$, we want to
find $k$ spanning trees on $G$, not necessarily
disjoint, of minimum total weight, such that the weight
of each edge is subject to a penalty given by $w_p$ if
it belongs to more than one tree. The objective
function to be minimized is $\sum_{e \in E} W_e(i_e)$,
where $i_e$ is the number of times edge $e$ appears in
the solution and $W_e(i_e) = i_e w_p(e, i_e)$ is the
aggregate cost of using edge $e$ $i_e$ times. For the
case when $W_e$ is weakly convex, which should have
wide application in congestion problems, we present a
polynomial time algorithm; the algorithm's complexity
is quadratic in $k$. We also present two heuristics
with complexity linear in $k$. In an experimental study
we show that these heuristics are much faster than the
exact algorithm also in practice. These experiments
present a diverse combination of input families (four),
varying $k$ (up to 1000), and penalty functions (two).
In most inputs tested the solutions given by the
heuristics were within 1\% of optimal or much better,
especially for large $k$. The worst quality observed
was 3.2\% of optimal.",
acknowledgement = ack-nhfb,
articleno = "11",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Schulz:2000:DAL,
author = "Frank Schulz and Dorothea Wagner and Karsten Weihe",
title = "{Dijkstra}'s algorithm on-line: an empirical case
study from public railroad transport",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "12:1--12:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384254",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Traffic information systems are among the most
prominent real-world applications of Dijkstra's
algorithm for shortest paths. We consider the scenario
of a central information server in the realm of public
railroad transport on wide-area networks. Such a system
has to process a large number of on-line queries for
optimal travel connections in real time. In practice,
this problem is usually solved by heuristic variations
of Dijkstra's algorithm, which do not guarantee an
optimal result. We report results from a pilot study,
in which we focused on the travel time as the only
optimization criterion. In this study, various speed-up
techniques for Dijkstra's algorithm were analysed
empirically. This analysis was based on the timetable
data of all German trains and on a 'snapshot' of half a
million customer queries.",
acknowledgement = ack-nhfb,
articleno = "12",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Flato:2000:DIP,
author = "Eyal Flato and Dan Halperin and Iddo Hanniel and Oren
Nechushtan and Eti Ezra",
title = "The design and implementation of planar maps in
{CGAL}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "13:1--13:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384255",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Planar maps are fundamental structures in
computational geometry. They are used to represent the
subdivision of the plane into regions and have numerous
applications. We describe the planar map package of
CGAL--a Computational Geometry Algorithms Library. We
discuss its modular design and implementation. In
particular we introduce the two main classes of the
design--planar maps and topological maps that enable
the convenient separation between geometry and
topology. The modular design is implemented using a
generic programming approach. By switching a template
parameter--the geometric traits class, one can use the
same code for planar maps of different objects such as
line segments or circular arcs. More flexibility is
achieved by choosing a point location algorithm out of
three implemented algorithms or plugging in an
algorithm implemented by the user. The user of the
planar maps package can benefit both from its
flexibility and robustness. We present several examples
of geometric traits classes and point location
algorithms which demonstrate the possibility to adapt
the general package to specific needs.",
acknowledgement = ack-nhfb,
articleno = "13",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Rahman:2000:ACE,
author = "Naila Rahman and Rajeev Raman",
title = "Analysing cache effects in distribution sorting",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "14:1--14:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384256",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We study cache effects in distribution sorting
algorithms for sorting keys drawn independently at
random from a uniform distribution (`uniform keys'). We
note that the performance of a recently-published
distribution sorting algorithm, Flashsort1, which sorts
$n$ uniform floating-point keys in $O(n)$ expected
time, does not scale well with the input size due to
poor cache utilisation. We present an approximate
analysis for distribution sorting uniform keys which,
as validated by simulation results, predicts the
expected cache misses of Flashsort1 quite well. Using
this analysis, we design a multiple-pass variant of
Flashsort1 which outperforms Flashsort1 and
comparison-based algorithms on uniform floating-point
keys for moderate to large values of $n$. Using
experimental results we also show that the integer
distribution sorting algorithm MSB radix sort performs
well on both uniform integer and uniform floating-point
keys.",
acknowledgement = ack-nhfb,
articleno = "14",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "cache; efficient sorting algorithms; external-memory
algorithms; memory hierarchy",
}
@Article{Bojesen:2000:PEC,
author = "Jesper Bojesen and Jyrki Katajainen and Maz Spork",
title = "Performance engineering case study: heap
construction",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "15:1--15:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384257",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The behaviour of three methods for constructing a
binary heap on a computer with a hierarchical memory is
studied. The methods considered are the original one
proposed by Williams [1964], in which elements are
repeatedly inserted into a single heap; the improvement
by Floyd [1964], in which small heaps are repeatedly
merged to bigger heaps; and a recent method proposed,
e.g., by Fadel et al. [1999] in which a heap is built
layerwise. Both the worst-case number of instructions
and that of cache misses are analysed. It is well-known
that Floyd's method has the best instruction count. Let
N denote the size of the heap to be constructed, B the
number of elements that fit into a cache line, and let
c and d be some positive constants. Our analysis shows
that, under reasonable assumptions, repeated insertion
and layerwise construction both incur at most cN/B
cache misses, whereas repeated merging, as programmed
by Floyd, can incur more than (dN log2 B)/B cache
misses. However, for our memory-tuned versions of
repeated insertion and repeated merging the number of
cache misses incurred is close to the optimal bound
N/B. In addition to these theoretical findings, we
communicate many practical experiences which we hope to
be valuable for others doing experimental algorithmic
work.",
acknowledgement = ack-nhfb,
articleno = "15",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; binary heaps; code tuning;
experimentation; memory tuning; performance; theory",
}
@Article{Boghossian:2000:RSP,
author = "N. P. Boghossian and O. Kohlbacher and H. P. Lenhof",
title = "Rapid software prototyping in molecular modeling using
the biochemical algorithms library {(BALL)}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "16:1--16:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384258",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In the next century, virtual laboratories will play a
key role in biotechnology. Computer experiments will
not only replace some of the time-consuming and
expensive real-world experiments, but they will also
provide insights that cannot be obtained using 'wet'
experiments. The field that deals with the modeling of
atoms, molecules, and their reactions is called
Molecular Modeling. The advent of Life Sciences gave
rise to numerous new developments in this area.
However, the implementation of new simulation tools is
extremely time-consuming. This is mainly due to the
large amount of supporting code that is required in
addition to the code necessary to implement the new
idea. The only way to reduce the development time is to
reuse reliable code, preferably using object-oriented
approaches. We have designed and implemented BALL, the
first object-oriented application framework for rapid
prototyping in Molecular Modeling. By the use of the
composite design pattern and polymorphism we were able
to model the multitude of complex biochemical concepts
in a well-structured and comprehensible class
hierarchy, the BALL kernel classes. The isomorphism
between the biochemical structures and the kernel
classes leads to an intuitive interface. Since BALL was
designed for rapid software prototyping, ease of use,
extensibility, and robustness were our principal design
goals. Besides the kernel classes, BALL provides
fundamental components for import/export of data in
various file formats, Molecular Mechanics simulations,
three-dimensional visualization, and more complex ones
like a numerical solver for the Poisson--Boltzmann
equation.",
acknowledgement = ack-nhfb,
articleno = "16",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "libraries; molecular modeling; rapid software
prototyping",
}
@Article{Brengel:2000:ESP,
author = "Klaus Brengel and Andreas Crauser and Paolo Ferragina
and Ulrich Meyer",
title = "An experimental study of priority queues in external
memory",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "5",
pages = "17:1--17:??",
month = "????",
year = "2000",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/351827.384259",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:09 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this paper we compare the performance of eight
different priority queue implementations: four of them
are explicitly designed to work in an external-memory
setting, the others are standard internal-memory queues
available in the LEDA library [Mehlhorn and N{\"a}her
1999]. Two of the external-memory priority queues are
obtained by engineering known internal-memory priority
queues with the aim of achieving effective performance
on external storage devices (i.e., Radix heaps [Ahuja
et al. 1990] and array heaps [Thorup 1996]). Our
experimental framework includes some simple tests, like
random sequences of insert or delete-minimum
operations, as well as more advanced tests consisting
of intermixed sequences of update operations and
'application driven' update sequences originated by
simulations of Dijkstra's algorithm on large graph
instances. Our variegate spectrum of experimental
results gives a good picture of the features of these
priority queues, thus being helpful to anyone
interested in the use of such data structures on very
large data sets.",
acknowledgement = ack-nhfb,
articleno = "17",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Arge:2001:EAP,
author = "Lars Arge and Laura Toma and Jeffrey Scott Vitter",
title = "{I/O}-Efficient Algorithms for Problems on Grid-Based
Terrains",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "6",
pages = "1:1--1:??",
month = "????",
year = "2001",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/945394.945395",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:55 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The potential and use of Geographic Information
Systems is rapidly increasing due to the increasing
availability of massive amounts of geospatial data from
projects like NASA's Mission to Planet Earth. However,
the use of these massive datasets also exposes
scalability problems with existing GIS algorithms.
These scalability problems are mainly due to the fact
that most GIS algorithms have been designed to minimize
internal computation time, while I/O communication
often is the bottleneck when processing massive amounts
of data. In this paper, we consider I/O-efficient
algorithms for problems on grid-based terrains.
Detailed grid-based terrain data is rapidly becoming
available for much of the Earth's surface. We describe
[EQUATION] I/O algorithms for several problems on
[EQUATION] grids for which only $O(N)$ algorithms were
previously known. Here $M$ denotes the size of the main
memory and $B$ the size of a disk block. We demonstrate
the practical merits of our work by comparing the
empirical performance of our new algorithm for the {\em
flow accumulation\/} problem with that of the
previously best known algorithm. Flow accumulation,
which models flow of water through a terrain, is one of
the most basic hydrologic attributes of a terrain. We
present the results of an extensive set of experiments
on real-life terrain datasets of different sizes and
characteristics. Our experiments show that while our
new algorithm scales nicely with dataset size, the
previously known algorithm 'breaks down' once the size
of the dataset becomes bigger than the available main
memory. For example, while our algorithm computes the
flow accumulation for the Appalachian Mountains in
about three hours, the previously known algorithm takes
several weeks.",
acknowledgement = ack-nhfb,
articleno = "1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Demestrescu:2001:BCM,
author = "Camil Demestrescu and Irene Finocchi",
title = "Breaking cycles for minimizing crossings",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "6",
pages = "2:1--2:??",
month = "????",
year = "2001",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/945394.945396",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:55 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We consider the one-sided crossing minimization
problem (CP): given a bipartite graph $G$ and a
permutation $x_0$ of the vertices on a layer, find a
permutation $x_1$ of the vertices on the other layer
which minimizes the number of edge crossings in any
straightline drawing of $G$ where vertices are placed
on two parallel lines and sorted according to $x_0$ and
$x_1$. Solving CP represents a fundamental step in the
construction of aesthetically pleasing layouts of
hierarchies and directed graphs, but unfortunately this
problem has been proved to be NP-complete.\par
In this paper we address the strong relation between CP
and the problem of computing minimum feedback arc sets
in directed graphs and we devise a new approximation
algorithm for CP, called PM, that exploits this
dependency. We experimentally and visually compare the
performance of PM with the performance of well-known
algorithms and of recent attractive strategies.
Experiments are carried out on different families of
randomly generated graphs, on pathological instances,
and on real test sets. Performance indicators include
both number of edge crossings and running time, as well
as structural measures of the problem instances. We
found CP to be a very interesting and rich problem from
a combinatorial point of view. Our results clearly
separate the behavior of the algorithms, proving the
effectiveness of PM on most test sets and showing
tradeoffs between quality of the solutions and running
time. However, if the visual complexity of the drawings
is considered, we found no clear winner. This confirms
the importance of optimizing also other aesthetic
criteria such as symmetry, edge length, and angular
resolution.",
acknowledgement = ack-nhfb,
articleno = "2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "bipartite graphs; crossing minimization; experimental
algorithms",
}
@Article{Gabow:2001:NFB,
author = "Harold Gabow and Tadayoshi Kohno",
title = "A Network-Flow-Based Scheduler: Design, Performance
History, and Experimental Analysis",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "6",
pages = "3:1--3:??",
month = "????",
year = "2001",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/945394.945397",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:55 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We describe a program that schedules physician
attending teams at Denver Health Medical Center. The
program uses network flow techniques to prune an
exponentially sized search space. We describe the
program design, its performance history at the
hospital, and experiments on a simplified version of
the program.",
acknowledgement = ack-nhfb,
articleno = "3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "graphs; matroids; scheduling",
}
@Article{Iyer:2001:ESP,
author = "Raj Iyer and David Karger and Hariharan Rahul and
Mikkel Thorup",
title = "An Experimental Study of Polylogarithmic, Fully
Dynamic, Connectivity Algorithms",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "6",
pages = "4:1--4:??",
month = "????",
year = "2001",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/945394.945398",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:55 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present an experimental study of different variants
of the amortized $O(\log^n)$-time fully-dynamic
connectivity algorithm of Holm, de Lichtenberg, and
Thorup (STOC'98). The experiments build upon
experiments provided by Alberts, Cattaneo, and Italiano
(SODA'96) on the randomized amortized $O(\log^3 n)$
fully-dynamic connectivity algorithm of Henzinger and
King (STOC'95). Our experiments shed light upon
similarities and differences between the two
algorithms. We also present a slightly modified version
of the Henzinger--King algorithm that runs in $O(\log^2
n)$ time, which resulted from our experiments.",
acknowledgement = ack-nhfb,
articleno = "4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Liberatore:2001:CSB,
author = "Vincenzo Liberatore",
title = "Caching and Scheduling for Broadcast Disk Systems",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "6",
pages = "5:1--5:??",
month = "????",
year = "2001",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/945394.945399",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:55 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Unicast connections lead to performance and
scalability problems when a large client population
attempts to access the same data. Broadcast push and
broadcast disk technology address the problem by
broadcasting data items from a server to a large number
of clients. Broadcast disk performance depends mainly
on caching strategies at the client site and on how the
broadcast is scheduled at the server site. An on-line
broadcast disk paging strategy makes caching decisions
without knowing future page requests or access
probabilities. This paper gives new implementations of
existing on-line algorithms and reports on extensive
empirical investigations. The gray algorithm [Khanna
and Liberatore 2000] always outperformed other on-line
strategies on both synthetic and Web traces. Moreover,
caching limited the skewness of broadcast schedules,
and led to favor efficient caching algorithms over
refined scheduling strategies when the cache was
large.",
acknowledgement = ack-nhfb,
articleno = "5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "broadcast disk; caching; scheduling",
}
@Article{Narasimhan:2001:GMS,
author = "Giri Narasimhan and Martin Zachariasen",
title = "Geometric Minimum Spanning Trees via Well-Separated
Pair Decompositions",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "6",
pages = "6:1--6:??",
month = "????",
year = "2001",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/945394.945400",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:55 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Let $S$ be a set of $n$ points in $\Re^d$. We present
an algorithm that uses the well-separated pair
decomposition and computes the minimum spanning tree of
$S$ under any $L_p$ or polyhedral metric. A theoretical
analysis shows that it has an expected running time of
$O(n \log n)$ for uniform point distributions; this is
verified experimentally. Extensive experimental results
show that this approach is practical. Under a variety
of input distributions, the resulting implementation is
robust and performs well for points in higher
dimensional space.",
acknowledgement = ack-nhfb,
articleno = "6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Rahman:2001:ARS,
author = "Naila Rahman and Rajeev Raman",
title = "Adapting Radix Sort to the Memory Hierarchy",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "6",
pages = "7:1--7:??",
month = "????",
year = "2001",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/945394.945401",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:55 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We demonstrate the importance of reducing misses in
the translation-lookaside buffer (TLB) for obtaining
good performance on modern computer architectures. We
focus on least-significant bit first (LSB) radix sort,
standard implementations of which make many TLB misses.
We give three techniques which simultaneously reduce
cache and TLB misses for LSB radix sort: reducing
working set size, explicit block transfer and
pre-sorting. We note that: \item All the techniques
above yield algorithms whose implementations outperform
optimised cache-tuned implementations of LSB radix sort
and comparison-based sorting algorithms. The fastest
running times are obtained by the pre-sorting approach
and these are over twice as fast as optimised
cache-tuned implementations of LSB radix sort and
quicksort. Even the simplest optimisation, using the
TLB size to guide the choice of radix in standard
implementations of LSB radix sort, gives good
improvements over cache-tuned algorithms. \item One of
the pre-sorting algorithms and explicit block transfer
make few cache and TLB misses in the worst case. This
is not true of standard implementations of LSB radix
sort. We also apply these techniques to the problem of
permuting an array of integers, and obtain gains of
over 30\% relative to the naive algorithm by using
explicit block transfer.",
acknowledgement = ack-nhfb,
articleno = "7",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "cache; efficient sorting algorithms; external-memory
algorithms; locality of reference; memory hierarchy;
radix sort; translation-lookaside buffer (TLB)",
}
@Article{Stallmann:2001:HES,
author = "Matthias Stallmann and Franc Brglez and Debabrata
Ghosh",
title = "Heuristics, Experimental Subjects, and Treatment
Evaluation in Bigraph Crossing Minimization",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "6",
pages = "8:1--8:??",
month = "????",
year = "2001",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/945394.945402",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:55 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The bigraph crossing problem, embedding the two node
sets of a bipartite graph along two parallel lines so
that edge crossings are minimized, has applications to
circuit layout and graph drawing. Experimental results
for several previously known and two new heuristics
suggest continued exploration of the problem,
particularly sparse instances. We emphasize careful
design of experimental subject classes and present
novel views of the results. All source code, data, and
scripts are available on-line",
acknowledgement = ack-nhfb,
articleno = "8",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "crossing number; design of experiments; graph drawing;
graph embedding; graph equivalence classes; layout",
}
@Article{Frigioni:2001:ESD,
author = "Daniele Frigioni and Tobias Miller and Christos
Zaroliagis",
title = "An Experimental Study of Dynamic Algorithms for
Transitive Closure",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "6",
pages = "9:1--9:??",
month = "????",
year = "2001",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/945394.945403",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:55 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We perform an extensive experimental study of several
dynamic algorithms for transitive closure. In
particular, we implemented algorithms given by
Italiano, Yellin, Cicerone et al., and two recent
randomized algorithms by Henzinger and King. We propose
a fine-tuned version of Italiano's algorithms as well
as a new variant of them, both of which were always
faster than any of the other implementations of the
dynamic algorithms. We also considered simple-minded
algorithms that were easy to implement and likely to be
fast in practice. Wetested and compared the above
implementations on random inputs, on non-random inputs
that are worst-case inputs for the dynamic algorithms,
and on an input motivated by a real-world graph.",
acknowledgement = ack-nhfb,
articleno = "9",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "dynamic algorithm; experimentation; transitive
closure",
}
@Article{Matias:2001:EFP,
author = "Yossi Matias and Nasir Rajpoot and Cenk Sahinalp",
title = "The Effect of Flexible Parsing for Dynamic
Dictionary-Based Data Compression",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "6",
pages = "10:1--10:??",
month = "????",
year = "2001",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/945394.945404",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:03:55 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We report on the performance evaluation of greedy
parsing with a single step lookahead (which we call
flexible Parsing or {\em FP\/}) as an alternative to
the commonly used greedy parsing (with no-lookaheads)
scheme. Greedy parsing is the basis of most popular
compression programs including UNIX {\tt compress} and
{\tt gzip}, however it usually results in far from
optimal parsing\slash compression with regard to the
dictionary construction scheme in use. Flexible
parsing, however, is optimal [MS99], i.e. partitions
any given input to the smallest number of phrases
possible, for dictionary construction schemes which
satisfy the prefix property throughout their
execution.\par
We focus on the application of {\em FP\/} in the
context of the LZW variant of the Lempel--Ziv'78
dictionary construction method [Wel84, ZL78], which is
of considerable practical interest. We implement two
compression algorithms which use (1) {\em FP\/} with
LZW dictionary (LZW-{\em FP\/}), and (2) {\em FP\/}
with an alternative flexible dictionary (FPA as
introduced in [Hor95]). Our implementations are based
on novel on-line data structures enabling us to use
linear time and space. We test our implementations on a
collection of input sequences which includes textual
files, DNA sequences, medical images, and pseudorandom
binary files, and compare our results with two of the
most popular compression programs UNIX {\tt compress}
and {\tt gzip}. Our results demonstrate that flexible
parsing is especially useful for non-textual data, on
which it improves over the compression rates of {\tt
compress} and {\tt gzip} by up to 20\% and 35\%,
respectively.",
acknowledgement = ack-nhfb,
articleno = "10",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Backes:2002:HLB,
author = "Werner Backes and Susanne Wetzel",
title = "Heuristics on lattice basis reduction in practice",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "7",
pages = "1--1",
month = "????",
year = "2002",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/944618.944619",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this paper we provide a survey on LLL lattice basis
reduction in practice. We introduce several new
heuristics as to speed up known lattice basis reduction
methods and improve the quality of the computed reduced
lattice basis in practice. We analyze substantial
experimental data and to our knowledge, we are the
first to present general heuristics for determining
which variant of the reduction algorithm, for varied
parameter choices, yields the most efficient reduction
strategy for reducing a particular problem instance.",
acknowledgement = ack-nhfb,
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "dynamic approximation; general reduction heuristics;
lattice basis reduction; modular and iterative
heuristics",
}
@Article{Iwama:2002:PLS,
author = "Kazuo Iwama and Daisuke Kawai and Shuichi Miyazaki and
Yasuo Okabe and Jun Umemoto",
title = "Parallelizing local search for {CNF} satisfiability
using vectorization and {PVM}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "7",
pages = "2--2",
month = "????",
year = "2002",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/944618.944620",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The purpose of this paper is to speed up the local
search algorithm for the CNF Satisfiability problem.
Our basic strategy is to run some 10$^5$ independent
search paths simultaneously using PVM on a vector
supercomputer VPP800, which consists of 40 vector
processors. Using the above parallelization and
vectorization together with some improvement of data
structure, we obtained 600-times speedup in terms of
the number of flips the local search can make per
second, compared to the original GSAT by Selman and
Kautz. We ran our parallel GSAT for benchmark instances
and compared the running time with those of existing
SAT programs. We could observe an apparent benefit of
parallelization: Especially, we were able to solve two
instances that have never been solved before this
paper. We also tested parallel local search for the SAT
encoding of the class scheduling problem. Again we were
able to get almost the best answer in reasonable
time.",
acknowledgement = ack-nhfb,
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; CNF Satisfiability; distributed computing;
experimentation; local search algorithms;
parallelization; PVM; vector supercomputer;
vectorization",
}
@Article{Albers:2002:ESO,
author = "Susanne Albers and Bianca Schr{\"o}der",
title = "An experimental study of online scheduling
algorithms",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "7",
pages = "3--3",
month = "????",
year = "2002",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/944618.944621",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present the first comprehensive experimental study
of online algorithms for Graham's scheduling problem.
Graham's scheduling problem is a fundamental problem in
scheduling theory where a sequence of jobs has to be
scheduled on $m$ identical parallel machines so as to
minimize the makespan. Graham gave an elegant algorithm
that is $(2 - 1 / m)$-competitive. Recently a number of
new online algorithms were developed that achieve
competitive ratios around 1.9. Since competitive
analysis can only capture the worst case behavior of an
algorithm a question often asked is: Are these new
algorithms geared only towards a pathological case or
do they perform better in practice, too?We address this
question by analyzing the algorithms on various job
sequences. In our actual tests, we analyzed the
algorithms (1) on real world jobs and (2) on jobs
generated by probability distributions. It turns out
that the performance of the algorithms depends heavily
on the characteristics of the respective work load. On
job sequences that are generated by standard
probability distributions, Graham's strategy is clearly
the best. However, on the real world jobs the new
algorithms often outperform Graham's strategy. Our
experimental study confirms theoretical results in the
sense that there are also job sequences in practice on
which the new online algorithms perform better. Our
study can help to inform practitioners about the new
scheduling strategies as an alternative to Graham's
algorithm.",
acknowledgement = ack-nhfb,
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; experimentation; online algorithms;
performance; scheduling",
}
@Article{Mehlhorn:2002:IWM,
author = "Kurt Mehlhorn and Guido Sch{\"a}fer",
title = "Implementation of {$O(nm \log n)$} weighted matchings
in general graphs: the power of data structures",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "7",
pages = "4--4",
month = "????",
year = "2002",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/944618.944622",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We describe the implementation of an algorithm which
solves the weighted matching problem in general graphs
with $n$ vertices and $m$ edges in time $O(nm \log n)$.
Our algorithm is a variant of the algorithm of Galil,
Micali and Gabow [Galil et al. 1986] and extensively
uses sophisticated data structures, in particular {\em
concatenable priority queues}, so as to reduce the time
needed to perform dual adjustments and to find tight
edges in Edmonds' blossom-shrinking algorithm. We
compare our implementation to the experimentally
fastest implementation, named {\em Blossom IV}, due to
Cook and Rohe [Cook and Rohe 1997]. Blossom IV requires
only very simple data structures and has an asymptotic
running time of $O(n^2 m)$. Our experiments show that
our new implementation is superior to Blossom IV. A
closer inspection reveals that the running time of
Edmonds' blossom-shrinking algorithm in practice
heavily depends on the time spent to perform dual
adjustments and to find tight edges. Therefore,
optimizing these operations, as is done in our
implementation, indeed speeds-up the practical
performance of implementations of Edmonds' algorithm.",
acknowledgement = ack-nhfb,
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Edelkamp:2002:IHQ,
author = "Stefan Edelkamp and Patrick Stiegeler",
title = "Implementing {{\em HEAPSORT\/}} with $(n \log n - 0.9
n)$ and {{\em QUICKSORT}\/} with $(n \log n + 0.2 n)$
comparisons",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "7",
pages = "5--5",
month = "????",
year = "2002",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/944618.944623",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "With refinements to the {\em WEAK-HEAPSORT\/}
algorithm we establish the general and practical
relevant sequential sorting algorithm {\em
INDEX-WEAK-HEAPSORT\/} with exactly $n \lceil \log n
\rceil - 2^{\lceil \log n \rceil} + 1 \leq n \log n 0.9
n$ comparisons and at most $n \log n + 0.1 n$
transpositions on any given input. It comprises an
integer array of size $n$ and is best used to generate
an index for the data set. With {\em
RELAXED-WEAK-HEAPSORT\/} and {\em
GREEDY-WEAK-HEAPSORT\/} we discuss modifications for a
smaller set of pending element transpositions. If extra
space to create an index is not available, with {\em
QUICK-WEAK-HEAPSORT\/} we propose an efficient {\em
QUICKSORT\/} variant with $n \log n + 0.2 n + o(n)$
comparisons on the average. Furthermore, we present
data showing that {\em WEAK-HEAPSORT,
INDEX-WEAK-HEAPSORT\/} and {\em QUICK-WEAK-HEAPSORT\/}
compete with other performant {\em QUICKSORT\/} and
{\em HEAPSORT\/} variants.",
acknowledgement = ack-nhfb,
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Erlebach:2002:IAA,
author = "Thomas Erlebach and Klaus Jansen",
title = "Implementation of approximation algorithms for
weighted and unweighted edge-disjoint paths in
bidirected trees",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "7",
pages = "6--6",
month = "????",
year = "2002",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/944618.944624",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Given a set of weighted directed paths in a bidirected
tree, the maximum weight edge-disjoint paths problem
(MWEDP) is to select a subset of the given paths such
that the selected paths are edge-disjoint and the total
weight of the selected paths is maximized. MWEDP is
{\em NP\/}-hard for bidirected trees of unbounded
degree, even if all weights are the same (the
unweighted case). Three different approximation
algorithms are implemented: a known combinatorial $(5/3
+ \epsilon)$-approximation algorithm $A_1$ for the
unweighted case, a new combinatorial 2-approximation
algorithm $A_2$ for the weighted case, and a known $(5
/ 3 + \epsilon)$-approximation algorithm $A_3$ for the
weighted case that is based on linear programming. For
algorithm $A_1$, it is shown how efficient data
structures can be used to obtain a worst-case
running-time of $O(m + n + 4^{1/\epsilon} \sqrt n c m)$
for instances consisting of $m$ paths in a tree with
$n$ nodes. Experimental results regarding the
running-times and the quality of the solutions obtained
by the three approximation algorithms are reported.
Where possible, the approximate solutions are compared
to the optimal solutions, which were computed by
running CPLEX on an integer linear programming
formulation of MWEDP.",
acknowledgement = ack-nhfb,
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; combinatorial optimization;
experimentation; linear programming",
}
@Article{Lassous:2002:PLR,
author = "Isabelle Gu{\'e}rin Lassous and Jens Gustedt",
title = "Portable list ranking: an experimental study",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "7",
pages = "7--7",
month = "????",
year = "2002",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/944618.944625",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present and analyze two portable algorithms for the
List Ranking Problem in the Coarse Grained
Multicomputer model (CGM). We report on implementations
of these algorithms and experiments that were done with
these on a variety of parallel and distributed
architectures, ranging from PC clusters to a mainframe
parallel machine. With these experiments, we validate
the chosen CGM model, and also show the possible gains
and limits of such algorithms.",
acknowledgement = ack-nhfb,
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Vahrenhold:2002:PPL,
author = "Jan Vahrenhold and Klaus H. Hinrichs",
title = "Planar point location for large data sets: to seek or
not to seek",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "7",
pages = "8--8",
month = "????",
year = "2002",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/944618.944626",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present an algorithm for external memory planar
point location that is both effective and easy to
implement. The base algorithm is an external memory
variant of the bucket method by Edahiro, Kokubo and
Asano that is combined with Lee and Yang's batched
internal memory algorithm for planar point location.
Although our algorithm is not optimal in terms of its
worst-case behavior, we show its efficiency for both
batched and single-shot queries by experiments with
real-world data. The experiments show that the
algorithm benefits from the mainly sequential disk
access pattern and significantly outperforms the
fastest algorithm for internal memory. Due to its
simple concept, the algorithm can take advantage of
multiple disks and processors in a rather
straightforward yet efficient way.",
acknowledgement = ack-nhfb,
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Wickremesinghe:2002:ESU,
author = "Rajiv Wickremesinghe and Lars Arge and Jeffrey S.
Chase and Jeffrey Scott Vitter",
title = "Efficient sorting using registers and caches",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "7",
pages = "9--9",
month = "????",
year = "2002",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/944618.944627",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Modern computer systems have increasingly complex
memory systems. Common machine models for algorithm
analysis do not reflect many of the features of these
systems, e.g., large register sets, lockup-free caches,
cache hierarchies, associativity, cache line fetching,
and streaming behavior. Inadequate models lead to poor
algorithmic choices and an incomplete understanding of
algorithm behavior on real machines. A key step toward
developing better models is to quantify the performance
effects of features not reflected in the models. This
paper explores the effect of memory system features on
sorting performance. We introduce a new cache-conscious
sorting algorithm, R-MERGE, which achieves better
performance in practice over algorithms that are
superior in the theoretical models. R-MERGE is designed
to minimize memory stall cycles rather than cache
misses by considering features common to many system
designs.",
acknowledgement = ack-nhfb,
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Herrmann:2002:FCN,
author = "Francine Herrmann and Alain Hertz",
title = "Finding the chromatic number by means of critical
graphs",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "7",
pages = "10--10",
month = "????",
year = "2002",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/944618.944628",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We propose a new exact algorithm for finding the
chromatic number of a graph $G$. The algorithm attempts
to determine the smallest possible induced subgraph
$G'$ of $G$ which has the same chromatic number as $G$.
Such a subgraph is said critical since all proper
induced sub-graph of $G'$ have a chromatic number
strictly smaller than $G'$. The proposed method is
particularly helpful when a $k$-coloring of a
non-critical graph is known, and it has to be proved
that no $(k - 1)$-coloring of $G$ exists. Computational
experiments on random graphs and on DIMACS benchmark
problems demonstrate that the new proposed algorithm
can solve larger problem than previous known exact
methods.",
acknowledgement = ack-nhfb,
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; experimentation; performance",
}
@Article{Fekete:2002:SHP,
author = "S{\'a}ndor P. Fekete and Henk Meijer and Andr{\'e}
Rohe and Walter Tietze",
title = "Solving a 'Hard' problem to approximate an 'Easy' one:
heuristics for maximum matchings and maximum traveling
salesman problems",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "7",
pages = "11--11",
month = "????",
year = "2002",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/944618.944629",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We consider geometric instances of the Maximum
Weighted Matching Problem (MWMP) and the Maximum
Traveling Salesman Problem (MTSP) with up to 3,000,000
vertices. Making use of a geometric duality
relationship between MWMP, MTSP, and the
Fermat--Weber-Problem (FWP), we develop a heuristic
approach that yields in near-linear time solutions as
well as upper bounds. Using various computational
tools, we get solutions within considerably less than
1\% of the optimum. An interesting feature of our
approach is that, even though an FWP is hard to compute
in theory and Edmonds' algorithm for maximum weighted
matching yields a polynomial solution for the MWMP, the
practical behavior is just the opposite, and we can
solve the FWP with high accuracy in order to find a
good heuristic solution for the MWMP.",
acknowledgement = ack-nhfb,
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "approximation; Fermat--Weber problem; geometric
optimization; geometric problems; heuristics; maximum
traveling salesman problem (MTSP); maximum weighted
matching; near-linear algorithms",
}
@Article{Neri:2002:RCL,
author = "Filippo Neri",
title = "Relational concept learning by cooperative evolution",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "7",
pages = "12--12",
month = "????",
year = "2002",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/944618.944630",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Concept learning is a computationally demanding task
that involves searching large hypothesis spaces
containing candidate descriptions. Stochastic search
combined with parallel processing provide a promising
approach to successfully deal with such computationally
intensive tasks. Learning systems based on distributed
genetic algorithms (GA) were able to find concept
descriptions as accurate as the ones found by
state-of-the-art learning systems based on alternative
approaches. However, genetic algorithms' exploitation
has the drawback of being computationally demanding. We
show how a suitable architectural choice, named
cooperative evolution, allows to solve complex
applications in an acceptable user waiting time and
with a reasonable computational cost by using GA-based
learning systems because of the effective exploitation
of distributed computation. A variety of experimental
settings is analyzed and an explanation for the
empirical observations is proposed.",
acknowledgement = ack-nhfb,
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "distributed genetic algorithm; first order logic
concept learning; relational concept learning",
}
@Article{Kumar:2003:AME,
author = "Piyush Kumar and Joseph S. B. Mitchell and E. Alper
Yildirim",
title = "Approximate minimum enclosing balls in high dimensions
using core-sets",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "8",
pages = "1.1:1--1.1:??",
month = "????",
year = "2003",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/996546.996548",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:56 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We study the minimum enclosing ball (MEB) problem for
sets of points or balls in high dimensions. Using
techniques of second-order cone programming and
'core-sets', we have developed $(1 +
\epsilon)$-approximation algorithms that perform well
in practice, especially for very high dimensions, in
addition to having provable guarantees. We prove the
existence of core-sets of size $O(1/\epsilon)$,
improving the previous bound of $O(1/\epsilon^2)$, and
we study empirically how the core-set size grows with
dimension. We show that our algorithm, which is simple
to implement, results in fast computation of nearly
optimal solutions for point sets in much higher
dimension than previously computable using exact
techniques.",
acknowledgement = ack-nhfb,
articleno = "1.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "approximation algorithms; minimum enclosing ball;
second-order cone programming",
}
@Article{Arge:2003:EPL,
author = "Lars Arge and Andrew Danner and Sha-Mayn Teh",
title = "{I/O}-efficient point location using persistent
{B}-trees",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "8",
pages = "1.2:1--1.2:??",
month = "????",
year = "2003",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/996546.996549",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:56 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present an external planar point location data
structure that is I/O-efficient both in theory and
practice. The developed structure uses linear space and
answers a query in optimal $O(\log B N)$ I/Os, where
$B$ is the disk block size. It is based on a persistent
B-tree, and all previously developed such structures
assume a total order on the elements in the structure.
As a theoretical result of independent interest, we
show how to remove this assumption. Most previous
theoretical I/O-efficient planar point location
structures are relatively complicated and have not been
implemented. Based on a bucket approach, Vahrenhold and
Hinrichs therefore developed a simple and practical,
but theoretically non-optimal, heuristic structure. We
present an extensive experimental evaluation that shows
that, on a range of real-world Geographic Information
Systems (GIS) data, our structure uses a similar number
of I/Os as the structure of Vahrenhold and Hinrichs to
answer a query. On a synthetically generated worst-case
dataset our structure uses significantly fewer I/Os.",
acknowledgement = ack-nhfb,
articleno = "1.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Buchsbaum:2003:FPM,
author = "Adam L. Buchsbaum and Glenn S. Fowler and Balachannder
Kirishnamurthy and Kiem-Phong Vo and Jia Wang",
title = "Fast prefix matching of bounded strings",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "8",
pages = "1.3:1--1.3:??",
month = "????",
year = "2003",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/996546.996550",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:56 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Longest Prefix Matching (LPM) is the problem of
finding which string from a given set is the longest
prefix of another, given string. LPM is a core problem
in many applications, including IP routing, network
data clustering, and telephone network management.
These applications typically require very fast matching
of bounded strings, i.e., strings that are short and
based on small alphabets. We note a simple
correspondence between bounded strings and natural
numbers that maps prefixes to nested intervals so that
computing the longest prefix matching a string is
equivalent to finding the shortest interval containing
its corresponding integer value. We then present {\em
retries}, a fast and compact data structure for LPM on
general alphabets. Performance results show that
retries often outperform previously published data
structures for IP look-up. By extending LPM to general
alphabets, retries admit new applications that could
not exploit prior LPM solutions designed for IP
look-ups.",
acknowledgement = ack-nhfb,
articleno = "1.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "IP routing; prefix matching; table look-up; tries",
}
@Article{Breimer:2003:LAL,
author = "Eric A. Breimer and Mark K. Goldberg and Darren T.
Lim",
title = "A learning algorithm for the longest common
subsequence problem",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "8",
pages = "2.1:1--2.1:??",
month = "????",
year = "2003",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/996546.996552",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:56 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present an experimental study of a learning
algorithm for the longest common subsequence problem,
{\em LCS}. Given an arbitrary input domain, the
algorithm learns an {\em LCS\/}-procedure tailored to
that domain. The learning is done with the help of an
oracle, which can be any {\em LCS\/}-algorithm. After
solving a limited number of training inputs using an
oracle, the learning algorithm outputs a new {\em
LCS\/}-procedure. Our experiments demonstrate that, by
allowing a slight loss of optimality, learning yields a
procedure which is significantly faster than the
oracle. The oracle used for the experiments is the {\em
np\/}-procedure by Wu {\em et al.}, a modification of
Myers' classical {\em LCS\/}-algorithm. We show how to
scale up the results of learning on small inputs to
inputs of arbitrary lengths. For the domain of two
random 2-symbol inputs of length $n$, learning yields a
program with 0.999 expected accuracy, which runs in
$O(n^{1.41})$-time, in contrast with $O(n^2 \log n)$
running time of the fastest theoretical algorithm that
produces optimal solutions. For the domain of random
2-symbol inputs of length 100,000, the program runs
10.5 times faster than the {\em np\/}-procedure,
producing 0.999- accurate outputs. The scaled version
of the evolved algorithm applied to random inputs of
length 1 million runs approximately 30 times faster
than the {\em np\/}-procedure while constructing 0.999-
accurate solutions. We apply the evolved algorithm to
DNA sequences of various lengths by training on random
4-symbol sequences of up to length 10,000. The evolved
algorithm, scaled up to the lengths of up to 1.8
million, produces solutions with the 0.998-accuracy in
a fraction of the time used by the {\em np}.",
acknowledgement = ack-nhfb,
articleno = "2.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Venkataraman:2003:BAP,
author = "Gayathri Venkataraman and Sartaj Sahni and Srabani
Mukhopadhyaya",
title = "A blocked all-pairs shortest-paths algorithm",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "8",
pages = "2.2:1--2.2:??",
month = "????",
year = "2003",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/996546.996553",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:56 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We propose a blocked version of Floyd's all-pairs
shortest-paths algorithm. The blocked algorithm makes
better utilization of cache than does Floyd's original
algorithm. Experiments indicate that the blocked
algorithm delivers a speedup (relative to the unblocked
Floyd's algorithm) between 1.6 and 1.9 on a Sun Ultra
Enterprise 4000/5000 for graphs that have between 480
and 3200 vertices. The measured speedup on an SGI O2
for graphs with between 240 and 1200 vertices is
between 1.6 and 2.",
acknowledgement = ack-nhfb,
articleno = "2.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "all pairs shortest paths; blocking; cache; speedup",
}
@Article{Petit:2003:EML,
author = "Jordi Petit",
title = "Experiments on the minimum linear arrangement
problem",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "8",
pages = "2.3:1--2.3:??",
month = "????",
year = "2003",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/996546.996554",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:04:56 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "This paper deals with the Minimum Linear Arrangement
problem from an experimental point of view. Using a
testsuite of sparse graphs, we experimentally compare
several algorithms to obtain upper and lower bounds for
this problem. The algorithms considered include
Successive Augmentation heuristics, Local Search
heuristics and Spectral Sequencing. The testsuite is
based on two random models and 'real life' graphs. As a
consequence of this study, two main conclusions can be
drawn: On one hand, the best approximations are usually
obtained using Simulated Annealing, which involves a
large amount of computation time. Solutions found with
Spectral Sequencing are close to the ones found with
Simulated Annealing and can be obtained in
significantly less time. On the other hand, we notice
that there exists a big gap between the best obtained
upper bounds and the best obtained lower bounds. These
two facts together show that, in practice, finding
lower and upper bounds for the Minimum Linear
Arrangement problem is hard.",
acknowledgement = ack-nhfb,
articleno = "2.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Brandes:2004:GNC,
author = "Ulrik Brandes and Frank Schulz and Dorothea Wagner and
Thomas Willhalm",
title = "Generating node coordinates for shortest-path
computations in transportation networks",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "9",
pages = "1.1:1--1.1:??",
month = "????",
year = "2004",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1005813.1005815",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:22 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Speed-up techniques that exploit given node
coordinates have proven useful for shortest-path
computations in transportation networks and geographic
information systems. To facilitate the use of such
techniques when coordinates are missing from some, or
even all, of the nodes in a network we generate
artificial coordinates using methods from graph
drawing. Experiments on a large set of German train
timetables indicate that the speed-up achieved with
coordinates from our drawings is close to that achieved
with the true coordinates---and in some special cases
even better.",
acknowledgement = ack-nhfb,
articleno = "1.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "graph drawing; shortest paths; transportation
networks; travel planning",
}
@Article{Niewiadomski:2004:PSD,
author = "Robert Niewiadomski and Jos{\'e} Nelson Amaral and
Robert C. Holte",
title = "A performance study of data layout techniques for
improving data locality in refinement-based
pathfinding",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "9",
pages = "1.2:1--1.2:??",
month = "????",
year = "2004",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1005813.1041511",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:22 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The widening gap between processor speed and memory
latency increases the importance of crafting data
structures and algorithms to exploit temporal and
spatial locality. Refinement-based pathfinding
algorithms, such as Classic Refinement (CR), find
quality paths in very large sparse graphs where
traditional search techniques fail to generate paths in
acceptable time. In this paper, we present a
performance evaluation study of three simple data
structure transformations aimed at improving the data
reference locality of CR. These transformations are
robust to changes in computer architecture and the
degree of compiler optimization. We test our
alternative designs on four contemporary architectures,
using two compilers for each machine. In our
experiments, the application of these techniques
results in performance improvements of up to 67\% with
consistent improvements above 15\%. Analysis reveals
that these improvements stem from improved data
reference locality at the page level and to a lesser
extent at the cache line level.",
acknowledgement = ack-nhfb,
articleno = "1.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "cache-conscious algorithms; classical refinement;
pathfinding",
}
@Article{Marathe:2004:ESS,
author = "Madhav V. Marathe and Alessandro Panconesi and Larry
D. {Risinger, Jr.}",
title = "An experimental study of a simple, distributed
edge-coloring algorithm",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "9",
pages = "1.3:1--1.3:??",
month = "????",
year = "2004",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1005813.1041515",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:22 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We conduct an experimental analysis of a distributed
randomized algorithm for edge coloring simple
undirected graphs. The algorithm is extremely simple
yet, according to the probabilistic analysis, it
computes nearly optimal colorings very quickly [Grable
and Panconesi 1997]. We test the algorithm on a number
of random as well as nonrandom graph families. The test
cases were chosen based on two objectives: (i) to
provide insights into the worst-case behavior (in terms
of time and quality) of the algorithm and (ii) to test
the performance of the algorithm with instances that
are likely to arise in practice. Our main results
include the following:(1) The empirical results
obtained compare very well with the recent empirical
results reported by other researchers [Durand et al.
1994, 1998; Jain and Werth 1995].(2) The empirical
results confirm the bounds on the running time and the
solution quality as claimed in the theoretical paper.
Our results show that for certain classes of graphs the
algorithm is likely to perform much better than the
analysis suggests.(3) The results demonstrate that the
algorithm might be well suited (from a theoretical as
well as practical standpoint) for edge coloring graphs
quickly and efficiently in a distributed setting. Based
on our empirical study, we propose a simple
modification of the original algorithm with
substantially improved performance in practice.",
acknowledgement = ack-nhfb,
articleno = "1.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "distributed algorithms; edge coloring; experimental
analysis of algorithms; high performance computing;
randomized algorithms; scheduling",
}
@Article{Fredriksson:2004:AOS,
author = "Kimmo Fredriksson and Gonzalo Navarro",
title = "Average-optimal single and multiple approximate string
matching",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "9",
pages = "1.4:1--1.4:??",
month = "????",
year = "2004",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1005813.1041513",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:22 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present a new algorithm for multiple approximate
string matching. It is based on reading backwards
enough l-grams from text windows so as to prove that no
occurrence can contain the part of the window read, and
then shifting the window. We show analytically that our
algorithm is optimal on average. Hence our first
contribution is to fill an important gap in the area,
since no average-optimal algorithm existed for multiple
approximate string matching. We consider several
variants and practical improvements to our algorithm,
and show experimentally that they are resistant to the
number of patterns and the fastest for low difference
ratios, displacing the long-standing best algorithms.
Hence our second contribution is to give a practical
algorithm for this problem, by far better than any
existing alternative in many cases of interest. On
real-life texts, our algorithm is especially
interesting for computational biology applications. In
particular, we show that our algorithm can be
successfully used to search for one pattern, where many
more competing algorithms exist. Our algorithm is also
average-optimal in this case, being the second after
that of Chang and Marr. However, our algorithm permits
higher difference ratios than Chang and Marr, and this
is our third contribution. In practice, our algorithm
is competitive in this scenario too, being the fastest
for low difference ratios and moderate alphabet sizes.
This is our fourth contribution, which also answers
affirmatively the question of whether a practical
average-optimal approximate string-matching algorithm
existed.",
acknowledgement = ack-nhfb,
articleno = "1.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; approximate string matching; biological
sequences; multiple string matching; optimality",
}
@Article{Sinha:2004:CCS,
author = "Ranjan Sinha and Justin Zobel",
title = "Cache-conscious sorting of large sets of strings with
dynamic tries",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "9",
pages = "1.5:1--1.5:??",
month = "????",
year = "2004",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1005813.1041517",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:22 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Ongoing changes in computer architecture are affecting
the efficiency of string-sorting algorithms. The size
of main memory in typical computers continues to grow
but memory accesses require increasing numbers of
instruction cycles, which is a problem for the most
efficient of the existing string-sorting algorithms as
they do not utilize cache well for large data sets. We
propose a new sorting algorithm for strings, burstsort,
based on dynamic construction of a compact trie in
which strings are kept in buckets. It is simple, fast,
and efficient. We experimentally explore key
implementation options and compare burstsort to
existing string-sorting algorithms on large and small
sets of strings with a range of characteristics. These
experiments show that, for large sets of strings,
burstsort is almost twice as fast as any previous
algorithm, primarily due to a lower rate of cache
miss.",
acknowledgement = ack-nhfb,
articleno = "1.5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Goh:2004:TAP,
author = "Rick Siow Mong Goh and Ian Li-Jin Thng",
title = "Twol-amalgamated priority queues",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "9",
pages = "1.6:1--1.6:??",
month = "????",
year = "2004",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1005813.1057625",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:22 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Priority queues are essential function blocks in
numerous applications such as discrete event
simulations. This paper describes and exemplifies the
ease of obtaining high performance priority queues
using a two-tier list-based structure. This new
implementation, called the {\em Twol\/} structure, is
amalgamated with three priority queues, namely, the
Henriksen's queue, splay tree and skew heap, to enhance
the efficiency of these {\em basal\/} priority queue
structures. Using a model that combines traditional
average case and amortized complexity analysis,
Twol-amalgamated priority queues that maintain $N$
active events are theoretically proven to offer $O(1)$
{\em expected amortized complexity\/} under reasonable
assumptions. They are also demonstrated empirically to
offer stable near $O(1)$ performance for widely varying
priority increment distributions and for queue sizes
ranging from 10 to 10 million. Extensive empirical
results show that the Twol-amalgamated priority queues
consistently outperform those basal structures (i.e.,
without the Twol structure) with an average speedup of
about three to five times on widely different hardware
architectures. These results provide testimony that the
Twol-amalgamated priority queues are suitable for
implementation in sizable application scenarios such
as, but not limited to, large-scale discrete event
simulation.",
acknowledgement = ack-nhfb,
articleno = "1.6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithm analysis; calendar queue; discrete event
simulation; future event list; Henriksen's; pending
event set; priority queue; simulator; skew heap; splay
tree; tree",
}
@Article{Ioannidis:2005:ADS,
author = "Ioannis Ioannidis and Ananth Grama and Mikhail
Atallah",
title = "Adaptive data structures for {IP} lookups",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "1.1:1--1.1:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1064548",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The problem of efficient data structures for IP
lookups has been well studied in the literature.
Techniques such as LC tries and extensible hashing are
commonly used. In this paper, we address the problem of
generalizing LC tries, based on traces of past lookups,
to provide performance guarantees for memory suboptimal
structures. As a specific example, if a memory-optimal
(LC) trie takes 6 MB and the total memory at the router
is 8 MB, how should the trie be modified to make best
use of the 2 MB of excess memory? We present a greedy
algorithm for this problem and prove that, if for the
optimal data structure there are $b$ fewer memory
accesses on average for each lookup compared with the
original trie, the solution produced by the greedy
algorithm will have at least $9 \times b /11$ fewer
memory accesses on average (compared to the original
trie). An efficient implementation of this algorithm
presents significant additional challenges. We describe
an implementation with a time complexity of $O(\xi(d) n
\log n)$ and a space complexity of $O(n)$, where $n$ is
the number of nodes of the trie and $d$ its depth. The
depth of a trie is fixed for a given version of the
Internet protocol and is typically $O(\log n)$. In this
case, $\xi(d) = O(\log^2 n)$. We also demonstrate
experimentally the performance and scalability of the
algorithm on actual routing data.",
acknowledgement = ack-nhfb,
articleno = "1.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "IP lookups; level compression",
}
@Article{Lesh:2005:NHI,
author = "N. Lesh and J. Marks and A. McMahon and M.
Mitzenmacher",
title = "New heuristic and interactive approaches to {$2$D}
rectangular strip packing",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "1.2:1--1.2:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1083322",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this paper, we consider the two-dimensional
rectangular strip packing problem. A standard simple
heuristic, Bottom-Left-Decreasing (BLD), has been shown
to perform quite well in practice. We introduce and
demonstrate the effectiveness of BLD*, a stochastic
search variation of BLD. While BLD places the
rectangles in decreasing order of height, width, area,
and perimeter, BLD* successively tries random
orderings, chosen from a distribution determined by
their Kendall-tau distance from one of these fixed
orderings. Our experiments on benchmark problems show
that BLD* produces significantly better packings than
BLD after only 1 min of computation. Furthermore, we
also show that BLD* outperforms recently reported
metaheuristics. Furthermore, we observe that people
seem able to reason about packing problems extremely
well. We incorporate our new algorithms in an
interactive system that combines the advantages of
computer speed and human reasoning. Using the
interactive system, we are able to quickly produce
significantly better solutions than BLD* by itself.",
acknowledgement = ack-nhfb,
articleno = "1.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "2D rectangular strip packing; cutting stock/trim;
interactive methods",
}
@Article{Wagner:2005:GCE,
author = "Dorothea Wagner and Thomas Willhalm and Christos
Zaroliagis",
title = "Geometric containers for efficient shortest-path
computation",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "1.3:1--1.3:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1103378",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "A fundamental approach in finding efficiently best
routes or optimal itineraries in traffic information
systems is to reduce the search space (part of graph
visited) of the most commonly used shortest path
routine (Dijkstra's algorithm) on a suitably defined
graph. We investigate reduction of the search space
while simultaneously retaining data structures, created
during a preprocessing phase, of size linear (i.e.,
optimal) to the size of the graph. We show that the
search space of Dijkstra's algorithm can be
significantly reduced by extracting geometric
information from a given layout of the graph and by
encapsulating precomputed shortest-path information in
resulted geometric objects (containers). We present an
extensive experimental study comparing the impact of
different types of geometric containers using test data
from real-world traffic networks. We also present new
algorithms as well as an empirical study for the
dynamic case of this problem, where edge weights are
subject to change and the geometric containers have to
be updated and show that our new methods are two to
three times faster than recomputing everything from
scratch. Finally, in an appendix, we discuss the
software framework that we developed to realize the
implementations of all of our variants of Dijkstra's
algorithm. Such a framework is not trivial to achieve
as our goal was to maintain a common code base that is,
at the same time, small, efficient, and flexible, as we
wanted to enhance and combine several variants in any
possible way.",
acknowledgement = ack-nhfb,
articleno = "1.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "data structures and algorithms; Dijkstra's algorithm;
geometric container; graph algorithms; shortest path;
traffic network",
}
@Article{Lopez-Ortiz:2005:FSS,
author = "Alejandro L{\'o}pez-Ortiz and Mehdi Mirzazadeh and
Mohammad Ali Safari and Hossein Sheikhattar",
title = "Fast string sorting using order-preserving
compression",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "1.4:1--1.4:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1180611",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We give experimental evidence for the benefits of
order-preserving compression in sorting algorithms.
While, in general, any algorithm might benefit from
compressed data because of reduced paging requirements,
we identified two natural candidates that would further
benefit from order-preserving compression, namely
string-oriented sorting algorithms and word-RAM
algorithms for keys of bounded length. The word-RAM
model has some of the fastest known sorting algorithms
in practice. These algorithms are designed for keys of
bounded length, usually 32 or 64 bits, which limits
their direct applicability for strings. One possibility
is to use an order-preserving compression scheme, so
that a bounded-key-length algorithm can be applied. For
the case of standard algorithms, we took what is
considered to be the among the fastest nonword RAM
string sorting algorithms, Fast MKQSort, and measured
its performance on compressed data. The Fast MKQSort
algorithm of Bentley and Sedgewick is optimized to
handle text strings. Our experiments show that
order-compression techniques results in savings of
approximately 15\% over the same algorithm on
noncompressed data. For the word-RAM, we modified
Andersson's sorting algorithm to handle variable-length
keys. The resulting algorithm is faster than the
standard Unix sort by a factor of 1.5 $X$. Last, we
used an order-preserving scheme that is within a
constant additive term of the optimal Hu--Tucker, but
requires linear time rather than $O(m \log m)$, where
$m = |\Sigma|$ is the size of the alphabet.",
acknowledgement = ack-nhfb,
articleno = "1.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "order-preserving compression; sorting; unit-cost RAM;
word-RAM",
}
@Article{Ribeiro:2005:P,
author = "Celso C. Ribeiro and Simone L. Martins",
title = "Preface",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "2.1:1--2.1:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1180620",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
acknowledgement = ack-nhfb,
articleno = "2.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Sinha:2005:URS,
author = "Ranjan Sinha and Justin Zobel",
title = "Using random sampling to build approximate tries for
efficient string sorting",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "2.10:1--2.10:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1180622",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Algorithms for sorting large datasets can be made more
efficient with careful use of memory hierarchies and
reduction in the number of costly memory accesses. In
earlier work, we introduced burstsort, a new
string-sorting algorithm that on large sets of strings
is almost twice as fast as previous algorithms,
primarily because it is more cache efficient. Burstsort
dynamically builds a small trie that is used to rapidly
allocate each string to a bucket. In this paper, we
introduce new variants of our algorithm: SR-burstsort,
DR-burstsort, and DRL-burstsort. These algorithms use a
random sample of the strings to construct an
approximation to the trie prior to sorting. Our
experimental results with sets of over 30 million
strings show that the new variants reduce, by up to
37\%, cache misses further than did the original
burstsort, while simultaneously reducing instruction
counts by up to 24\%. In pathological cases, even
further savings can be obtained.",
acknowledgement = ack-nhfb,
articleno = "2.10",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "cache-aware; cache-conscious; data structure;
in-memory; sorting; string",
}
@Article{Bracht:2005:GAA,
author = "Evandro C. Bracht and Luis and A. A. Meira and F. K.
Miyazawa",
title = "A greedy approximation algorithm for the uniform
metric labeling problem analyzed by a primal-dual
technique",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "2.11:1--2.11:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1180623",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We consider the uniform metric labeling problem. This
NP-hard problem considers how to assign objects to
labels respecting assignment and separation costs. The
known approximation algorithms are based on solutions
of large linear programs and are impractical for
moderate- and large-size instances. We present an 8log
$n$-approximation algorithm that can be applied to
large-size instances. The algorithm is greedy and is
analyzed by a primal-dual technique. We implemented the
presented algorithm and two known approximation
algorithms and compared them at randomized instances.
The gain of time was considerable with small error
ratios. We also show that the analysis is tight, up to
a constant factor.",
acknowledgement = ack-nhfb,
articleno = "2.11",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "approximation algorithms; graph labeling",
}
@Article{deSouza:2005:DMP,
author = "Cid C. de Souza and Andre M. Lima and Guido Araujo and
Nahri B. Moreano",
title = "The datapath merging problem in reconfigurable
systems: {Complexity}, dual bounds and heuristic
evaluation",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "2.2:1--2.2:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1180613",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this paper, we investigate the data path merging
problem (DPM) in reconfigurable systems. DPM is modeled
as a graph optimization problem and is shown to be {\em
NP\/}-hard. An Integer Programming (IP) formulation of
the problem is presented and some valid inequalities
for the convex hull of integer solutions are
introduced. These inequalities form the basis of a
branch-and-cut algorithm that we implemented. This
algorithm was used to compute lower bounds for a set of
DPM instances, allowing us to assess the performance of
two heuristics proposed earlier in the literature for
the problem. Moreover, the branch-and-cut algorithm
also was proved to be a valuable tool to solve
small-sized DPM instances to optimality.",
acknowledgement = ack-nhfb,
articleno = "2.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "data path merging; heuristics; lower bounds;
reconfigurable systems",
}
@Article{Du:2005:IAA,
author = "Jingde Du and Stavros G. Kolliopoulos",
title = "Implementing approximation algorithms for the
single-source unsplittable flow problem",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "2.3:1--2.3:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1180614",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In the {\em single-source unsplittable flow\/}
problem, commodities must be routed simultaneously from
a common source vertex to certain sinks in a given
graph with edge capacities. The demand of each
commodity must be routed along a single path so that
the total flow through any edge is at most, its
capacity. This problem was introduced by Kleinberg
[1996a] and generalizes several NP-complete problems. A
cost value per unit of flow may also be defined for
every edge. In this paper, we implement the
2-approximation algorithm of Dinitz et al. [1999] for
congestion, which is the best known, and the (3,
1)-approximation algorithm of Skutella [2002] for
congestion and cost, which is the best known bicriteria
approximation. We experimentally study the quality of
approximation achieved by the algorithms and the effect
of heuristics on their performance. We also compare
these algorithms against the previous best ones by
Kolliopoulos and Stein [1999].",
acknowledgement = ack-nhfb,
articleno = "2.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "approximation algorithms; network flow; unsplittable
flow",
}
@Article{Duch:2005:IPM,
author = "Amalia Duch and Conrado Mart{\'\i}nez",
title = "Improving the performance of multidimensional search
using fingers",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "2.4:1--2.4:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1180615",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We propose two variants of $K$-d trees where {\em
fingers\/} are used to improve the performance of
orthogonal range search and nearest neighbor queries
when they exhibit locality of reference. The
experiments show that the second alternative yields
significant savings. Although it yields more modest
improvements, the first variant does it with much less
memory requirements and great simplicity, which makes
it more attractive on practical grounds.",
acknowledgement = ack-nhfb,
articleno = "2.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "experimental algorithmics; Finger search; K-d trees;
locality; multidimensional data structures;
nearest-neighbors searching; orthogonal range
searching",
}
@Article{Holzer:2005:CST,
author = "Martin Holzer and Frank Schulz and Dorothea Wagner and
Thomas Willhalm",
title = "Combining speed-up techniques for shortest-path
computations",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "2.5:1--2.5:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1180616",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In practice, computing a shortest path from one node
to another in a directed graph is a very common task.
This problem is classically solved by Dijkstra's
algorithm. Many techniques are known to speed up this
algorithm heuristically, while optimality of the
solution can still be guaranteed. In most studies, such
techniques are considered individually. The focus of
our work is {\em combination\/} of speed-up techniques
for Dijkstra's algorithm. We consider all possible
combinations of four known techniques, namely, {\em
goal-directed search}, {\em bidirectional search}, {\em
multilevel approach}, and {\em shortest-path
containers}, and show how these can be implemented. In
an extensive experimental study, we compare the
performance of the various combinations and analyze how
the techniques harmonize when jointly applied. Several
real-world graphs from road maps and public transport
and three types of generated random graphs are taken
into account.",
acknowledgement = ack-nhfb,
articleno = "2.5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "combination; Dijkstra's algorithm; shortest path;
speed-up",
}
@Article{Hyyro:2005:IBP,
author = "Heikki Hyyr{\"o} and Kimmo Fredriksson and Gonzalo
Navarro",
title = "Increased bit-parallelism for approximate and multiple
string matching",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "2.6:1--2.6:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1180617",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Bit-parallelism permits executing several operations
simultaneously over a set of bits or numbers stored in
a single computer word. This technique permits
searching for the approximate occurrences of a pattern
of length $m$ in a text of length $n$ in time $O(\lceil
m / w \rceil n)$, where $w$ is the number of bits in
the computer word. Although this is asymptotically the
optimal bit-parallel speedup over the basic $O(mn)$
time algorithm, it wastes bit-parallelism's power in
the common case where $m$ is much smaller than $w$,
since $w - m$ bits in the computer words are unused. In
this paper, we explore different ways to increase the
bit-parallelism when the search pattern is short.
First, we show how multiple patterns can be packed into
a single computer word so as to search for all them
simultaneously. Instead of spending $O(rn)$ time to
search for $r$ patterns of length $m \leq w / 2$, we
need $O(\lceil rm / w \rceil n)$ time. Second, we show
how the mechanism permits boosting the search for a
single pattern of length $m \leq w / 2$, which can be
searched for in $O(\lceil n / \lfloor w / m \rfloor
\rceil)$ bit-parallel steps instead of $O(n)$. Third,
we show how to extend these algorithms so that the time
bounds essentially depend on $k$ instead of $m$, where
$k$ is the maximum number of differences permitted.
Finally, we show how the ideas can be applied to other
problems such as multiple exact string matching and
one-against-all computation of edit distance and
longest common subsequences. Our experimental results
show that the new algorithms work well in practice,
obtaining significant speedups over the best existing
alternatives, especially on short patterns and moderate
number of differences allowed. This work fills an
important gap in the field, where little work has
focused on very short patterns.",
acknowledgement = ack-nhfb,
articleno = "2.6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "approximate string matching; bit-parallelism; multiple
string matching",
}
@Article{Nikolov:2005:SEH,
author = "Nikola S. Nikolov and Alexandre Tarassov and
J{\"u}rgen Branke",
title = "In search for efficient heuristics for minimum-width
graph layering with consideration of dummy nodes",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "2.7:1--2.7:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1180618",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We propose two fast heuristics for solving the NP-hard
problem of graph layering with the minimum width and
consideration of dummy nodes. Our heuristics can be
used at the layer-assignment phase of the Sugiyama
method for drawing of directed graphs. We evaluate our
heuristics by comparing them to the widely used
fast-layering algorithms in an extensive computational
study with nearly 6000 input graphs. We also
demonstrate how the well-known longest-path and
Coffman--Graham algorithms can be used for finding
narrow layerings with acceptable aesthetic
properties.",
acknowledgement = ack-nhfb,
articleno = "2.7",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "dummy vertices; hierarchical graph drawing; layer
assignment; layered graphs; layering",
}
@Article{Pemmaraju:2005:AIC,
author = "Sriram V. Pemmaraju and Sriram Penumatcha and Rajiv
Raman",
title = "Approximating interval coloring and max-coloring in
chordal graphs",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "2.8:1--2.8:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1180619",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We consider two coloring problems: interval coloring
and max-coloring for chordal graphs. Given a graph $G =
(V, E)$ and positive-integral vertex weights $w: V
\rightarrow N$, the {\em interval-coloring\/} problem
seeks to find an assignment of a real interval $I(u)$
to each vertex $u \in V$, such that two constraints are
satisfied: (i) for every vertex $u \in V$, $|I(u)| =
w(u)$ and (ii) for every pair of adjacent vertices $u$
and $v$, $I(u) \cap I(v) = \emptyset$. The goal is to
minimize the {\em span\/} $|\cup_{v \in V} I(v)|$. The
{\em max-coloring problem\/} seeks to find a proper
vertex coloring of $G$ whose color classes $C_1$,
$C_2$, \ldots{}, $C_k$, minimize the sum of the weights
of the heaviest vertices in the color classes, that is,
$\sum^k_i = 1 \hbox{max}_{v \epsilon C i w (v)}$. Both
problems arise in efficient memory allocation for
programs. The interval-coloring problem models the
compile-time memory allocation problem and has a rich
history dating back at least to the 1970s. The
max-coloring problem arises in minimizing the total
buffer size needed by a dedicated memory manager for
programs. In another application, this problem models
scheduling of conflicting jobs in batches to minimize
the {\em makespan}. Both problems are NP-complete even
for interval graphs, although there are constant-factor
approximation algorithms for both problems on interval
graphs. In this paper, we consider these problems for
{\em chordal graphs}, a subclass of perfect graphs.
These graphs naturally generalize interval graphs and
can be defined as the class of graphs that have no
induced cycle of length $> 3$. Recently, a
4-approximation algorithm (which we call GeomFit) has
been presented for the max-coloring problem on perfect
graphs (Pemmaraju and Raman 2005). This algorithm can
be used to obtain an interval coloring as well, but
without the constant-factor approximation guarantee. In
fact, there is no known constant-factor approximation
algorithm for the interval-coloring problem on perfect
graphs. We study the performance of GeomFit and several
simple $O(\log(n))$-factor approximation algorithms for
both problems. We experimentally evaluate and compare
four simple heuristics: first-fit, best-fit, GeomFit,
and a heuristic based on partitioning the graph into
vertex sets of similar weight. Both for max-coloring
and for interval coloring, GeomFit deviates from OPT by
about 1.5\%, on average. The performance of first-fit
comes close second, deviating from OPT by less than
6\%, on average, for both problems. Best-fit comes
third and graph-partitioning heuristic comes a distant
last. Our basic data comes from about 10,000 runs of
each of the heuristics for each of the two problems on
randomly generated chordal graphs of various sizes,
sparsity, and structure.",
acknowledgement = ack-nhfb,
articleno = "2.8",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "chordal graphs; dynamic storage allocation; graph
coloring; perfect graphs",
}
@Article{Santos:2005:TSH,
author = "Haroldo G. Santos and Luiz S. Ochi and Marcone J. F.
Souza",
title = "A {Tabu} search heuristic with efficient
diversification strategies for the class\slash teacher
timetabling problem",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "10",
pages = "2.9:1--2.9:??",
month = "????",
year = "2005",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1064546.1180621",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:05:40 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The Class/Teacher Timetabling Problem (CTTP) deals
with the weekly scheduling of encounters between
teachers and classes of an educational institution.
Since CTTP is a NP-hard problem for nearly all of its
variants, the use of heuristic methods for its
resolution is justified. This paper presents an
efficient Tabu Search (TS) heuristic with two different
memory based diversification strategies for CTTP.
Results obtained through an application of the method
to a set of real world problems show that it produces
better solutions than a previously proposed TS found in
the literature and faster times are observed in the
production of good quality solutions.",
acknowledgement = ack-nhfb,
articleno = "2.9",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "metaheuristics; tabu search; timetabling",
}
@Article{Salmela:2006:MSM,
author = "Leena Salmela and Jorma Tarhio and Jari Kyt{\"o}joki",
title = "Multipattern string matching with $q$-grams",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "1.1:1--1.1:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1187438",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present three algorithms for exact string matching
of multiple patterns. Our algorithms are filtering
methods, which apply $q$-grams and bit parallelism. We
ran extensive experiments with them and compared them
with various versions of earlier algorithms, e.g.,
different trie implementations of the Aho--Corasick
algorithm. All of our algorithms appeared to be
substantially faster than earlier solutions for sets of
1,000--10,000 patterns and the good performance of two
of them continues to 100,000 patterns. The gain is
because of the improved filtering efficiency caused by
$q$-grams.",
acknowledgement = ack-nhfb,
articleno = "1.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "content scanning; intrusion detection; multiple string
matching",
}
@Article{Sinha:2006:CES,
author = "Ranjan Sinha and Justin Zobel and David Ring",
title = "Cache-efficient string sorting using copying",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "1.2:1--1.2:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1187439",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Burstsort is a cache-oriented sorting technique that
uses a dynamic trie to efficiently divide large sets of
string keys into related subsets small enough to sort
in cache. In our original burstsort, string keys
sharing a common prefix were managed via a bucket of
pointers represented as a list or array; this approach
was found to be up to twice as fast as the previous
best string sorts, mostly because of a sharp reduction
in out-of-cache references. In this paper, we introduce
C-burstsort, which copies the unexamined tail of each
key to the bucket and discards the original key to
improve data locality. On both Intel and PowerPC
architectures, and on a wide range of string types, we
show that sorting is typically twice as fast as our
original burstsort and four to five times faster than
multikey quicksort and previous radixsorts. A variant
that copies both suffixes and record pointers to
buckets, CP-burstsort, uses more memory, but provides
stable sorting. In current computers, where performance
is limited by memory access latencies, these new
algorithms can dramatically reduce the time needed for
internal sorting of large numbers of strings.",
acknowledgement = ack-nhfb,
articleno = "1.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; cache; experimental algorithms; sorting;
string management; tries",
}
@Article{Penner:2006:CFI,
author = "Michael Penner and Viktor K. Prasanna",
title = "Cache-Friendly implementations of transitive closure",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "1.3:1--1.3:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1210586",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The topic of cache performance has been well studied
in recent years. Compiler optimizations exist and
optimizations have been done for many problems. Much of
this work has focused on dense linear algebra problems.
At first glance, the Floyd--Warshall algorithm appears
to fall into this category. In this paper, we begin by
applying two standard cache-friendly optimizations to
the Floyd--Warshall algorithm and show limited
performance improvements. We then discuss the
unidirectional space time representation (USTR). We
show analytically that the USTR can be used to reduce
the amount of processor-memory traffic by a factor of
$O(\sqrt C)$, where $C$ is the cache size, for a large
class of algorithms. Since the USTR leads to a tiled
implementation, we develop a tile size selection
heuristic to intelligently narrow the search space for
the tile size that minimizes total execution time.
Using the USTR, we develop a cache-friendly
implementation of the Floyd--Warshall algorithm. We
show experimentally that this implementation minimizes
the level-1 and level-2 cache misses and TLB misses
and, therefore, exhibits the best overall performance.
Using this implementation, we show a $2 \times$
improvement in performance over the best compiler
optimized implementation on three different
architectures. Finally, we show analytically that our
implementation of the Floyd--Warshall algorithm is
asymptotically optimal with respect to processor-memory
traffic. We show experimental results for the Pentium
III, Alpha, and MIPS R12000 machines using problem
sizes between 1024 and 2048 vertices. We demonstrate
improved cache performance using the Simplescalar
simulator.",
acknowledgement = ack-nhfb,
articleno = "1.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "data structures; Floyd--Warshall algorithm; systolic
array algorithms",
}
@Article{Goshi:2006:ADM,
author = "Justin Goshi and Richard E. Ladner",
title = "Algorithms for dynamic multicast key distribution",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "1.4:1--1.4:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1210587",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We study the problem of multicast key distribution for
group security. Secure group communication systems
typically rely on a group key, which is a secret shared
among the members of the group. This key is used to
provide privacy by encrypting all group communications.
Because groups can be large and highly dynamic, it
becomes necessary to change the group key in a scalable
and secure fashion when members join and leave the
group. We present a series of algorithms for solving
this problem based on key trees. The algorithms attempt
to minimize the worst-case communication cost of
updates by maintaining balanced key tree structures. We
focus on the trade-off between the communication cost
because of the structure of the tree and that due to
the overhead of restructuring the tree to maintain its
balanced structure. The algorithms are analyzed for
worst-case tree structure bounds and evaluated
empirically via simulations.",
acknowledgement = ack-nhfb,
articleno = "1.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "dynamic key distribution; experimental algorithms;
multicast",
}
@Article{Aleksandrov:2006:PPG,
author = "Lyudmil Aleksandrov and Hristo Djidjev and Hua Guo and
Anil Maheshwari",
title = "Partitioning planar graphs with costs and weights",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "1.5:1--1.5:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1210588",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "A graph separator is a set of vertices or edges whose
removal divides an input graph into components of
bounded size. This paper describes new algorithms for
computing separators in planar graphs as well as
techniques that can be used to speed up the
implementation of graph partitioning algorithms and
improve the partition quality. In particular, we
consider planar graphs with costs and weights on the
vertices, where weights are used to estimate the sizes
of the partitions and costs are used to estimate the
size of the separator. We show that in these graphs one
can always find a small cost separator (consisting of
vertices or edges) that partitions the graph into
components of bounded weight. We describe
implementations of the partitioning algorithms and
discuss results of our experiments.",
acknowledgement = ack-nhfb,
articleno = "1.5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "graph algorithms; graph partitioning algorithms; graph
separators; implementation",
}
@Article{Ilinkin:2006:HEC,
author = "Ivayio Ilinkin and Ravi Janardan and Michiel Smid and
Eric Johnson and Paul Castillo and J{\"o}rg Schwerdt",
title = "Heuristics for estimating contact area of supports in
layered manufacturing",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "1.6:1--1.6:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1210589",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Layered manufacturing is a technology that allows
physical prototypes of three-dimensional(3D) models to
be built directly from their digital representation, as
a stack of two-dimensional(2D) layers. A key design
problem here is the choice of a suitable direction in
which the digital model should be oriented and built so
as to minimize the area of contact between the
prototype and temporary support structures that are
generated during the build. Devising an efficient
algorithm for computing such a direction has remained a
difficult problem for quite some time. In this paper, a
suite of efficient and practical heuristics is
presented for estimating the minimum contact area. Also
given is a technique for evaluating the quality of the
estimate provided by any heuristic, which does not
require knowledge of the (unknown and hard-to-compute)
optimal solution; instead, it provides an indirect
upper bound on the quality of the estimate via two
relatively easy-to-compute quantities. The algorithms
are based on various techniques from computational
geometry, such as ray-shooting, convex hulls, boolean
operations on polygons, and spherical arrangements, and
have been implemented and tested. Experimental results
on a wide range of real-world models show that the
heuristics perform quite well in practice.",
acknowledgement = ack-nhfb,
articleno = "1.6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithm implementation and testing; computational
geometry",
}
@Article{Pearce:2006:DTS,
author = "David J. Pearce and Paul H. J. Kelly",
title = "A dynamic topological sort algorithm for directed
acyclic graphs",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "1.7:1--1.7:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1210590",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We consider the problem of maintaining the topological
order of a directed acyclic graph (DAG) in the presence
of edge insertions and deletions. We present a new
algorithm and, although this has inferior time
complexity compared with the best previously known
result, we find that its simplicity leads to better
performance in practice. In addition, we provide an
empirical comparison against the three main
alternatives over a large number of random DAGs. The
results show our algorithm is the best for sparse
digraphs and only a constant factor slower than the
best on dense digraphs.",
acknowledgement = ack-nhfb,
articleno = "1.7",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "dynamic graph algorithms; topological sort",
}
@Article{Flammini:2006:RAF,
author = "Michele Flammini and Alfredo Navarra and Stephane
Perennes",
title = "The ``real'' approximation factor of the {MST}
heuristic for the minimum energy broadcasting",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "2.10:1--2.10:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1216587",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "This paper deals with one of the most studied problems
in the last few years in the field of wireless
communication in ad-hoc networks. The problem consists
of reducing the total energy consumption of wireless
radio stations distributed over a given area of
interest in order to perform the basic pattern of
communication by a broadcast. Recently, a tight
6-approximation of the minimum spanning tree heuristic
has been proven. While such a bound is theoretically
optimal if compared to the known lower bound of 6,
there is an obvious gap with practical experimental
results. By extensive experiments, proposing a new
technique to generate input instances and supported by
theoretical results, we show how the approximation
ratio can be actually considered close to 4 for a
``real-world'' set of instances. We consider, in fact,
instances more representative of common practices.
Those are usually composed by considerable number of
nodes uniformly and randomly distributed inside the
area of interest.",
acknowledgement = ack-nhfb,
articleno = "2.10",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "ad-hoc networks; broadcast; energy saving; spanning
tree",
}
@Article{Nikoletseas:2006:JSS,
author = "Sotiris Nikoletseas",
title = "{JEA Special Section}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "2.1:1--2.1:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1216578",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
acknowledgement = ack-nhfb,
articleno = "2.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Fahle:2006:FBB,
author = "Torsten Fahle and Karsten Tiemann",
title = "A faster branch-and-bound algorithm for the test-cover
problem based on set-covering techniques",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "2.2:1--2.2:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1216579",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The test-cover problem asks for the minimal number of
tests needed to uniquely identify a disease, infection,
etc. A collection of branch-and-bound algorithms was
proposed by De Bontridder et al. [2002]. Based on their
work, we introduce several improvements that are
compatible with all techniques described in De
Bontridder et al. [2002] and the more general setting
of {\em weighted\/} test-cover problems. We present a
faster data structure, cost-based variable fixing, and
adapt well-known set-covering techniques, including
Lagrangian relaxation and upper-bound heuristics. The
resulting algorithm solves benchmark instances up to 10
times faster than the former approach and up to 100
times faster than a general MIP solver.",
acknowledgement = ack-nhfb,
articleno = "2.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "branch-and-bound; Lagrangian relaxation; set-cover
problem; test-cover problem; variable fixing",
}
@Article{Leone:2006:FPN,
author = "Pierre Leone and Jose Rolim and Paul Albuquerque and
Christian Mazza",
title = "A framework for probabilistic numerical evaluation of
sensor networks: a case study of a localization
protocol",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "2.3:1--2.3:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1216580",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this paper we show how to use stochastic estimation
methods to investigate topological properties of sensor
networks as well as the behavior of dynamical processes
on these networks. The framework is particularly
important to study problems for which no theoretical
results are known, or cannot be directly applied in
practice, for instance, when only asymptotic results
are available. We also interpret Russo's formula in the
context of sensor networks and thus obtain practical
information on their reliability. As a case study, we
analyze a localization protocol for wireless sensor
networks and validate our approach by numerical
experiments. Finally, we mention three applications of
our approach: estimating the number of pivotal sensors
in a real network, minimizing the number of such
sensors for robustness purposes during the network
design and estimating the distance between successive
localized positions for mobile sensor networks.",
acknowledgement = ack-nhfb,
articleno = "2.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "localization process and reliability; sensor networks;
stochastic recursive estimation",
}
@Article{Festa:2006:GPR,
author = "Paola Festa and Panos M. Pardalos and Leonidas S.
Pitsoulis and Mauricio G. C. Resende",
title = "{GRASP} with path relinking for the weighted {MAXSAT}
problem",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "2.4:1--2.4:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1216581",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "A GRASP with path relinking for finding good-quality
solutions of the weighted maximum satisfiability
problem (MAX-SAT) is described in this paper. GRASP, or
Greedy Randomized Adaptive Search Procedure, is a
randomized multistart metaheuristic, where, at each
iteration, locally optimal solutions are constructed,
each independent of the others. Previous experimental
results indicate its effectiveness for solving weighted
MAX-SAT instances. Path relinking is a procedure used
to intensify the search around good-quality isolated
solutions that have been produced by the GRASP
heuristic. Experimental comparison of the pure GRASP
(without path relinking) and the GRASP with path
relinking illustrates the effectiveness of path
relinking in decreasing the average time needed to find
a good-quality solution for the weighted maximum
satisfiability problem.",
acknowledgement = ack-nhfb,
articleno = "2.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; experimentation; GRASP; heuristics; path
relinking; performance; time-to-target plots",
}
@Article{Mehlhorn:2006:IMC,
author = "Kurt Mehlhorn and Dimitrios Michail",
title = "Implementing minimum cycle basis algorithms",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "2.5:1--2.5:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1216582",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this paper, we consider the problem of computing a
minimum cycle basis of an undirected graph $G$ = ($V$,
$E$) with $n$ vertices and $m$ edges. We describe an
efficient implementation of an $O(m^3 + mn^2 \log n)$
algorithm. For sparse graphs, this is the currently
best-known algorithm. This algorithm's running time can
be partitioned into two parts with time $O(m^3)$ and
$O(m^2 n + mn^2 \log n)$, respectively. Our
experimental findings imply that for random graphs the
true bottleneck of a sophisticated implementation is
the $O(m^2 n + mn^2 \log n)$ part. A straightforward
implementation would require $\Omega(n m)$
shortest-path computations. Thus, we develop several
heuristics in order to get a practical algorithm. Our
experiments show that in random graphs our techniques
result in a significant speed-up. Based on our
experimental observations, we combine the two
fundamentally different approaches to compute a minimum
cycle basis to obtain a new hybrid algorithm with
running time $O(m^2 n^2)$. The hybrid algorithm is very
efficient, in practice, for random dense unweighted
graphs. Finally, we compare these two algorithms with a
number of previous implementations for finding a
minimum cycle basis of an undirected graph.",
acknowledgement = ack-nhfb,
articleno = "2.5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "cycle basis; graph algorithms",
}
@Article{Heinrich-Litan:2006:RCR,
author = "Laura Heinrich-Litan and Marco E. L{\"u}bbecke",
title = "Rectangle covers revisited computationally",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "2.6:1--2.6:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1216583",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We consider the problem of covering an orthogonal
polygon with a minimum number of axis-parallel
rectangles from a computational point of view. We
propose an integer program which is the first general
approach to obtain provably optimal solutions to this
well-studied NP-hard problem. It applies to common
variants like covering only the corners or the boundary
of the polygon and also to the weighted case. In
experiments, it turns out that the linear programming
relaxation is extremely tight and rounding a fractional
solution is an immediate high-quality heuristic. We
obtain excellent experimental results for polygons
originating from VLSI design, fax data sheets, black
and white images, and for random instances. Making use
of the dual linear program, we propose a stronger lower
bound on the optimum, namely, the cardinality of a
fractional stable set. Furthermore, we outline ideas
how to make use of this bound in primal--dual-based
algorithms. We give partial results, which make us
believe that our proposals have a strong potential to
settle the main open problem in the area: To find a
constant factor approximation algorithm for the
rectangle cover problem.",
acknowledgement = ack-nhfb,
articleno = "2.6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "integer programming; linear programming",
}
@Article{Panagopoulou:2006:APN,
author = "Panagiota N. Panagopoulou and Paul G. Spirakis",
title = "Algorithms for pure {Nash} equilibria in weighted
congestion games",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "2.7:1--2.7:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1216584",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In large-scale or evolving networks, such as the
Internet, there is no authority possible to enforce a
centralized traffic management. In such situations,
game theory, and especially the concepts of Nash
equilibria and congestion games [Rosenthal 1973] are a
suitable framework for analyzing the equilibrium
effects of selfish routes selection to network delays.
We focus here on {\em single-commodity\/} networks
where selfish users select paths to route their loads
(represented by arbitrary integer {\em weights\/}). We
assume that individual link delays are equal to the
total load of the link. We then focus on the algorithm
suggested in Fotakis et al. [2005], i.e., a
potential-based method for finding {\em pure\/} Nash
equilibria in such networks. A superficial analysis of
this algorithm gives an upper bound on its time, which
is polynomial in $n$ (the number of users) and the sum
of their weights $W$. This bound can be exponential in
$n$ when some weights are exponential. We provide
strong experimental evidence that this algorithm
actually converges to a pure Nash equilibrium in {\em
polynomial time}. More specifically, our experimental
findings suggest that the running time is a polynomial
function of $n$ and $\log W$. In addition, we propose
an initial allocation of users to paths that
dramatically accelerates this algorithm, compared to an
arbitrary initial allocation. A by-product of our
research is the discovery of a weighted potential
function when link delays are {\em exponential\/} to
their loads. This asserts the existence of pure Nash
equilibria for these delay functions and extends the
result of Fotakis et al. [2005].",
acknowledgement = ack-nhfb,
articleno = "2.7",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "congestion games; game theory; pure Nash equilibria",
}
@Article{Mohring:2006:PGS,
author = "Rolf H. M{\"o}hring and Heiko Schilling and Birk
Sch{\"u}tz and Dorothea Wagner and Thomas Willhalm",
title = "Partitioning graphs to speedup {Dijkstra}'s
algorithm",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "2.8:1--2.8:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1216585",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We study an acceleration method for point-to-point
shortest-path computations in large and sparse directed
graphs with given nonnegative arc weights. The
acceleration method is called the {\em arc-flag
approach\/} and is based on Dijkstra's algorithm. In
the arc-flag approach, we allow a preprocessing of the
network data to generate additional information, which
is then used to speedup shortest-path queries. In the
preprocessing phase, the graph is divided into regions
and information is gathered on whether an arc is on a
shortest path into a given region. The arc-flag method
combined with an appropriate partitioning and a
bidirected search achieves an average speedup factor of
more than 500 compared to the standard algorithm of
Dijkstra on large networks (1 million nodes, 2.5
million arcs). This combination narrows down the search
space of Dijkstra's algorithm to almost the size of the
corresponding shortest path for long-distance
shortest-path queries. We conduct an experimental study
that evaluates which partitionings are best suited for
the arc-flag method. In particular, we examine
partitioning algorithms from computational geometry and
a multiway arc separator partitioning. The evaluation
was done on German road networks. The impact of
different partitions on the speedup of the shortest
path algorithm are compared. Furthermore, we present an
extension of the speedup technique to multiple levels
of partitions. With this multilevel variant, the same
speedup factors can be achieved with smaller space
requirements. It can, therefore, be seen as a
compression of the precomputed data that preserves the
correctness of the computed shortest paths.",
acknowledgement = ack-nhfb,
articleno = "2.8",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "acceleration method; Dijkstra's algorithm; road
network; shortest path",
}
@Article{Boukerche:2006:ICC,
author = "Azzedine Boukerche and Alba Cristina Magalhaes {Alves
De Melo}",
title = "Integrating coordinated checkpointing and recovery
mechanisms into {DSM} synchronization barriers",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "11",
pages = "2.9:1--2.9:??",
month = "????",
year = "2006",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1187436.1216586",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:06:20 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Distributed shared memory (DSM) creates an abstraction
of a physical shared memory that parallel programmers
can access. Most recent software DSM systems provide
relaxed-memory models that guarantee consistency only
at synchronization operations, such as locks and
barriers. As the main goal of DSM systems is to provide
support for long-term computation-intensive
applications, checkpointing and recovery mechanisms are
highly desirable. This article presents and evaluates
the integration of a coordinated checkpointing
mechanism to the barrier primitive that is usually
provided with many DSM systems. Our results on some
popular benchmarks and a real parallel application show
that the overhead introduced during the failure-free
execution is often small.",
acknowledgement = ack-nhfb,
articleno = "2.9",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "barrier synchronization; distributed shared memory",
}
@Article{Anonymous:2008:EGC,
author = "Anonymous",
title = "Engineering graph clustering: {Models} and
experimental evaluation",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "1.1:1--1.1:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1227162",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "A promising approach to graph clustering is based on
the intuitive notion of intracluster density versus
intercluster sparsity. As for the weighted case,
clusters should accumulate lots of weight, in contrast
to their connection to the remaining graph, which
should be light. While both formalizations and
algorithms focusing on particular aspects of this
rather vague concept have been proposed, no conclusive
argument on their appropriateness has been given. In
order to deepen the understanding of particular
concepts, including both quality assessment as well as
designing new algorithms, we conducted an experimental
evaluation of graph-clustering approaches. By combining
proved techniques from graph partitioning and geometric
clustering, we also introduce a new approach that
compares favorably.",
acknowledgement = ack-nhfb,
articleno = "1.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "clustering algorithms; experimental evaluation; graph
clustering; quality measures",
}
@Article{Barsky:2008:GAT,
author = "Marina Barsky and Ulrike Stege and Alex Thomo and
Chris Upton",
title = "A graph approach to the threshold all-against-all
substring matching problem",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "1.10:1--1.10:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1370596.1370601",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present a novel graph model and an efficient
algorithm for solving the ``threshold all against all''
problem, which involves searching two strings (with
length $M$ and $N$, respectively) for all maximal
approximate substring matches of length at least $S$,
with up to $K$ differences. Our algorithm solves the
problem in time $O(MNK_3)$, which is a considerable
improvement over the previous known bound for this
problem. We also provide experimental evidence that, in
practice, our algorithm exhibits a better performance
than its worst-case running time.",
acknowledgement = ack-nhfb,
articleno = "1.10",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "bioinformatics; complexity; string matching",
}
@Article{Dietzfelbinger:2008:DIB,
author = "Martin Dietzfelbinger and Martin H{\"u}hne and
Christoph Weidling",
title = "A dictionary implementation based on dynamic perfect
hashing",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "1.11:1--1.11:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1370596.1370602",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We describe experimental results on an implementation
of a dynamic dictionary. The basis of our
implementation is ``dynamic perfect hashing'' as
described by Dietzfelbinger et al. ({\em SIAM J.
Computing 23}, 1994, pp. 738--761), an extension of the
storage scheme proposed by Fredman et al. ({\em J.
ACM\/} 31, 1984, pp. 538--544). At the top level, a
hash function is used to partition the keys to be
stored into several sets. On the second level, there is
a perfect hash function for each of these sets. This
technique guarantees $O(1)$ worst-case time for lookup
and expected $O(1)$ amortized time for insertion and
deletion, while only linear space is required. We study
the practical performance of dynamic perfect hashing
and describe improvements of the basic scheme. The
focus is on the choice of the hash function (both for
integer and string keys), on the efficiency of
rehashing, on the handling of small buckets, and on the
space requirements of the implementation.",
acknowledgement = ack-nhfb,
articleno = "1.11",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "data structures; dictionaries; dynamic hashing; hash
functions; implementation",
}
@Article{Maniscalco:2008:EVA,
author = "Michael A. Maniscalco and Simon J. Puglisi",
title = "An efficient, versatile approach to suffix sorting",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "1.2:1--1.2:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1278374",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Sorting the suffixes of a string into lexicographical
order is a fundamental task in a number of contexts,
most notably lossless compression (Burrows--Wheeler
transformation) and text indexing (suffix arrays). Most
approaches to suffix sorting produce a sorted array of
suffixes directly, continually moving suffixes into
their final place in the array until the ordering is
complete. In this article, we describe a novel and
resource-efficient (time and memory) approach to suffix
sorting, which works in a complementary way --- by
assigning each suffix its rank in the final ordering,
before converting to a sorted array, if necessary, once
all suffixes are ranked. We layer several powerful
extensions on this basic idea and show experimentally
that our approach is superior to other leading
algorithms in a variety of real-world contexts.",
acknowledgement = ack-nhfb,
articleno = "1.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "Burrows--Wheeler transform; suffix array; suffix
sorting; suffix tree",
}
@Article{Aloul:2008:SBP,
author = "Fadi A. Aloul and Arathi Ramani and Igor L. Markov and
Karem A. Sakallah",
title = "Symmetry breaking for pseudo-{Boolean} formulas",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "1.3:1--1.3:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1278375",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Many important tasks in design automation and
artificial intelligence can be performed in practice
via reductions to Boolean satisfiability (SAT).
However, such reductions often omit
application-specific structure, thus handicapping tools
in their competition with creative engineers.
Successful attempts to represent and utilize additional
structure on Boolean variables include recent work on
0-1 integer linear programming (ILP) and symmetries in
SAT. Those extensions gracefully accommodate well-known
advances in SAT solving, however, no previous work has
attempted to combine both extensions. Our work shows
(i) how one can detect and use symmetries in instances
of 0-1 ILP, and (ii) what benefits this may bring.",
acknowledgement = ack-nhfb,
articleno = "1.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "graph automorphism",
}
@Article{Pellegrini:2008:EIT,
author = "Marco Pellegrini and Giordano Fusco",
title = "Efficient {IP} table lookup via adaptive stratified
trees with selective reconstructions",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "1.4:1--1.4:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1278376",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "IP address lookup is a critical operation for
high-bandwidth routers in packet-switching networks,
such as Internet. The lookup is a nontrivial operation,
since it requires searching for the longest prefix,
among those stored in a (large) given table, matching
the IP address. Ever increasing routing table size,
traffic volume, and links speed demand new and more
efficient algorithms. Moreover, the imminent move to
IPv6 128-bit addresses will soon require a rethinking
of previous technical choices. This article describes a
the new data structure for solving the IP table lookup
problem christened the adaptive stratified tree (AST).
The proposed solution is based on casting the problem
in geometric terms and on repeated application of
efficient local geometric optimization routines.
Experiments with this approach have shown that in terms
of storage, query time, and update time the AST is at a
par with state of the art algorithms based on data
compression or string manipulations (and often it is
better on some of the measured quantities).",
acknowledgement = ack-nhfb,
articleno = "1.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "data structures; IP table lookup",
}
@Article{Navarro:2008:DSA,
author = "Gonzalo Navarro and Nora Reyes",
title = "Dynamic spatial approximation trees",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "1.5:1--1.5:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1322337",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Metric space searching is an emerging technique to
address the problem of efficient similarity searching
in many applications, including multimedia databases
and other repositories handling complex objects.
Although promising, the metric space approach is still
immature in several aspects that are well established
in traditional databases. In particular, most indexing
schemes are static, that is, few of them tolerate
insertion or deletion of elements at reasonable cost
over an existing index. The spatial approximation tree
({\em sa--tree\/}) has been experimentally shown to
provide a good tradeoff between construction cost,
search cost, and space requirement. However, the {\em
sa--tree\/} is static, which renders it unsuitable for
many database applications. In this paper, we study
different methods to handle insertions and deletions on
the {\em sa--tree\/} at low cost. In many cases, the
dynamic construction (by successive insertions) is even
faster than the previous static construction, and both
are similar elsewhere. In addition, the dynamic version
significantly improves the search performance of {\em
sa--trees\/} in virtually all cases. The result is a
much more practical data structure that can be useful
in a wide range of database applications.",
acknowledgement = ack-nhfb,
articleno = "1.5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "multimedia databases; similarity or proximity search;
spatial and multidimensional search; spatial
approximation tree",
}
@Article{Li:2008:EAC,
author = "Keqin Li",
title = "Experimental average-case performance evaluation of
online algorithms for routing and wavelength assignment
and throughput maximization in {WDM} optical networks",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "1.7:1--1.7:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1370596.1370598",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We investigate the problem of online routing and
wavelength assignment and the related throughput
maximization problem in wavelength division
multiplexing optical networks. It is pointed out that
these problems are highly inapproximable, that is, the
competitive ratio of any algorithm is at least a
polynomial. We evaluate the average-case performance of
several online algorithms, which have no knowledge of
future arriving connection requests when processing the
current connection request. Our experimental results on
a wide range of optical networks demonstrate that the
average-case performance of these algorithms are very
close to optimal.",
acknowledgement = ack-nhfb,
articleno = "1.7",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "average-case performance; competitive ratio; online
algorithm; optical network; routing; wavelength
assignment; wavelength division multiplexing",
}
@Article{Biggar:2008:ESS,
author = "Paul Biggar and Nicholas Nash and Kevin Williams and
David Gregg",
title = "An experimental study of sorting and branch
prediction",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "1.8:1--1.8:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1370599",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Sorting is one of the most important and well-studied
problems in computer science. Many good algorithms are
known which offer various trade-offs in efficiency,
simplicity, memory use, and other factors. However,
these algorithms do not take into account features of
modern computer architectures that significantly
influence performance. Caches and branch predictors are
two such features and, while there has been a
significant amount of research into the cache
performance of general purpose sorting algorithms,
there has been little research on their branch
prediction properties. In this paper, we empirically
examine the behavior of the branches in all the most
common sorting algorithms. We also consider the
interaction of cache optimization on the predictability
of the branches in these algorithms. We find insertion
sort to have the fewest branch mispredictions of any
comparison-based sorting algorithm, that bubble and
shaker sort operate in a fashion that makes their
branches highly unpredictable, that the
unpredictability of shellsort's branches improves its
caching behavior, and that several cache optimizations
have little effect on mergesort's branch
mispredictions. We find also that optimizations to
quicksort, for example the choice of pivot, have a
strong influence on the predictability of its branches.
We point out a simple way of removing branch
instructions from a classic heapsort implementation and
also show that unrolling a loop in a cache-optimized
heapsort implementation improves the predicitability of
its branches. Finally, we note that when sorting random
data two-level adaptive branch predictors are usually
no better than simpler bimodal predictors. This is
despite the fact that two-level adaptive predictors are
almost always superior to bimodal predictors, in
general.",
acknowledgement = ack-nhfb,
articleno = "1.8",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "branch prediction; caching; pipeline architectures;
sorting",
}
@Article{Hazel:2008:TCL,
author = "Thomas Hazel and Laura Toma and Jan Vahrenhold and
Rajiv Wickremesinghe",
title = "Terracost: {Computing} least-cost-path surfaces for
massive grid terrains",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "1.9:1--1.9:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1370596.1370600",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "This paper addresses the problem of computing
least-cost-path surfaces for massive grid terrains.
Consider a grid terrain $T$ and let $C$ be a cost grid
for $T$ such that every point in $C$ stores a value
that represents the cost of traversing the
corresponding point in $T$. Given $C$ and a set of
sources $S \in T$, a least-cost-path grid $\Delta$ for
$T$ is a grid such that every point in $\Delta$
represents the distance to the source in $S$ that can
be reached with minimal cost. We present a scalable
approach to computing least-cost-path grids. Our
algorithm, terracost, is derived from our previous work
on I/O-efficient shortest paths on grids and uses
$O(\hbox{sort}(n))$ I/Os, where $\hbox{sort}(n)$ is the
complexity of sorting $n$ items of data in the
I/O-model of Aggarwal and Vitter. We present the
design, the analysis, and an experimental study of
terracost. An added benefit of the algorithm underlying
terracost is that it naturally lends itself to
parallelization. We have implemented terracost in a
distributed environment using our cluster management
tool and report on experiments that show that it
obtains speedup near-linear with the size of the
cluster. To the best of our knowledge, this is the
first experimental evaluation of a multiple-source
least-cost-path algorithm in the external memory
setting.",
acknowledgement = ack-nhfb,
articleno = "1.9",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "data structures and algorithms; Dijkstra's algorithm;
I/O-efficiency; shortest paths; terrain data",
}
@Article{Arge:2008:P,
author = "Lars Arge and Giuseppe F. Italiano",
title = "Preface",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "2.1:1--2.1:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1227163",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
acknowledgement = ack-nhfb,
articleno = "2.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Brodal:2008:ECO,
author = "Gerth St{\o}lting Brodal and Rolf Fagerberg and
Kristoffer Vinther",
title = "Engineering a cache-oblivious sorting algorithm",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "2.2:1--2.2:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1227164",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "This paper is an algorithmic engineering study of
cache-oblivious sorting. We investigate by empirical
methods a number of implementation issues and parameter
choices for the cache-oblivious sorting algorithm Lazy
Funnelsort and compare the final algorithm with
Quicksort, the established standard for
comparison-based sorting, as well as with recent
cache-aware proposals. The main result is a carefully
implemented cache-oblivious sorting algorithm, which,
our experiments show, can be faster than the best
Quicksort implementation we are able to find for input
sizes well within the limits of RAM. It is also at
least as fast as the recent cache-aware implementations
included in the test. On disk, the difference is even
more pronounced regarding Quicksort and the cache-aware
algorithms, whereas the algorithm is slower than a
careful implementation of multiway Mergesort, such as
TPIE.",
acknowledgement = ack-nhfb,
articleno = "2.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "cache-oblivious algorithms; funnelsort; quicksort",
}
@Article{Bender:2008:SSH,
author = "Michael A. Bender and Bryan Bradley and Geetha
Jagannathan and Krishnan Pillaipakkamnatt",
title = "Sum-of-squares heuristics for bin packing and memory
allocation",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "2.3:1--2.3:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1227165",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The sum-of-squares algorithm (SS) was introduced by
Csirik, Johnson, Kenyon, Shor, and Weber for online bin
packing of integral-sized items into integral-sized
bins. First, we show the results of experiments from
two new variants of the SS algorithm. The first
variant, which runs in time $O(n \sqrt{B \log B})$,
appears to have almost identical expected waste as the
sum-of-squares algorithm on all the distributions
mentioned in the original papers on this topic. The
other variant, which runs in $O(n \log B)$ time,
performs well on most, but not on all of those
distributions. We also apply SS to the online
memory-allocation problem. Our experimental comparisons
between SS and Best Fit indicate that neither algorithm
is consistently better than the other. If the amount of
randomness in item sizes is low, SS appears to have
lower waste than Best Fit, whereas, if the amount of
randomness is high Best Fit appears to have lower waste
than SS. Our experiments suggest that in both real and
synthetic traces, SS does not seem to have an
asymptotic advantage over Best Fit, in contrast with
the bin-packing problem.",
acknowledgement = ack-nhfb,
articleno = "2.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "bin packing; memory allocation; sum of squares",
}
@Article{Pyrga:2008:EMT,
author = "Evangelia Pyrga and Frank Schulz and Dorothea Wagner
and Christos Zaroliagis",
title = "Efficient models for timetable information in public
transportation systems",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "2.4:1--2.4:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1227166",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We consider two approaches that model timetable
information in public transportation systems as
shortest-path problems in weighted graphs. In the {\em
time-expanded\/} approach, every event at a station,
e.g., the departure of a train, is modeled as a node in
the graph, while in the {\em time-dependent\/} approach
the graph contains only one node per station. Both
approaches have been recently considered for (a
simplified version of) the earliest arrival problem,
but little is known about their relative performance.
Thus far, there are only theoretical arguments in favor
of the time-dependent approach. In this paper, we
provide the first extensive experimental comparison of
the two approaches. Using several real-world data sets,
we evaluate the performance of the basic models and of
several new extensions towards realistic modeling.
Furthermore, new insights on solving bicriteria
optimization problems in both models are presented. The
time-expanded approach turns out to be more robust for
modeling more complex scenarios, whereas the
time-dependent approach shows a clearly better
performance.",
acknowledgement = ack-nhfb,
articleno = "2.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "itinerary query; public transportation system;
shortest path; timetable information",
}
@Article{Leaver-Fay:2008:FPH,
author = "Andrew Leaver-Fay and Yuanxin Liu and Jack Snoeyink
and Xueyi Wang",
title = "Faster placement of hydrogens in protein structures by
dynamic programming",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "2.5:1--2.5:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1227167",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "M. Word and coauthors from the Richardsons' 3D Protein
Structure laboratory at Duke University propose {\em
dot scores\/} to measure interatomic interactions in
molecular structures. Their program REDUCE uses these
scores in a brute-force search to solve instances of
the {\em NP\/}-hard problem of finding the optimal
placement of hydrogen atoms in molecular structures
determined by X-ray crystallography. We capture the
central combinatorial optimization in the hydrogen
placement problem with an abstraction that we call an
interaction (hyper)graph. REDUCE's dot-based scoring
function cannot be decomposed into the sum of pair
interactions, but because the function is short ranged
we are able to decompose it into the sum of single,
pair, triple, and quadruple interactions that we
represent by graph hyperedges. Almost every interaction
graph we have observed has had a small treewidth. This
fact allows us to replace the brute-force search by
dynamic programming, giving speedups of nearly ten
orders of magnitude. This dynamic programming has been
incorporated into REDUCE and is available for
download.",
acknowledgement = ack-nhfb,
articleno = "2.5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "dynamic programming; hard-sphere model; hydrogen
bonds; hydrogen placement; protein structure;
treewidth",
}
@Article{Demetrescu:2008:PA,
author = "Camil Demetrescu and Roberto Tamassia",
title = "Papers from {ALENEX 2005}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "3.1:1--3.1:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1402293",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
acknowledgement = ack-nhfb,
articleno = "3.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Brodal:2008:AQ,
author = "Gerth St{\o}lting Brodal and Rolf Fagerberg and
Gabriel Moruz",
title = "On the adaptiveness of {Quicksort}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "3.2:1--3.2:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1402294",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Quicksort was first introduced in 1961 by Hoare. Many
variants have been developed, the best of which are
among the fastest generic-sorting algorithms available,
as testified by the choice of Quicksort as the default
sorting algorithm in most programming libraries. Some
sorting algorithms are adaptive, i.e., they have a
complexity analysis that is better for inputs, which
are nearly sorted, according to some specified measure
of presortedness. Quicksort is not among these, as it
uses $\Omega (n \log n)$ comparisons even for sorted
inputs. However, in this paper, we demonstrate
empirically that the actual running time of Quicksort
{\em is\/} adaptive with respect to the presortedness
measure Inv. Differences close to a factor of two are
observed between instances with low and high Inv value.
We then show that for the randomized version of
Quicksort, the number of element {\em swaps\/}
performed is {\em provably\/} adaptive with respect to
the measure $\hbox{Inv}$. More precisely, we prove that
randomized Quicksort performs expected $O(n (1 + \log(1
+ \hbox{Inv} / n)))$ element swaps, where $\hbox{Inv}$
denotes the number of inversions in the input sequence.
This result provides a theoretical explanation for the
observed behavior and gives new insights on the
behavior of Quicksort. We also give some empirical
results on the adaptive behavior of Heapsort and
Mergesort.",
acknowledgement = ack-nhfb,
articleno = "3.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "adaptive sorting; branch mispredictions; Quicksort",
}
@Article{Codenotti:2008:ESD,
author = "Bruno Codenotti and Benton Mccune and Sriram Pemmaraju
and Rajiv Raman and Kasturi Varadarajan",
title = "An experimental study of different approaches to solve
the market equilibrium problem",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "3.3:1--3.3:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1402295",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Over the last few years, the problem of computing
market equilibrium prices for exchange economies has
received much attention in the theoretical computer
science community. Such activity led to a flurry of
polynomial time algorithms for various restricted, yet
significant, settings. The most important restrictions
arise either when the traders' utility functions
satisfy a property known as {\em gross
substitutability\/} or when the initial endowments are
proportional (the Fisher model). In this paper, we
experimentally compare the performance of some of these
recent algorithms against that of the most used
software packages. In particular, we evaluate the
following approaches: (1) the solver PATH, available
under GAMS/MPSGE, a popular tool for computing market
equilibrium prices; (2) a discrete version of a simple
iterative price update scheme called t{\^a}tonnement;
(3) a discrete version of the welfare adjustment
process; (4) convex feasibility programs that
characterize the equilibrium in some special cases. We
analyze the performance of these approaches on models
of exchange economies where the consumers are equipped
with utility functions, which are widely used in real
world applications. The outcomes of our experiments
consistently show that many market settings allow for
an efficient computation of the equilibrium, well
beyond the restrictions under which the theory provides
polynomial time guarantees. For some of the approaches,
we also identify models where they are prone to
failure.",
acknowledgement = ack-nhfb,
articleno = "3.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "market equilibrium",
}
@Article{Dementiev:2008:BEM,
author = "Roman Dementiev and Juha K{\"a}rkk{\"a}inen and Jens
Mehnert and Peter Sanders",
title = "Better external memory suffix array construction",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "3.4:1--3.4:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1402296",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Suffix arrays are a simple and powerful data structure
for text processing that can be used for full text
indexes, data compression, and many other applications,
in particular, in bioinformatics. However, so far, it
has appeared prohibitive to build suffix arrays for
huge inputs that do not fit into main memory. This
paper presents design, analysis, implementation, and
experimental evaluation of several new and improved
algorithms for suffix array construction. The
algorithms are asymptotically optimal in the worst case
or on average. Our implementation can construct suffix
arrays for inputs of up to 4-GB in hours on a low-cost
machine. As a tool of possible independent interest, we
present a systematic way to design, analyze, and
implement {\em pipelined\/} algorithms.",
acknowledgement = ack-nhfb,
articleno = "3.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithm engineering; algorithms for strings;
external memory; I/O-efficient; large data sets;
secondary memory; suffix array",
}
@Article{Swenson:2008:ATE,
author = "Krister M. Swenson and Mark Marron and Joel V.
Earnest-Deyoung and Bernard M. E. Moret",
title = "Approximating the true evolutionary distance between
two genomes",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "3.5:1--3.5:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1227161.1402297",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "As more and more genomes are sequenced, evolutionary
biologists are becoming increasingly interested in
evolution at the level of whole genomes, in scenarios
in which the genome evolves through insertions,
duplications, deletions, and movements of genes along
its chromosomes. In the mathematical model pioneered by
Sankoff and others, a unichromosomal genome is
represented by a signed permutation of a multiset of
genes; Hannenhalli and Pevzner showed that the edit
distance between two signed permutations of the same
set can be computed in polynomial time when all
operations are inversions. El-Mabrouk extended that
result to allow deletions and a limited form of
insertions (which forbids duplications); in turn we
extended it to compute a nearly optimal edit sequence
between an arbitrary genome and the identity
permutation. In this paper we generalize our approach
to compute distances between two arbitrary genomes, but
focus on approximating the true evolutionary distance
rather than the edit distance. We present experimental
results showing that our algorithm produces excellent
estimates of the true evolutionary distance up to a
(high) threshold of saturation; indeed, the distances
thus produced are good enough to enable the simple
neighbor-joining procedure to reconstruct our test
trees with high accuracy.",
acknowledgement = ack-nhfb,
articleno = "3.5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "duplications; evolution; inversions; pairwise
distances; whole-genome data",
}
@Article{Krommidas:2008:ESA,
author = "Ioannis Krommidas and Christos Zaroliagis",
title = "An experimental study of algorithms for fully dynamic
transitive closure",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "12",
pages = "16:1--16:??",
month = jun,
year = "2008",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1370596.1370597",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:17:58 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We have conducted an extensive experimental study on
algorithms for fully dynamic transitive closure. We
have implemented the recent fully dynamic algorithms by
King [1999], Roditty [2003], Roditty and Zwick [2002,
2004], and Demetrescu and Italiano [2000, 2005] along
with several variants and compared them to pseudo fully
dynamic and simple-minded algorithms developed in a
previous study [Frigioni et al. 2001]. We tested and
compared these implementations on random inputs,
synthetic (worst-case) inputs, and on inputs motivated
by real-world graphs. Our experiments reveal that some
of the dynamic algorithms can really be of practical
value in many situations.",
acknowledgement = ack-nhfb,
articleno = "16",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "dynamic algorithm; path; reachability; transitive
closure",
}
@Article{Gottlob:2008:BBA,
author = "Georg Gottlob and Marko Samer",
title = "A backtracking-based algorithm for hypertree
decomposition",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "13",
pages = "1:1--1:??",
month = sep,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1412228.1412229",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:18:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Hypertree decompositions of hypergraphs are a
generalization of tree decompositions of graphs. The
corresponding hypertree-width is a measure for the
acyclicity and therefore an indicator for the
tractability of the associated computation problem.
Several NP-hard decision and computation problems are
known to be tractable on instances whose structure is
represented by hypergraphs of bounded hypertree-width.
Roughly speaking, the smaller the hypertree-width, the
faster the computation problem can be solved. In this
paper, we present the new backtracking-based algorithm
det-$k$-decomp for computing hypertree decompositions
of small width. Our benchmark evaluations have shown
that det-$k$-decomp significantly outperforms opt-
$k$-decomp, the only exact hypertree decomposition
algorithm so far. Even compared to the best heuristic
algorithm, we obtained competitive results as long as
the hypergraphs are sufficiently simple.",
acknowledgement = ack-nhfb,
articleno = "1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "constraint satisfaction; hypertree decomposition",
}
@Article{Raman:2008:P,
author = "Rajeev Raman and Matt Stallmann",
title = "Preface",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "13",
pages = "1:1--1:??",
month = sep,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1412228.1412235",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:18:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
acknowledgement = ack-nhfb,
articleno = "1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Gramm:2008:DRE,
author = "Jens Gramm and Jiong Guo and Falk H{\"u}ffner and Rolf
Niedermeier",
title = "Data reduction and exact algorithms for clique cover",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "13",
pages = "2:1--2:??",
month = sep,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1412228.1412236",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:18:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "To cover the edges of a graph with a minimum number of
cliques is an NP-hard problem with many applications.
For this problem we develop efficient and effective
polynomial-time data reduction rules that, combined
with a search tree algorithm, allow for exact problem
solutions in competitive time. This is confirmed by
experiments with real-world and synthetic data.
Moreover, we prove the fixed-parameter tractability of
covering edges by cliques.",
acknowledgement = ack-nhfb,
articleno = "2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "clique cover; data reduction; fixed-parameter
tractability",
}
@Article{Haran:2008:ESP,
author = "Idit Haran and Dan Halperin",
title = "An experimental study of point location in planar
arrangements in {CGAL}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "13",
pages = "3:1--3:??",
month = sep,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1412228.1412237",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:18:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We study the performance in practice of various
point-location algorithms implemented in CGAL (the
Computational Geometry Algorithms Library), including a
newly devised {\em landmarks\/} algorithm. Among the
other algorithms studied are: a na{\"\i}ve approach, a
``walk along a line'' strategy, and a trapezoidal
decomposition-based search structure. The current
implementation addresses general arrangements of planar
curves, including arrangements of nonlinear segments
(e.g., conic arcs) and allows for degenerate input (for
example, more than two curves intersecting in a single
point or overlapping curves). The algorithms use exact
geometric computation and thus result in the correct
point location. In our landmarks algorithm (a.k.a. jump
\& walk), special points, ``landmarks,'' are chosen in
a preprocessing stage, their place in the arrangement
is found, and they are inserted into a data structure
that enables efficient nearest-neighbor search. Given a
query point, the nearest landmark is located and a
``walk'' strategy is applied from the landmark to the
query point. We report on various experiments with
arrangements composed of line segments or conic arcs.
The results indicate that compared to the other
algorithms tested, the landmarks approach is the most
efficient, when the overall (amortized) cost of a query
is taken into account, combining both preprocessing and
query time. The simplicity of the algorithm enables an
almost straightforward implementation and rather easy
maintenance. The generic programming implementation
allows versatility both in the selected type of
landmarks and in the choice of the nearest-neighbor
search structure. The end result is an efficient
point-location algorithm that bypasses the alternative
CGAL implementations in most practical aspects.",
acknowledgement = ack-nhfb,
articleno = "3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "arrangements; CGAL; computational geometry; generic
programming; point location",
}
@Article{Lanthier:2008:CAC,
author = "Mark A. Lanthier and Doron Nussbaum and Tsuo-Jung
Wang",
title = "Computing an approximation of the $1$-center problem
on weighted terrain surfaces",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "13",
pages = "3:1--3:??",
month = sep,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1412228.1412231",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:18:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this article, we discuss the problem of determining
a meeting point of a set of scattered robots $R = r_1,
r _2, \ldots{}, r_s$ in a weighted terrain $P$, which
has $n > s$ triangular faces. Our algorithmic approach
is to produce a discretization of $P$ by producing a
graph $G = \{V^G, E^G\}$, which lies on the surface of
$P$. For a chosen vertex $p' \in V^G$, we define
$|\Pi(r_i, p')|$ as the minimum weight cost of
traveling from $r_i$ to $p'$. We show that min$_{p'}
\in V^G$ \hbox{max}$_{1\leq i \leq s} |\Pi(r_i, p')|
\leq \hbox{min}_p *\in P \hbox{max}_{1\leq i \leq s}
|{\Pi}(r_i, p*)| + 2 W |L|$, where $L$ is the longest
edge of $P$, $W$ is the maximum cost weight of a face
of $P$, and $p*$ is the optimal solution. Our algorithm
requires $O(s n m \log(s n m) + s n m^2)$ time to run,
where $m = n$ in the Euclidean metric and $m = n^2$ in
the weighted metric. However, we show, through
experimentation, that only a constant value of $m$ is
required (e.g., $m = 8$) in order to produce very
accurate solutions.",
acknowledgement = ack-nhfb,
articleno = "3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "1-Center; algorithms; approximation; meeting point;
robots; shortest path; terrain; weighted",
}
@Article{Hershberger:2008:SSD,
author = "John Hershberger and Nisheeth Shrivastava and Subhash
Suri",
title = "Summarizing spatial data streams using
{ClusterHulls}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "13",
pages = "4:1--4:??",
month = sep,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1412228.1412238",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:18:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We consider the following problem: given an on-line,
possibly unbounded stream of two-dimensional (2D)
points, how can we summarize its spatial distribution
or {\em shape\/} using a small, bounded amount of
memory? We propose a novel scheme, called {\em
ClusterHull}, which represents the shape of the stream
as a dynamic collection of convex hulls, with a total
of at most $m$ vertices, where $m$ is the size of the
memory. The algorithm dynamically adjusts both the
number of hulls and the number of vertices in each hull
to best represent the stream using its fixed-memory
budget. This algorithm addresses a problem whose
importance is increasingly recognized, namely, the
problem of summarizing real-time data streams to enable
on-line analytical processing. As a motivating example,
consider habitat monitoring using wireless sensor
networks. The sensors produce a steady stream of
geographic data, namely, the locations of objects being
tracked. In order to conserve their limited resources
(power, bandwidth, and storage), the sensors can
compute, store, and exchange ClusterHull summaries of
their data, without losing important geometric
information. We are not aware of other schemes
specifically designed for capturing shape information
in geometric data streams and so we compare ClusterHull
with some of the best general-purpose clustering
schemes, such as CURE, $k$-medians, and LSEARCH. We
show through experiments that ClusterHull is able to
represent the shape of two-dimensional data streams
more faithfully and flexibly than the stream versions
of these clustering algorithms.",
acknowledgement = ack-nhfb,
articleno = "4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "convex hull; data streams; geometric data",
}
@Article{Safro:2008:MAL,
author = "Ilya Safro and Dorit Ron and Achi Brandt",
title = "Multilevel algorithms for linear ordering problems",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "13",
pages = "4:1--4:??",
month = sep,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1412228.1412232",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:18:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Linear ordering problems are combinatorial
optimization problems that deal with the minimization
of different functionals by finding a suitable
permutation of the graph vertices. These problems are
widely used and studied in many practical and
theoretical applications. In this paper, we present a
variety of linear--time algorithms for these problems
inspired by the Algebraic Multigrid approach, which is
based on weighted-edge contraction. The experimental
result for four such problems turned out to be better
than every known result in almost all cases, while the
short (linear) running time of the algorithms enables
testing very large graphs.",
acknowledgement = ack-nhfb,
articleno = "4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algebraic multigrid; linear ordering; multilevel
algorithm",
}
@Article{Holzer:2008:EMO,
author = "Martin Holzer and Frank Schulz and Dorothea Wagner",
title = "Engineering multilevel overlay graphs for
shortest-path queries",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "13",
pages = "5:1--5:??",
month = sep,
year = "2008",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1412228.1412239",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Oct 6 16:18:31 MDT 2008",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "An overlay graph of a given graph $G$ = ($V$, $E$) on
a subset $S \subseteq V$ is a graph with vertex set $S$
and edges corresponding to shortest paths in $G$. In
particular, we consider variations of the multilevel
overlay graph used in Schulz et al. [2002] to speed up
shortest-path computation. In this work, we follow up
and present several vertex selection criteria, along
with two general strategies of applying these criteria,
to determine a subset $S$ of a graph's vertices. The
main contribution is a systematic experimental study
where we investigate the impact of selection criteria
and strategies on multilevel overlay graphs and the
resulting speed-up achieved for shortest-path
computation: Depending on selection strategy and graph
type, a centrality index criterion, selection based on
planar separators, and vertex degree turned out to
perform best.",
acknowledgement = ack-nhfb,
articleno = "5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "Dijkstra's algorithm; hierarchical; multilevel;
overlay graph; preprocessing; shortest path; speed-up
technique; vertex selection",
}
@Article{Julstrom:2009:GHB,
author = "Bryant A. Julstrom",
title = "Greedy heuristics for the bounded diameter minimum
spanning tree problem",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
pages = "1:1--1:??",
month = may,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed Jun 3 16:21:43 MDT 2009",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Given a connected, weighted, undirected graph G and a
bound $D$, the bounded diameter minimum spanning tree
problem seeks a spanning tree on $G$ of minimum weight
among the trees in which no path between two vertices
contains more than $D$ edges. In Prim's algorithm, the
diameter of the growing spanning tree can always be
known, so it is a good starting point from which to
develop greedy heuristics for the bounded diameter
problem. Abdalla, Deo, and Gupta described such an
algorithm. It imitates Prim's algorithm but avoids
edges whose inclusion in the spanning tree would
violate the diameter bound. Running the algorithm from
one start vertex requires time that is $O(n^3)$. A
modification of this approach uses the start vertex as
the center of the spanning tree (if $D$ is even) or as
one of the two center vertices (if $D$ is odd). This
yields a simpler algorithm whose time is $O(n^2)$. A
further modification chooses each next vertex at random
rather than greedily, though it still connects each
vertex to the growing tree with the lowest-weight
feasible edge. On Euclidean problem instances with
small diameter bounds, the randomized heuristic is
superior to the two fully greedy algorithms, though its
advantage fades as the diameter bound grows. On
instances whose edge weights have been chosen at
random, the fully greedy algorithms outperform the
randomized heuristic.",
acknowledgement = ack-nhfb,
articleno = "1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Munro:2009:PSS,
author = "J. Ian Munro and Dorothea Wagner",
title = "Preface: Section 2 --- Selected Papers from {ALENEX
2008}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
pages = "1:1--1:??",
month = may,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed Jun 3 16:21:43 MDT 2009",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
acknowledgement = ack-nhfb,
articleno = "1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Dumitriu:2009:HMG,
author = "Daniel Dumitriu and Stefan Funke and Martin Kutz and
Nikola Milosavljevi{\'c}",
title = "How much geometry it takes to reconstruct a
$2$-manifold in {$R^3$}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
pages = "2:1--2:??",
month = may,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed Jun 3 16:21:43 MDT 2009",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Known algorithms for reconstructing a 2-manifold from
a point sample in $R^3$ are naturally based on
decisions/predicates that take the geometry of the
point sample into account. Facing the always present
problem of round-off errors that easily compromise the
exactness of those predicate decisions, an exact and
robust implementation of these algorithms is far from
being trivial and typically requires employment of
advanced datatypes for exact arithmetic, as provided by
libraries like CORE, LEDA, or GMP. In this article, we
present a new reconstruction algorithm, one whose main
novelties is to throw away geometry information early
on in the reconstruction process and to mainly operate
combinatorially on a graph structure. More precisely,
our algorithm only requires distances between the
sample points and not the actual embedding in $R^3$. As
such, it is less susceptible to robustness problems due
to round-off errors and also benefits from not
requiring expensive exact arithmetic by faster running
times. A more theoretical view on our algorithm
including correctness proofs under suitable sampling
conditions can be found in a companion article.",
acknowledgement = ack-nhfb,
articleno = "2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Irving:2009:FLS,
author = "Robert W. Irving and David F. Manlove",
title = "Finding large stable matchings",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
pages = "2:1--2:??",
month = may,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed Jun 3 16:21:43 MDT 2009",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "When ties and incomplete preference lists are
permitted in the stable marriage and
hospitals/residents problems, stable matchings can have
different sizes. The problem of finding a maximum
cardinality stable matching in this context is known to
be NP-hard, even under very severe restrictions on the
number, size, and position of ties. In this article, we
present two new heuristics for finding large stable
matchings in variants of these problems in which ties
are on one side only. We describe an empirical study
involving these heuristics and the best existing
approximation algorithm for this problem. Our results
indicate that all three of these algorithms perform
significantly better than naive tie-breaking algorithms
when applied to real-world and randomly-generated data
sets and that one of the new heuristics fares slightly
better than the other algorithms, in most cases. This
study, and these particular problem variants, are
motivated by important applications in large-scale
centralized matching schemes.",
acknowledgement = ack-nhfb,
articleno = "2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Basu:2009:GAO,
author = "Amitabh Basu and Joseph S. B. Mitchell and Girish
Kumar Sabhnani",
title = "Geometric algorithms for optimal airspace design and
air traffic controller workload balancing",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
pages = "3:1--3:??",
month = may,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed Jun 3 16:21:43 MDT 2009",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The National Airspace System (NAS) is designed to
accommodate a large number of flights over North
America. For purposes of workload limitations for air
traffic controllers, the airspace is partitioned into
approximately 600 sectors; each sector is observed by
one or more controllers. In order to satisfy workload
limitations for controllers, it is important that
sectors be designed carefully according to the traffic
patterns of flights, so that no sector becomes
overloaded. We formulate and study the airspace
sectorization problem from an algorithmic
point-of-view, modeling the problem of optimal
sectorization as a geometric partition problem with
constraints. The novelty of the problem is that it
partitions data consisting of trajectories of moving
points, rather than static point set partitioning that
is commonly studied. First, we formulate and solve the
1D version of the problem, showing how to partition a
line into ``sectors'' (intervals) according to
historical trajectory data. Then, we apply the 1D
solution framework to design a 2D sectorization
heuristic based on binary space partitions. We also
devise partitions based on balanced ``pie partitions''
of a convex polygon. We evaluate our 2D algorithms
experimentally, applying our algorithms to actual
historical flight track data for the NAS. We compare
the workload balance of our methods to that of the
existing set of sectors for the NAS and find that our
resectorization yields competitive and improved
workload balancing. In particular, our methods yield an
improvement by a factor between 2 and 3 over the
current sectorization in terms of the time-average and
the worst-case workloads of the maximum workload
sector. An even better improvement is seen in the
standard deviations (over all sectors) of both
time-average and worst-case workloads.",
acknowledgement = ack-nhfb,
articleno = "3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Bauer:2009:SFR,
author = "Reinhard Bauer and Daniel Delling",
title = "{SHARC}: Fast and robust unidirectional routing",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
pages = "4:1--4:??",
month = may,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed Jun 3 16:21:43 MDT 2009",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "During recent years, impressive speed-up techniques
for Dijkstra's have been developed. Unfortunately, the
most advanced techniques use bidirectional search,
which makes it hard to use them in scenarios where a
backward search is prohibited. Even worse, such
scenarios are widely spread (e.g.,
timetable-information systems or time-dependent
networks). In this work, we present a unidirectional
speed-up technique, which competes with bidirectional
approaches. Moreover, we show how to exploit the
advantage of unidirectional routing for fast exact
queries in timetable information systems and for fast
approximative queries in time-dependent scenarios. By
running experiments on several inputs other than road
networks, we show that our approach is very robust to
the input.",
acknowledgement = ack-nhfb,
articleno = "4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Coleman:2009:RTL,
author = "Tom Coleman and Anthony Wirth",
title = "Ranking tournaments: Local search and a new
algorithm",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
pages = "6:1--6:??",
month = may,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed Jun 3 16:21:43 MDT 2009",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Ranking is a fundamental activity for organizing and,
later, understanding data. Advice of the form `` a
should be ranked before b '' is given. If this advice
is consistent, and complete, then there is a total
ordering on the data and the ranking problem is
essentially a sorting problem. If the advice is
consistent, but incomplete, then the problem becomes
topological sorting. If the advice is inconsistent,
then we have the feedback arc set (FAS) problem: The
aim is then to rank a set of items to satisfy as much
of the advice as possible. An instance in which there
is advice about every pair of items is known as a
tournament. This ranking task is equivalent to ordering
the nodes of a given directed graph from left to right,
while minimizing the number of arcs pointing left. In
the past, much work focused on finding good, effective
heuristics for solving the problem. Recently, a proof
of the NP-completeness of the problem (even when
restricted to tournaments) has accompanied new
algorithms with approximation guarantees, culminating
in the development of a PTAS (polynomial time
approximation scheme) for solving FAS on tournaments.
In this article, we reexamine many existing algorithms
and develop some new techniques for solving FAS. The
algorithms are tested on both synthetic and
nonsynthetic datasets. We find that, in practice,
local-search algorithms are very powerful, even though
we prove that they do not have approximation
guarantees. Our new algorithm is based on reversing
arcs whose nodes have large in-degree differences,
eventually leading to a total ordering. Combining this
with a powerful local-search technique yields an
algorithm that is as strong, or stronger than, existing
techniques on a variety of data sets.",
acknowledgement = ack-nhfb,
articleno = "6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Cherkassky:2009:SPF,
author = "Boris V. Cherkassky and Loukas Georgiadis and Andrew
V. Goldberg and Robert E. Tarjan and Renato F.
Werneck",
title = "Shortest-path feasibility algorithms: An experimental
evaluation",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
pages = "7:1--7:??",
month = may,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed Jun 3 16:21:43 MDT 2009",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "This is an experimental study of algorithms for the
shortest-path feasibility problem: Given a directed
weighted graph, find a negative cycle or present a
short proof that none exists. We study previously known
and new algorithms. Our testbed is more extensive than
those previously used, including both static and
incremental problems, as well as worst-case instances.
We show that, while no single algorithm dominates, a
small subset (including new algorithms) has very robust
performance in practice. Our work advances the state of
the art in the area.",
acknowledgement = ack-nhfb,
articleno = "7",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Demetrescu:2009:P,
author = "Camil Demetrescu",
title = "Preface",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "1:1--1:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
acknowledgement = ack-nhfb,
articleno = "1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Serna:2009:PSS,
author = "Maria Serna and Carme {\'A}lvarez",
title = "Preface to special section of selected papers from
{WEA 2006}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "1:1--1:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
acknowledgement = ack-nhfb,
articleno = "1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Maue:2009:GDS,
author = "Jens Maue and Peter Sanders and Domagoj Matijevic",
title = "Goal-directed shortest-path queries using precomputed
cluster distances",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "2:1--2:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We demonstrate how Dijkstra's algorithm for shortest
path queries can be accelerated by using precomputed
shortest path distances. Our approach allows a
completely flexible tradeoff between query time and
space consumption for precomputed distances. In
particular, sublinear space is sufficient to give the
search a strong ``sense of direction''. We evaluate our
approach experimentally using large, real-world road
networks.",
acknowledgement = ack-nhfb,
articleno = "2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Valimaki:2009:ECS,
author = "N. V{\"a}lim{\"a}ki and V. M{\"a}kinen and W. Gerlach
and K. Dixit",
title = "Engineering a compressed suffix tree implementation",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "2:1--2:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Suffix tree is one of the most important data
structures in string algorithms and biological sequence
analysis. Unfortunately, when it comes to implementing
those algorithms and applying them to real genomic
sequences, often the main memory size becomes the
bottleneck. This is easily explained by the fact that
while a DNA sequence of length $n$ from alphabet
$\Sigma = \{ A, C, G, T \}$ can be stored in $n \log
|\Sigma| = 2 n$ bits, its suffix tree occupies $O(n
\log n)$ bits. In practice, the size difference easily
reaches factor 50. We report on an implementation of
the compressed suffix tree very recently proposed by
Sadakane (2007). The compressed suffix tree occupies
space proportional to the text size, that is, $O(n \log
|\Sigma|)$ bits, and supports all typical suffix tree
operations with at most $\log n$ factor slowdown. Our
experiments show that, for example, on a 10 MB DNA
sequence, the compressed suffix tree takes 10\% of the
space of the normal suffix tree. At the same time, a
representative algorithm is slowed down by factor 30.
Our implementation follows the original proposal in
spirit, but some internal parts are tailored toward
practical implementation. Our construction algorithm
has time requirement $O(n \log n \log |\Sigma|)$ and
uses closely the same space as the final structure
while constructing it: on the 10MB DNA sequence, the
maximum space usage during construction is only 1.5
times the final product size. As by-products, we
develop a method to create Succinct Suffix Array
directly from Burrows--Wheeler transform and a
space-efficient version of the suffixes-insertion
algorithm to build balanced parentheses representation
of suffix tree from LCP information.",
acknowledgement = ack-nhfb,
articleno = "2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Eisenbrand:2009:ALO,
author = "Friedrich Eisenbrand and Andreas Karrenbauer and
Chihao Xu",
title = "Algorithms for longer {OLED} lifetime",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "3:1--3:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We consider an optimization problem arising in the
design of controllers for OLED displays. Our objective
is to minimize the amplitude of the electrical current
flowing through the diodes, which has a direct impact
on the lifetime of such a display. The optimization
problem consist of finding a decomposition of an image
into subframes with special structural properties that
allow the display driver to lower the stress on the
diodes. For monochrome images, we present an algorithm
that finds an optimal solution of this problem in
linear time. Moreover, we consider an online version of
the problem in which we have to take a decision for one
row based on a constant number of rows in the
lookahead. In this framework, this algorithm has a
tight competitive ratio. A generalization of this
algorithm computes near-optimal solutions of real-world
instances in real time.",
acknowledgement = ack-nhfb,
articleno = "3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Englert:2009:EOS,
author = "Matthias Englert and Heiko R{\"o}glin and Matthias
Westermann",
title = "Evaluation of online strategies for reordering
buffers",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "3:1--3:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "A sequence of objects that are characterized by their
color has to be processed. Their processing order
influences how efficiently they can be processed: Each
color change between two consecutive objects produces
costs. A reordering buffer, which is a random access
buffer with storage capacity for k objects, can be used
to rearrange this sequence online in such a way that
the total costs are reduced. This concept is useful for
many applications in computer science and economics.
The strategy with the best-known competitive ratio is
MAP. An upper bound of $O(\log k)$ on the competitive
ratio of MAP is known and a nonconstant lower bound on
the competitive ratio is not known. Based on
theoretical considerations and experimental
evaluations, we give strong evidence that the
previously used proof techniques are not suitable to
show an $o (\sqrt{\log k})$ upper bound on the
competitive ratio of MAP. However, we also give some
evidence that in fact MAP achieves a competitive ratio
of $O(1)$. Further, we evaluate the performance of
several strategies on random input sequences
experimentally. MAP and its variants RC and RR clearly
outperform the other strategies FIFO, LRU, and MCF. In
particular, MAP, RC, and RR are the only known
strategies whose competitive ratios do not depend on
the buffer size. Furthermore, MAP achieves the smallest
competitive ratio.",
acknowledgement = ack-nhfb,
articleno = "3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Farshi:2009:ESG,
author = "Mohammad Farshi and Joachim Gudmundsson",
title = "Experimental study of geometric $t$-spanners",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "3:1--3:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The construction of t -spanners of a given point set
has received a lot of attention, especially from a
theoretical perspective. In this article, we
experimentally study the performance and quality of the
most common construction algorithms for points in the
Euclidean plane. We implemented the most well-known t
-spanner algorithms and tested them on a number of
different point sets. The experiments are discussed and
compared to the theoretical results, and in several
cases, we suggest modifications that are implemented
and evaluated. The measures of quality that we consider
are the number of edges, the weight, the maximum
degree, the spanner diameter, and the number of
crossings. This is the first time an extensive
comparison has been made between the running times of
construction algorithms of t -spanners and the quality
of the generated spanners.",
acknowledgement = ack-nhfb,
articleno = "3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Cederman:2009:GQP,
author = "Daniel Cederman and Philippas Tsigas",
title = "{GPU-Quicksort}: a practical {Quicksort} algorithm for
graphics processors",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "4:1--4:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this article, we describe GPU-Quicksort, an
efficient Quicksort algorithm suitable for highly
parallel multicore graphics processors. Quicksort has
previously been considered an inefficient sorting
solution for graphics processors, but we show that in
CUDA, NVIDIA's programming platform for general-purpose
computations on graphical processors, GPU-Quicksort
performs better than the fastest-known sorting
implementations for graphics processors, such as radix
and bitonic sort. Quicksort can thus be seen as a
viable alternative for sorting large quantities of data
on graphics processors.",
acknowledgement = ack-nhfb,
articleno = "4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Chimani:2009:EEC,
author = "Markus Chimani and Carsten Gutwenger and Petra
Mutzel",
title = "Experiments on exact crossing minimization using
column generation",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "4:1--4:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The crossing number of a graph G is the smallest
number of edge crossings in any drawing of G into the
plane. Recently, the first branch-and-cut approach for
solving the crossing number problem has been presented
in Buchheim et al. [2005]. Its major drawback was the
huge number of variables out of which only very few
were actually used in the optimal solution. This
restricted the algorithm to rather small graphs with
low crossing number. In this article, we discuss two
column generation schemes; the first is based on
traditional algebraic pricing, and the second uses
combinatorial arguments to decide whether and which
variables need to be added. The main focus of this
article is the experimental comparison between the
original approach and these two schemes. In addition,
we evaluate the quality achieved by the best-known
crossing number heuristic by comparing the new results
with the results of the heuristic.",
acknowledgement = ack-nhfb,
articleno = "4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Putze:2009:CHS,
author = "Felix Putze and Peter Sanders and Johannes Singler",
title = "Cache-, hash-, and space-efficient {Bloom} filters",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "4:1--4:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "A Bloom filter is a very compact data structure that
supports approximate membership queries on a set,
allowing false positives. We propose several new
variants of Bloom filters and replacements with similar
functionality. All of them have a better
cache-efficiency and need less hash bits than regular
Bloom filters. Some use SIMD functionality, while the
others provide an even better space efficiency. As a
consequence, we get a more flexible trade-off between
false-positive rate, space-efficiency,
cache-efficiency, hash-efficiency, and computational
effort. We analyze the efficiency of Bloom filters and
the proposed replacements in detail, in terms of the
false-positive rate, the number of expected
cache-misses, and the number of required hash bits. We
also describe and experimentally evaluate the
performance of highly tuned implementations. For many
settings, our alternatives perform better than the
methods proposed so far.",
acknowledgement = ack-nhfb,
articleno = "4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Chimani:2009:OOC,
author = "Markus Chimani and Maria Kandyba and Ivana Ljubi{\'c}
and Petra Mutzel",
title = "Obtaining optimal $k$-cardinality trees fast",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "2.5:1--2.5:23",
month = dec,
year = "2009",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1498698.1537600",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Given an undirected graph G = (V, E) with edge weights
and a positive integer number k, the k -cardinality
tree problem consists of finding a subtree T of G with
exactly k edges and the minimum possible weight. Many
algorithms have been proposed to solve this NP-hard
problem, resulting in mainly heuristic and
metaheuristic approaches. In this article, we present
an exact ILP-based algorithm using directed cuts. We
mathematically compare the strength of our formulation
to the previously known ILP formulations of this
problem, and show the advantages of our approach.
Afterwards, we give an extensive study on the
algorithm's practical performance compared to the
state-of-the-art metaheuristics. In contrast to the
widespread assumption that such a problem cannot be
efficiently tackled by exact algorithms for medium and
large graphs (between 200 and 5,000 nodes), our results
show that our algorithm not only has the advantage of
proving the optimality of the computed solution, but
also often outperforms the metaheuristic approaches in
terms of running time.",
acknowledgement = ack-nhfb,
articleno = "2.5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Frias:2009:LRC,
author = "Leonor Frias and Jordi Petit and Salvador Roura",
title = "Lists revisited: Cache-conscious {STL} lists",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "5:1--5:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present three cache-conscious implementations of
STL standard compliant lists. Until now, one could
either find simple doubly linked list implementations
that easily cope with standard strict requirements, or
theoretical approaches that do not take into account
any of these requirements in their design. In contrast,
we have merged both approaches, paying special
attention to iterators constraints. In this article,
the competitiveness of our implementations is evinced
with an extensive experimental analysis. This shows,
for instance, 5 to 10 times faster traversals and 3 to
5 times faster internal sort.",
acknowledgement = ack-nhfb,
articleno = "5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Holzer:2009:EPS,
author = "Martin Holzer and Frank Schulz and Dorothea Wagner and
Grigorios Prasinos and Christos Zaroliagis",
title = "Engineering planar separator algorithms",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "5:1--5:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We consider classical linear-time planar separator
algorithms, determining for a given planar graph a
small subset of its nodes whose removal divides the
graph into two components of similar size. These
algorithms are based on planar separator theorems,
which guarantee separators of size $O(\sqrt n)$ and
remaining components of size at most $2 n / 3$ (where
$n$ denotes the number of nodes in the graph). In this
article, we present a comprehensive experimental study
of the classical algorithms applied to a large variety
of graphs, where our main goal is to find separators
that do not only satisfy upper bounds, but also possess
other desirable characteristics with respect to
separator size and component balance. We achieve this
by investigating a number of specific alternatives for
the concrete implementation and fine-tuning of certain
parts of the classical algorithms. It is also shown
that the choice of several parameters influences the
separation quality considerably. Moreover, we propose
as planar separators the usage of fundamental cycles,
whose size is at most twice the diameter of the graph:
For graphs of small diameter, the guaranteed bound is
better than the $O(\sqrt n)$ bounds, and it turns out
that this simple strategy almost always outperforms the
other algorithms, even for graphs with large
diameter.",
acknowledgement = ack-nhfb,
articleno = "5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Tarjan:2009:DTP,
author = "Robert E. Tarjan and Renato F. Werneck",
title = "Dynamic trees in practice",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "5:1--5:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Dynamic tree data structures maintain forests that
change over time through edge insertions and deletions.
Besides maintaining connectivity information in
logarithmic time, they can support aggregation of
information over paths, trees, or both. We perform an
experimental comparison of several versions of dynamic
trees: ST-trees, ET-trees, RC-trees, and two variants
of top trees (self-adjusting and worst-case). We
quantify their strengths and weaknesses through tests
with various workloads, most stemming from practical
applications. We observe that a simple, linear-time
implementation is remarkably fast for graphs of small
diameter, and that worst-case and randomized data
structures are best when queries are very frequent. The
best overall performance, however, is achieved by
self-adjusting ST-trees.",
acknowledgement = ack-nhfb,
articleno = "5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Avdil:2009:LSS,
author = "Alaubek Avdil and Karsten Weihe",
title = "Local search starting from an {LP} solution: Fast and
quite good",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "6:1--6:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present and evaluate a specific way to generate
good start solutions for local search. The start
solution is computed from a certain LP, which is
related to the underlying problem. We consider three
optimization problems: the directed MAX-CUT problem
with a source and a sink and two variations of the MAX-
k -SAT problem with k = 2 and k = 3. To compare our
technique, we run local search repeatedly with random
start solutions. Our technique produces, consistently,
final solutions whose objective values are not too far
from the best solutions from repeated random starts.
The surprising degree of stability and uniformity of
this result throughout all of our experiments on
various classes of instances strongly suggests that we
have consistently achieved nearly optimal solutions. On
the other hand, the runtime of our technique is rather
small, so the technique is very efficient and probably
quite accurate.",
acknowledgement = ack-nhfb,
articleno = "6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Deineko:2009:FMW,
author = "Vladimir Deineko and Alexander Tiskin",
title = "Fast minimum-weight double-tree shortcutting for
metric {TSP}: Is the best one good enough?",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "6:1--6:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The Metric Traveling Salesman Problem (TSP) is a
classical NP-hard optimization problem. The double-tree
shortcutting method for Metric TSP yields an
exponentially-sized space of TSP tours, each of which
approximates the optimal solution within, at most, a
factor of 2. We consider the problem of finding among
these tours the one that gives the closest
approximation, that is, the minimum-weight double-tree
shortcutting. Burkard et al. gave an algorithm for this
problem, running in time $O(n^3 + 2^d n^2)$ and memory
$O(2^d n^2)$, where $d$ is the maximum node degree in
the rooted minimum spanning tree. We give an improved
algorithm for the case of small $d$ (including planar
Euclidean TSP, where $d \leq 4$), running in time
$O(4^d n^2)$ and memory $O(4^d n)$. This improvement
allows one to solve the problem on much larger
instances than previously attempted. Our computational
experiments suggest that in terms of the time-quality
trade-off, the minimum-weight double-tree shortcutting
method provides one of the best existing
tour-constructing heuristics.",
acknowledgement = ack-nhfb,
articleno = "6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Figueroa:2009:SSA,
author = "Karina Figueroa and Edgar Chavez and Gonzalo Navarro
and Rodrigo Paredes",
title = "Speeding up spatial approximation search in metric
spaces",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "6:1--6:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Proximity searching consists of retrieving from a
database those elements that are similar to a query
object. The usual model for proximity searching is a
metric space where the distance, which models the
proximity, is expensive to compute. An index uses
precomputed distances to speedup query processing.
Among all the known indices, the baseline for
performance for about 20 years has been AESA. This
index uses an iterative procedure, where at each
iteration it first chooses the next promising element
(``pivot'') to compare to the query, and then it
discards database elements that can be proved not
relevant to the query using the pivot. The next pivot
in AESA is chosen as the one minimizing the sum of
lower bounds to the distance to the query proved by
previous pivots. In this article, we introduce the new
index iAESA, which establishes a new performance
baseline for metric space searching. The difference
with AESA is the method to select the next pivot. In
iAESA, each candidate sorts previous pivots by
closeness to it, and chooses the next pivot as the
candidate whose order is most similar to that of the
query. We also propose a modification to AESA-like
algorithms to turn them into probabilistic algorithms.
Our empirical results confirm a consistent improvement
in query performance. For example, we perform as few as
60\% of the distance evaluations of AESA in a database
of documents, a very important and difficult real-life
instance of the problem. For the probabilistic
algorithm, we perform in a database of faces up to 40\%
of the comparisons made by the best alternative
algorithm to retrieve the same percentage of the
correct answer. Based on the empirical results, we
conjecture that the new probabilistic AESA-like
algorithms will become, as AESA had been for exact
algorithms, a reference point establishing, in
practice, a lower bound on how good a probabilistic
proximity search algorithm can be.",
acknowledgement = ack-nhfb,
articleno = "6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Barbay:2009:EIS,
author = "J{\'e}r{\'e}my Barbay and Alejandro L{\'o}pez-Ortiz
and Tyler Lu and Alejandro Salinger",
title = "An experimental investigation of set intersection
algorithms for text searching",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "7:1--7:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The intersection of large ordered sets is a common
problem in the context of the evaluation of boolean
queries to a search engine. In this article, we propose
several improved algorithms for computing the
intersection of sorted arrays, and in particular for
searching sorted arrays in the intersection context. We
perform an experimental comparison with the algorithms
from the previous studies from Demaine,
L{\'o}pez-Ortiz, and Munro [ALENEX 2001] and from
Baeza-Yates and Salinger [SPIRE 2005]; in addition, we
implement and test the intersection algorithm from
Barbay and Kenyon [SODA 2002] and its randomized
variant [SAGA 2003]. We consider both the random data
set from Baeza-Yates and Salinger, the Google queries
used by Demaine et al., a corpus provided by Google,
and a larger corpus from the TREC Terabyte 2006
efficiency query stream, along with its own query log.
We measure the performance both in terms of the number
of comparisons and searches performed, and in terms of
the CPU time on two different architectures. Our
results confirm or improve the results from both
previous studies in their respective context
(comparison model on real data, and CPU measures on
random data) and extend them to new contexts. In
particular, we show that value-based search algorithms
perform well in posting lists in terms of the number of
comparisons performed.",
acknowledgement = ack-nhfb,
articleno = "7",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Estivill-Castro:2009:RRD,
author = "Vladimir Estivill-Castro and Apichat Heednacram and
Francis Suraweera",
title = "Reduction rules deliver efficient {FPT}-algorithms for
covering points with lines",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "7:1--7:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present efficient algorithms to solve the Line
Cover Problem exactly. In this NP-complete problem, the
inputs are n points in the plane and a positive integer
k, and we are asked to answer if we can cover these n
points with at most k lines. Our approach is based on
fixed-parameter tractability and, in particular,
kernelization. We propose several reduction rules to
transform instances of Line Cover into equivalent
smaller instances. Once instances are no longer
susceptible to these reduction rules, we obtain a
problem kernel whose size is bounded by a polynomial
function of the parameter k and does not depend on the
size n of the input. Our algorithms provide exact
solutions and are easy to implement. We also describe
the design of algorithms to solve the corresponding
optimization problem exactly. We experimentally
evaluated ten variants of the algorithms to determine
the impact and trade-offs of several reduction rules.
We show that our approach provides tractability for a
larger range of values of the parameter and larger
inputs, improving the execution time by several orders
of magnitude with respect to earlier algorithms that
use less rules.",
acknowledgement = ack-nhfb,
articleno = "7",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{DeLoera:2009:CMM,
author = "Jes{\'u}s A. {De Loera} and David C. Haws and Jon Lee
and Allison O'Hair",
title = "Computation in multicriteria matroid optimization",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "14",
number = "1",
pages = "8:1--8:??",
month = dec,
year = "2009",
CODEN = "????",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:04:28 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Motivated by recent work on algorithmic theory for
nonlinear and multicriteria matroid optimization, we
have developed algorithms and heuristics aimed at
practical solution of large instances of some of these
difficult problems. Our methods primarily use the local
adjacency structure inherent in matroid polytopes to
pivot to feasible solutions, which may or may not be
optimal. We also present a modified
breadth-first-search heuristic that uses adjacency to
enumerate a subset of feasible solutions. We present
other heuristics and provide computational evidence
supporting our techniques. We implemented all of our
algorithms in the software package MOCHA.",
acknowledgement = ack-nhfb,
articleno = "8",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Jacobs:2010:ESR,
author = "Tobias Jacobs",
title = "An experimental study of recent hotlink assignment
algorithms",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "15",
number = "1",
pages = "1.1:1--1.1:??",
month = mar,
year = "2010",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1671970.1671971",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:05:50 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The concept of {\em hotlink assignment\/} aims at
enhancing the structure of Web sites such that the
user's expected navigation effort is minimized. We
concentrate on sites that are representable by trees
and assume that each leaf carries a weight representing
its popularity.\par
The problem of optimally adding at most one additional
outgoing edge (``hotlink'') to each inner node has been
widely studied. A considerable number of approximation
algorithms have been proposed and worst-case bounds for
the quality of the computed solutions have been given.
However, only little is known about the practical
behavior of most of these algorithms.\par
This article contributes to closing this gap by
evaluating all recently proposed strategies
experimentally. Our experiments are based on trees
extracted from real Web sites, as well as on synthetic
instances. The latter are generated by a new method
that simulates the growth of a Web site over time.
Finally, we present a new heuristic that is easy to
implement and exhibits excellent behavior in
practice.",
acknowledgement = ack-nhfb,
articleno = "1.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "approximation; hotlink; Search tree",
}
@Article{Spence:2010:SGS,
author = "Ivor Spence",
title = "{{\tt sgen1}}: a generator of small but difficult
satisfiability benchmarks",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "15",
number = "1",
pages = "1.2:1--1.2:??",
month = mar,
year = "2010",
CODEN = "????",
DOI = "http://doi.acm.org/10.1145/1671970.1671972",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:05:50 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The satisfiability problem is known to be NP-Complete;
therefore, there should be relatively small problem
instances that take a very long time to solve. However,
most of the smaller benchmarks that were once thought
challenging, especially the satisfiable ones, can be
processed quickly by modern SAT-solvers. We describe
and make available a generator that produces both
unsatisfiable and, more significantly, satisfiable
formulae that take longer to solve than any others
known. At the two most recent international SAT
Competitions, the smallest unsolved benchmarks were
created by this generator. We analyze the results of
all solvers in the most recent competition when applied
to these benchmarks and also present our own more
focused experiments.",
acknowledgement = ack-nhfb,
articleno = "1.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "SAT-solvers; Satisfiability benchmarks",
}
@Article{Langguth:2010:HIB,
author = "Johannes Langguth and Fredrik Manne and Peter
Sanders",
title = "Heuristic initialization for bipartite matching
problems",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "15",
number = "1",
pages = "1.3:1--1.3:??",
month = mar,
year = "2010",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1712655.1712656",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Mar 15 12:05:50 MDT 2010",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "It is a well-established result that improved pivoting
in linear solvers can be achieved by computing a
bipartite matching between matrix entries and positions
on the main diagonal. With the availability of
increasingly faster linear solvers, the speed of
bipartite matching computations must keep up to avoid
slowing down the main computation. Fast algorithms for
bipartite matching, which are usually initialized with
simple heuristics, have been known for a long time.
However, the performance of these algorithms is largely
dependent on the quality of the heuristic. We compare
combinations of several known heuristics and exact
algorithms to find fast combined methods, using
real-world matrices as well as randomly generated
instances. In addition, we present a new heuristic
aimed at obtaining high-quality matchings and compare
its impact on bipartite matching algorithms with that
of other heuristics. The experiments suggest that its
performance compares favorably to the best-known
heuristics, and that it is especially suited for
application in linear solvers.",
acknowledgement = ack-nhfb,
articleno = "1.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "Heuristics; matching",
}
@Article{Delbot:2010:AEC,
author = "Fran{\c{c}}ois Delbot and Christian Laforest",
title = "Analytical and experimental comparison of six
algorithms for the vertex cover problem",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "15",
number = "1",
pages = "14:1--14:??",
month = mar,
year = "2010",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1865970.1865971",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Dec 10 09:03:03 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The vertex cover is a well-known NP-complete
minimization problem in graphs that has received a lot
of attention these last decades. Many algorithms have
been proposed to construct vertex cover in different
contexts (offline, online, list algorithms, etc.)
leading to solutions of different level of quality.
This quality is traditionally measured in terms of
approximation ratio, that is, the worst possible ratio
between the quality of the solution constructed and the
optimal one. For the vertex cover problem the range of
such known ratios are between 2 (conjectured as being
the smallest constant ratio) and $\Delta$, the maximum
degree of the graph. Based on this measure of quality,
the hierarchy is almost clear (the smaller the ratio
is, the better the algorithm is). In this article, we
show that this measure, although of great importance,
is too macroscopic and does not reflect the practical
behavior of the methods. We prove this by analyzing
(known and recent) algorithms running on a particular
class of graphs: the paths. We obtain closed and exact
formulas for the mean of the sizes of vertex cover
constructed by these different algorithms. Then, we
assess their quality experimentally in several
well-chosen class of graphs (random, regular, trees,
BHOSLIB benchmarks, trap graphs, etc.). The synthesis
of all these results lead us to formulate a ``practical
hierarchy'' of the algorithms. We remark that it is,
more or less, the opposite to the one only based on
approximation ratios, showing that worst-case analysis
only gives partial information on the quality of an
algorithm.",
acknowledgement = ack-nhfb,
articleno = "1.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Arroyuelo:2010:PAR,
author = "Diego Arroyuelo and Gonzalo Navarro",
title = "Practical approaches to reduce the space requirement
of {Lempel--Ziv}-based compressed text indices",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "15",
number = "1",
pages = "15:1--15:??",
month = mar,
year = "2010",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1671970.1883684",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Dec 10 09:03:03 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Given a text $T [1.\,.n]$ over an alphabet of size
$\sigma$, the full-text search problem consists in
locating the occ occurrences of a given pattern
$P[1.\,.m]$ in $T$. Compressed full-text self-indices
are space-efficient representations of the text that
provide direct access to and indexed search on
it.\par
The LZ-index of Navarro is a compressed full-text
self-index based on the LZ78 compression algorithm.
This index requires about 5 times the size of the
compressed text (in theory, $4 n H_k(T) + o(n \log
\sigma)$ bits of space, where $H_k(T)$ is the $k$-th
order empirical entropy of $T$). In practice, the
average locating complexity of the LZ-index is
$O(\sigma m \log_\sigma n + {\rm occ} \sigma^{m / 2})$,
where {\em occ} is the number of occurrences of $P$. It
can extract text substrings of length $l$ in $O(l)$
time. This index outperforms competing schemes both to
locate short patterns and to extract text snippets.
However, the LZ-index can be up to 4 times larger than
the smallest existing indices (which use $n H_k(T) +
o(n \log \sigma)$ bits in theory), and it does not
offer space/time tuning options. This limits its
applicability.\par
In this article, we study practical ways to reduce the
space of the LZ-index. We obtain new LZ-index variants
that require $2(1 + \epsilon) n H_k(T) + o(n \log
\sigma)$ bits of space, for any $0 < \epsilon < 1$.
They have an average locating time of $O(1 / \epsilon
(m \log n + {\rm occ} \sigma^{m / 2}))$, while
extracting takes $O(l)$ time.\par
We perform extensive experimentation and conclude that
our schemes are able to reduce the space of the
original LZ-index by a factor of $2/3$, that is, around
$3$ times the compressed text size. Our schemes are
able to extract about 1 to 2 MB of the text per second,
being twice as fast as the most competitive
alternatives. Pattern occurrences are located at a rate
of up to 1 to 4 million per second. This constitutes
the best space\slash time trade-off when indices are
allowed to use 4 times the size of the compressed text
or more.",
acknowledgement = ack-nhfb,
articleno = "1.5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Ullmann:2010:BVA,
author = "Julian R. Ullmann",
title = "Bit-vector algorithms for binary constraint
satisfaction and subgraph isomorphism",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "15",
number = "1",
pages = "16:1--16:??",
month = mar,
year = "2010",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1671970.1921702",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Dec 10 09:03:03 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "A solution to a binary constraint satisfaction problem
is a set of discrete values, one in each of a given set
of domains, subject to constraints that allow only
prescribed pairs of values in specified pairs of
domains. Solutions are sought by backtrack search
interleaved with a process that removes from domains
those values that are currently inconsistent with
provisional choices already made in the course of
search. For each value in a given domain, a bit-vector
shows which values in another domain are or are not
permitted in a solution. Bit-vector representation of
constraints allows bit-parallel, therefore fast,
operations for editing domains during search. This
article revises and updates bit-vector algorithms
published in the 1970's, and introduces focus search,
which is a new bit-vector algorithm relying more on
search and less on domain-editing than previous
algorithms. Focus search is competitive within a
limited family of constraint satisfaction problems.
Determination of subgraph isomorphism is a specialized
binary constraint satisfaction problem for which
bit-vector algorithms have been widely used since the
1980s, particularly for matching molecular structures.
This article very substantially updates the author's
1976 subgraph isomorphism algorithm, and reports
experimental results with random and real-life data.",
acknowledgement = ack-nhfb,
articleno = "1.6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Askitis:2010:RSH,
author = "Nikolas Askitis and Justin Zobel",
title = "Redesigning the string hash table, burst trie, and
{BST} to exploit cache",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "15",
number = "1",
pages = "17:1--17:??",
month = mar,
year = "2010",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1671970.1921704",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Dec 10 09:03:03 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "A key decision when developing in-memory computing
applications is choice of a mechanism to store and
retrieve strings. The most efficient current data
structures for this task are the hash table with
move-to-front chains and the burst trie, both of which
use linked lists as a substructure, and variants of
binary search tree. These data structures are
computationally efficient, but typical implementations
use large numbers of nodes and pointers to manage
strings, which is not efficient in use of cache. In
this article, we explore two alternatives to the
standard representation: the simple expedient of
including the string in its node, and, for linked
lists, the more drastic step of replacing each list of
nodes by a contiguous array of characters. Our
experiments show that, for large sets of strings, the
improvement is dramatic. For hashing, in the best case
the total space overhead is reduced to less than 1 bit
per string. For the burst trie, over 300MB of strings
can be stored in a total of under 200MB of memory with
significantly improved search time. These results, on a
variety of data sets, show that cache-friendly variants
of fundamental data structures can yield remarkable
gains in performance.",
acknowledgement = ack-nhfb,
articleno = "1.7",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{McGeoch:2010:P,
author = "Catherine C. McGeoch",
title = "Preface",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "15",
number = "1",
pages = "2.1:1--2.1:??",
month = mar,
year = "2010",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1671970.1671974",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Dec 10 09:03:03 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
acknowledgement = ack-nhfb,
articleno = "2.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Chimani:2010:LFU,
author = "Markus Chimani and Carsten Gutwenger and Petra Mutzel
and Hoi-Ming Wong",
title = "Layer-free upward crossing minimization",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "15",
number = "1",
pages = "2.2:1--2.2:??",
month = mar,
year = "2010",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1671970.1671975",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Dec 10 09:03:03 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "An upward drawing of a DAG $G$ is a drawing of $G$ in
which all arcs are drawn as curves increasing
monotonically in the vertical direction. In this
article, we present a new approach for upward crossing
minimization, that is, finding an upward drawing of a
DAG $G$ with as few crossings as possible. Our
algorithm is based on a two-stage upward planarization
approach, which computes a feasible upward planar
subgraph in the first step and reinserts the remaining
arcs by computing constraint-feasible upward insertion
paths. An experimental study shows that the new
algorithm leads to much better results than existing
algorithms for upward crossing minimization, including
the classical Sugiyama approach.",
acknowledgement = ack-nhfb,
articleno = "2.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "Crossing number; planarization approach; upward
drawing; upward planarization",
}
@Article{Bauer:2010:CHG,
author = "Reinhard Bauer and Daniel Delling and Peter Sanders
and Dennis Schieferdecker and Dominik Schultes and
Dorothea Wagner",
title = "Combining hierarchical and goal-directed speed-up
techniques for {Dijkstra}'s algorithm",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "15",
number = "1",
pages = "2.3:1--2.3:??",
month = mar,
year = "2010",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1671970.1671976",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Dec 10 09:03:03 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In recent years, highly effective hierarchical and
goal-directed speed-up techniques for routing in large
road networks have been developed. This article makes a
systematic study of combinations of such techniques.
These combinations turn out to give the best results in
many scenarios, including graphs for unit disk graphs,
grid networks, and time-expanded timetables. Besides
these quantitative results, we obtain general insights
for successful combinations.",
acknowledgement = ack-nhfb,
articleno = "2.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "Dijkstra's algorithm; speed-up technique",
}
@Article{Nash:2010:CID,
author = "Nicholas Nash and David Gregg",
title = "Comparing integer data structures for 32- and 64-bit
keys",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "15",
number = "1",
pages = "2.4:1--2.4:??",
month = mar,
year = "2010",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1671970.1671977",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Dec 10 09:03:03 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this article, we experimentally compare a number of
data structures operating over keys that are 32- and
64-bit integers. We examine traditional
comparison-based search trees as well as data
structures that take advantage of the fact that the
keys are integers such as van Emde Boas trees and
various trie-based data structures. We propose a
variant of a burst trie that performs better in time
than all the alternative data structures. In addition,
even for small sets of keys, this burst trie variant
occupies less space than comparison-based data
structures such as red-black trees and $B$-trees. Burst
tries have previously been shown to provide a very
efficient base for implementing cache efficient string
sorting algorithms. We find that with suitable
engineering, they also perform excellently as a dynamic
ordered data structure operating over integer keys. We
provide experimental results when the data structures
operate over uniform random data. We also present
experimental results for other types of data, including
datasets arising from {\em Valgrind}, a widely used
suite of tools for the dynamic binary instrumentation
of programs.",
acknowledgement = ack-nhfb,
articleno = "2.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "Integer keys; level compression; searching; trees;
tries",
}
@Article{Sinha:2010:EBT,
author = "Ranjan Sinha and Anthony Wirth",
title = "Engineering burstsort: Toward fast in-place string
sorting",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "15",
number = "1",
pages = "2.5:1--2.5:??",
month = mar,
year = "2010",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1671970.1671978",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon Dec 10 09:03:03 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Burstsort is a trie-based string sorting algorithm
that distributes strings into small buckets whose
contents are then sorted in cache. This approach has
earlier been demonstrated to be efficient on modern
cache-based processors [Sinha \& Zobel, JEA 2004]. In
this article, we introduce improvements that reduce by
a significant margin the memory requirement of
Burstsort: It is now less than 1\% greater than an
in-place algorithm. These techniques can be applied to
existing variants of Burstsort, as well as other string
algorithms such as for string management.\par
We redesigned the buckets, introducing sub-buckets and
an index structure for them, which resulted in an
order-of-magnitude space reduction. We also show the
practicality of moving some fields from the trie nodes
to the insertion point (for the next string pointer) in
the bucket; this technique reduces memory usage of the
trie nodes by one-third. Importantly, the trade-off for
the reduction in memory use is only a very slight
increase in the running time of Burstsort on real-world
string collections. In addition, during the
bucket-sorting phase, the string suffixes are copied to
a small buffer to improve their spatial locality,
lowering the running time of Burstsort by up to 30\%.
These memory usage enhancements have enabled the
copy-based approach [Sinha et al., JEA 2006] to also
reduce the memory usage with negligible impact on
speed.",
acknowledgement = ack-nhfb,
articleno = "2.5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
keywords = "algorithms; cache; experimental algorithms; Sorting;
string management; tries",
}
@Article{Boytsov:2011:IMA,
author = "Leonid Boytsov",
title = "Indexing methods for approximate dictionary searching:
Comparative analysis",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "1.1:1--1.1:??",
month = may,
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.1963191",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon May 30 08:26:05 MDT 2011",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The primary goal of this article is to survey
state-of-the-art indexing methods for approximate
dictionary searching. To improve understanding of the
field, we introduce a taxonomy that classifies all
methods into direct methods and sequence-based
filtering methods. We focus on infrequently updated
dictionaries, which are used primarily for retrieval.
Therefore, we consider indices that are optimized for
retrieval rather than for update. The indices are
assumed to be associative, that is, capable of storing
and retrieving auxiliary information, such as string
identifiers. All solutions are lossless and guarantee
retrieval of strings within a specified edit distance
$k$. Benchmark results are presented for the
practically important cases of $k = 1, 2$, and $3$.",
acknowledgement = ack-nhfb,
articleno = "1.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Biro:2011:SMC,
author = "P{\'e}ter Bir{\'o} and Robert W. Irving and Ildik{\'o}
Schlotter",
title = "Stable matching with couples: an empirical study",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "12:1--12:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.1970372",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In practical applications, algorithms for the classic
version of the hospitals residents problem (the
many-one version of the stable marriage problem) may
have to be extended to accommodate the needs of couples
who wish to be allocated to (geographically) compatible
places. Such an extension has been in operation in the
National Resident Matching Problem (NRMP) matching
scheme in the United States for a number of years. In
this setting, a stable matching need not exist, and it
is an NP-complete problem to decide if one does.
However, the only previous empirical study in this
context (focused on the NRMP algorithm), together with
information from NRMP, suggest that, in practice,
stable matchings do exist and that an appropriate
heuristic can be used to find such a matching. The
study presented here was motivated by the recent
decision to accommodate couples in the Scottish
Foundation Allocation Scheme (SFAS), the Scottish
equivalent of the NRMP. Here, the problem is a special
case, since hospital preferences are derived from a
``master list'' of resident scores, but we show that
the existence problem remains NP-complete in this case.
We describe the algorithm used in SFAS and contrast it
with a version of the algorithm that forms the basis of
the NRMP approach. We also propose a third simpler
algorithm based on satisfying blocking pairs, and an
FPT algorithm when the number of couples is viewed as a
parameter. We present an empirical study of the
performance of a number of variants of these algorithms
using a range of datasets. The results indicate that,
not surprisingly, increasing the ratio of couples to
single applicants typically makes it harder to find a
stable matching (and, by inference, less likely that a
stable matching exists). However, the likelihood of
finding a stable matching is very high for realistic
values of this ratio, and especially so for particular
variants of the algorithms.",
acknowledgement = ack-nhfb,
articleno = "1.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Huber:2011:MGS,
author = "Stefan Huber and Martin Held",
title = "Motorcycle graphs: Stochastic properties motivate an
efficient yet simple implementation",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "13:1--13:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.2019578",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this article, we study stochastic properties of a
geometric setting that underpins random motorcycle
graphs and use it to motivate a simple but very
efficient algorithm for computing motorcycle graphs. An
analysis of the mean trace length of $n$ random
motorcycles suggests that, on average, a motorcycle
crosses only a constant number of cells within a $\sqrt
n \times \sqrt n$ rectangular grid, provided that the
motorcycles are distributed sufficiently uniformly over
the area covered by the grid. This analysis motivates a
simple algorithm for computing motorcycle graphs: We
use the standard priority-queue--based algorithm and
enhance it with geometric hashing by means of a
rectangular grid. If the motorcycles are distributed
sufficiently uniformly, then our stochastic analysis
predicts an $O(n \log n)$ runtime. Indeed, extensive
experiments run on 22,000 synthetic and real-world
datasets confirm a runtime of less than $10^{-5} n \log
n$ seconds for the vast majority of our datasets on a
standard PC. Further experiments with our software,
Moca, also confirm the mean trace length and average
number of cells crossed by a motorcycle, as predicted
by our analysis. This makes Moca the first
implementation that is efficient enough to be applied
in practice for computing motorcycle graphs of large
datasets. Actually, it is easy to extend Moca to make
it compute a generalized version of the original
motorcycle graph, thus enabling a significantly larger
field of applications.",
acknowledgement = ack-nhfb,
articleno = "1.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Michail:2011:ECS,
author = "Dimitrios Michail",
title = "An experimental comparison of single-sided preference
matching algorithms",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "14:1--14:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.2019579",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We experimentally study the problem of assigning
applicants to posts. Each applicant provides a
preference list, which may contain ties, ranking a
subset of the posts. Different optimization criteria
may be defined, which depend on the desired solution
properties. The main focus of this work is to assess
the quality of matchings computed by rank-maximal and
popular matching algorithms and compare this with the
minimum weight matching algorithm, which is a standard
matching algorithm that is used in practice. Both
rank-maximal and popular matching algorithms use common
algorithmic techniques, which makes them excellent
candidates for a running time comparison. Since popular
matchings do not always exist, we also study the
unpopularity of matchings computed by the
aforementioned algorithms. Finally, extra criteria like
total weight and cardinality are included, due to their
importance in practice. All experiments are performed
using structured random instances as well as instances
created using real-world datasets.",
acknowledgement = ack-nhfb,
articleno = "1.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Kot:2011:ECP,
author = "Andriy Kot and Andrey N. Chernikov and Nikos P.
Chrisochoides",
title = "Effective out-of-core parallel {Delaunay} mesh
refinement using off-the-shelf software",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "15:1--15:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.2019580",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present three related out-of-core parallel mesh
generation algorithms and their implementations for
small size computational clusters. Computing
out-of-core permits to solve larger problems than
otherwise possible on the same hardware setup. Also,
when using shared computing resources with high demand,
a problem can take longer to compute in terms of
wall-clock time when using an in-core algorithm on many
nodes instead of using an out-of-core algorithm on few
nodes. The difference is due to wait-in-queue delays
that can grow exponentially to the number of requested
nodes. In one specific case, using our best method and
only 16 nodes it can take several times less wall-clock
time to generate a 2 billion element mesh than to
generate the same size mesh in-core with 121 nodes.
Although our best out-of-core method exhibits
unavoidable overheads (could be as low as 19\% in some
cases) over the corresponding in-core method (for mesh
sizes that fit completely in-core), this is a modest
and expected performance penalty. We evaluated our
methods on traditional clusters of workstations as well
as presented preliminary performance evaluation on
[the] emerging BlueWaters supercomputer.",
acknowledgement = ack-nhfb,
articleno = "1.5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Prosser:2011:LDS,
author = "Patrick Prosser and Chris Unsworth",
title = "Limited discrepancy search revisited",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "16:1--16:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.2019581",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Harvey and Ginsberg's limited discrepancy search (LDS)
is based on the assumption that costly heuristic
mistakes are made early in the search process.
Consequently, LDS repeatedly probes the state space,
going against the heuristic (i.e., taking
discrepancies) a specified number of times in all
possible ways and attempts to take those discrepancies
as early as possible. LDS was improved by Richard Korf,
to become improved LDS (ILDS), but in doing so,
discrepancies were taken as late as possible, going
against the original assumption. Many subsequent
algorithms have faithfully inherited Korf's
interpretation of LDS, and take discrepancies late.
This then raises the question: Should we take our
discrepancies late or early? We repeat the original
experiments performed by Harvey and Ginsberg and those
by Korf in an attempt to answer this question. We also
investigate the early stopping condition of the YIELDS
algorithm, demonstrating that it is simple, elegant and
efficient.",
acknowledgement = ack-nhfb,
articleno = "1.6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Tabourier:2011:GCR,
author = "Lionel Tabourier and Camille Roth and Jean-Philippe
Cointet",
title = "Generating constrained random graphs using multiple
edge switches",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "17:1--17:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.2063515",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The generation of random graphs using edge swaps
provides a reliable method to draw uniformly random
samples of sets of graphs respecting some simple
constraints (e.g., degree distributions). However, in
general, it is not necessarily possible to access all
graphs obeying some given constraints through a
classical switching procedure calling on pairs of
edges. Therefore, we propose to get around this issue
by generalizing this classical approach through the use
of higher-order edge switches. This method, which we
denote by `` k -edge switching,'' makes it possible to
progressively improve the covered portion of a set of
constrained graphs, thereby providing an increasing,
asymptotically certain confidence on the statistical
representativeness of the obtained sample.",
acknowledgement = ack-nhfb,
articleno = "1.7",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Tsourakakis:2011:AAS,
author = "Charalampos E. Tsourakakis and Richard Peng and Maria
A. Tsiarli and Gary L. Miller and Russell Schwartz",
title = "Approximation algorithms for speeding up dynamic
programming and denoising {aCGH} data",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "18:1--18:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.2063517",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The development of cancer is largely driven by the
gain or loss of subsets of the genome, promoting
uncontrolled growth or disabling defenses against it.
Denoising array-based Comparative Genome Hybridization
(aCGH) data is an important computational problem
central to understanding cancer evolution. In this
article, we propose a new formulation of the denoising
problem that we solve with a ``vanilla'' dynamic
programming algorithm, which runs in $O(n^2)$ units of
time. Then, we propose two approximation techniques.
Our first algorithm reduces the problem into a
well-studied geometric problem, namely halfspace
emptiness queries, and provides an $\epsilon$ additive
approximation to the optimal objective value in
$\tilde{O}(n ^{4 / 3 + \delta} \log (U / \epsilon))$
time, where $\delta$ is an arbitrarily small positive
constant and $U = \max\{\sqrt C, (|P_i|)_{i =
1,\ldots{}, n}\} (P = (P_1, P_2, \ldots{}, P_n), P_i
\in \mathbb{R})$, is the vector of the noisy aCGH
measurements, $C$ a normalization constant. The second
algorithm provides a $(1 \pm \epsilon)$ approximation
(multiplicative error) and runs in $O(n \log n /
\epsilon)$ time. The algorithm decomposes the initial
problem into a small (logarithmic) number of Monge
optimization subproblems that we can solve in linear
time using existing techniques. Finally, we validate
our model on synthetic and real cancer datasets. Our
method consistently achieves superior precision and
recall to leading competitors on the data with ground
truth. In addition, it finds several novel markers not
recorded in the benchmarks but supported in the
oncology literature.",
acknowledgement = ack-nhfb,
articleno = "1.8",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Vahrenhold:2011:P,
author = "Jan Vahrenhold",
title = "Preface",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "21:1--21:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.1970374",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
acknowledgement = ack-nhfb,
articleno = "2.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Wang:2011:CEM,
author = "Bei Wang and Herbert Edelsbrunner and Dmitriy
Morozov",
title = "Computing elevation maxima by searching the {Gauss}
sphere",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "22:1--22:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.1970375",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The elevation function on a smoothly embedded
2-manifold in R$^3$ reflects the multiscale topography
of cavities and protrusions as local maxima. The
function has been useful in identifying coarse docking
configurations for protein pairs. Transporting the
concept from the smooth to the piecewise linear
category, this article describes an algorithm for
finding all local maxima. While its worst-case running
time is the same as of the algorithm used in prior
work, its performance in practice is orders of
magnitudes superior. We cast light on this improvement
by relating the running time to the total absolute
Gaussian curvature of the 2-manifold.",
acknowledgement = ack-nhfb,
articleno = "2.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Rotta:2011:MLS,
author = "Randolf Rotta and Andreas Noack",
title = "Multilevel local search algorithms for modularity
clustering",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "23:1--23:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.1970376",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Modularity is a widely used quality measure for graph
clusterings. Its exact maximization is NP-hard and
prohibitively expensive for large graphs. Popular
heuristics first perform a coarsening phase, where
local search starting from singleton clusters is used
to compute a preliminary clustering, and then
optionally a refinement phase, where this clustering is
improved by moving vertices between clusters. As a
generalization, multilevel heuristics coarsen in
several stages, and refine by moving entire clusters
from each of these stages, not only individual
vertices. This article organizes existing and new
single-level and multilevel heuristics into a coherent
design space, and compares them experimentally with
respect to their effectiveness (achieved modularity)
and runtime. For coarsening by iterated cluster
joining, it turns out that the most widely used
criterion for joining clusters (modularity increase) is
outperformed by other simple criteria, that a recent
multistep algorithm [Schuetz and Caflisch 2008] is no
improvement over simple single-step coarsening for
these criteria, and that the recent multilevel
coarsening by iterated vertex moving [Blondel et al.
2008] is somewhat faster but slightly less effective
(with refinement). The new multilevel refinement is
significantly more effective than the conventional
single-level refinement or no refinement, in reasonable
runtime. A comparison with published benchmark results
and algorithm implementations shows that multilevel
local search heuristics, despite their relative
simplicity, are competitive with the best algorithms in
the literature.",
acknowledgement = ack-nhfb,
articleno = "2.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Bertasi:2011:PYA,
author = "Paolo Bertasi and Marco Bressan and Enoch Peserico",
title = "{{\tt psort}}, yet another fast stable sorting
software",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "24:1--24:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.1970377",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "{\tt psort} is the fastest sorting software according
to the PennySort benchmark, sorting 181GB of data in
2008 and 224GB in 2009 for \$0.01 of computer time.
This article details its internals, and the careful
fitting of its architecture to the structure of modern
PC-class platforms, allowing it to outperform
state-of-the-art sorting software such as STXXL sort.",
acknowledgement = ack-nhfb,
articleno = "2.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Finocchi:2011:GEF,
author = "Irene Finocchi and John Hershberger",
title = "Guest editors' foreword",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "31:1--31:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.2025377",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
acknowledgement = ack-nhfb,
articleno = "3.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Belazzougui:2011:TPM,
author = "Djamal Belazzougui and Paolo Boldi and Rasmus Pagh and
Sebastiano Vigna",
title = "Theory and practice of monotone minimal perfect
hashing",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "32:1--32:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.2025378",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Minimal perfect hash functions have been shown to be
useful to compress data in several data management
tasks. In particular, order-preserving minimal perfect
hash functions (Fox et al. 1991) have been used to
retrieve the position of a key in a given list of keys;
however, the ability to preserve any given order leads
to an unavoidable $\Omega(n \log n)$ lower bound on the
number of bits required to store the function.
Recently, it was observed (Belazzougui et al. 2009)
that very frequently the keys to be hashed are sorted
in their intrinsic (i.e., lexicographical) order. This
is typically the case of dictionaries of search
engines, list of URLs of Web graphs, and so on. We
refer to this restricted version of the problem as
monotone minimal perfect hashing. We analyze
experimentally the data structures proposed in
Belazzougui et al. [2009], and along our way we propose
some new methods that, albeit asymptotically equivalent
or worse, perform very well in practice and provide a
balance between access speed, ease of construction, and
space usage.",
acknowledgement = ack-nhfb,
articleno = "3.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Doerr:2011:QRS,
author = "Benjamin Doerr and Tobias Friedrich and Marvin
K{\"u}nnemann and Thomas Sauerwald",
title = "Quasirandom rumor spreading: an experimental
analysis",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "33:1--33:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.2025379",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We empirically analyze two versions of the well-known
``randomized rumor spreading'' protocol to disseminate
a piece of information in networks. In the classical
model, in each round, each informed node informs a
random neighbor. In the recently proposed quasirandom
variant, each node has a (cyclic) list of its
neighbors. Once informed, it starts at a random
position of the list, but from then on informs its
neighbors in the order of the list. While for sparse
random graphs a better performance of the quasirandom
model could be proven, all other results show that,
independent of the structure of the lists, the same
asymptotic performance guarantees hold as for the
classical model. In this work, we compare the two
models experimentally. Not only does this show that the
quasirandom model generally is faster, but it also
shows that the runtime is more concentrated around the
mean. This is surprising given that much fewer random
bits are used in the quasirandom process. These
advantages are also observed in a lossy communication
model, where each transmission does not reach its
target with a certain probability, and in an
asynchronous model, where nodes send at random times
drawn from an exponential distribution. We also show
that typically the particular structure of the lists
has little influence on the efficiency.",
acknowledgement = ack-nhfb,
articleno = "3.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Haverkort:2011:FDH,
author = "Herman Haverkort and Freek V. Walderveen",
title = "Four-dimensional {Hilbert} curves for {$R$}-trees",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "34:1--34:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.2025380",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Two-dimensional R-trees are a class of spatial index
structures in which objects are arranged to enable fast
window queries: report all objects that intersect a
given query window. One of the most successful methods
of arranging the objects in the index structure is
based on sorting the objects according to the positions
of their centers along a two-dimensional Hilbert
space-filling curve. Alternatively, one may use the
coordinates of the objects' bounding boxes to represent
each object by a four-dimensional point, and sort these
points along a four-dimensional Hilbert-type curve. In
experiments by Kamel and Faloutsos and by Arge et al.,
the first solution consistently outperformed the latter
when applied to point data, while the latter solution
clearly outperformed the first on certain artificial
rectangle data. These authors did not specify which
four-dimensional Hilbert-type curve was used; many
exist. In this article, we show that the results of the
previous articles can be explained by the choice of the
four-dimensional Hilbert-type curve that was used and
by the way it was rotated in four-dimensional space. By
selecting a curve that has certain properties and
choosing the right rotation, one can combine the
strengths of the two-dimensional and the
four-dimensional approach into one, while avoiding
their apparent weaknesses. The effectiveness of our
approach is demonstrated with experiments on various
datasets. For real data taken from VLSI design, our new
curve yields R-trees with query times that are better
than those of R-trees that were obtained with
previously used curves.",
acknowledgement = ack-nhfb,
articleno = "3.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Negrucseri:2011:SMF,
author = "Cosmin Silvestru Negrucseri and Mircea Bogdan Pacsosi
and Barbara Stanley and Clifford Stein and Cristian
George Strat",
title = "Solving maximum flow problems on real-world bipartite
graphs",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "35:1--35:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.2025381",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this article, we present an experimental study of
several maximum-flow algorithms in the context of
unbalanced bipartite networks. Our experiments are
motivated by a real-world problem of managing
reservation-based inventory in Google content ad
systems. We are interested in observing the performance
of several push-relabel algorithms on our real-world
datasets and also on some generated ones. Previous work
suggested an important improvement for push-relabel
algorithms on unbalanced bipartite networks: the
two-edge push rule. We show how the two-edge push rule
improves the running time. While no single algorithm
dominates the results, we show there is one that has
very robust performance in practice.",
acknowledgement = ack-nhfb,
articleno = "3.5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Tazari:2011:DLH,
author = "Siamak Tazari and Matthias M{\"u}ller-Hannemann",
title = "Dealing with large hidden constants: engineering a
{Planar Steiner Tree (PTAS)}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "16",
number = "1",
pages = "36:1--36:??",
year = "2011",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/1963190.2025382",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Sat Feb 25 18:02:18 MST 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We present the first attempt on implementing a highly
theoretical polynomial-time approximation scheme (PTAS)
with huge hidden constants, namely, the PTAS for
Steiner tree in planar graphs by Borradaile, Klein, and
Mathieu (2009). Whereas this result, and several other
PTAS results of the recent years, are of high
theoretical importance, no practical applications or
even implementation attempts have been known to date,
due to the extremely large constants that are involved
in them. We describe techniques on how to circumvent
the challenges in implementing such a scheme. With
today's limitations on processing power and space, we
still have to sacrifice approximation guarantees for
improved running times by choosing some parameters
empirically. But our experiments show that with our
choice of parameters, we do get the desired
approximation ratios, suggesting that a much tighter
analysis might be possible. Our computational
experiments with benchmark instances from SteinLib and
large artificial instances well exceeded our own
expectations. We demonstrate that we are able to handle
instances with up to a million nodes and several
hundreds of terminals in 1.5 hours on a standard PC. On
the rectilinear preprocessed instances from SteinLib,
we observe a monotonous improvement for smaller values
of $\epsilon$, with an average gap below 1\% for
$\epsilon = 0.1$. We compare our implementation against
the well-known batched $1$-Steiner heuristic and
observe that on very large instances, we are able to
produce comparable solutions much faster. We also
present a thorough experimental evaluation of the
influence of the various parameters of the PTAS and
thus obtain a better understanding of their empirical
effects.",
acknowledgement = ack-nhfb,
articleno = "3.6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Reams:2012:AFD,
author = "Charles Reams",
title = "{Anatree}: a Fast Data Structure for Anagrams",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "17",
number = "1",
pages = "11:1--11:??",
month = mar,
year = "2012",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2133803.2133804",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Tue Mar 27 17:30:32 MDT 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Natural language is a rich source of constraint
satisfaction problems (CSPs), with a uniquely
structured solution domain. We describe a number of
approaches to satisfying the particular case of
unordered letter-level constraints, including anagrams,
but also relevant to typographical error correction,
password security and word puzzles among other fields.
We define the anatree, a data structure that can solve
many such problems in constant time with respect to the
size of the lexicon. The structure represents the
lexicon of a language in a format somewhat analogous to
a binary decision diagram (BDD) and, as with BDDs,
construction heuristics allow the real average-case
performance to vastly exceed the theoretical worst
case. We compare anatrees and their alternatives
empirically, explore the behavior of the construction
heuristics, and characterize the tasks for which each
is best suited.",
acknowledgement = ack-nhfb,
articleno = "1.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Geisberger:2012:RPF,
author = "Robert Geisberger and Michael N. Rice and Peter
Sanders and Vassilis J. Tsotras",
title = "Route planning with flexible edge restrictions",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "17",
number = "1",
pages = "12:1--12:??",
month = mar,
year = "2012",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2133803.2133805",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Tue Mar 27 17:30:32 MDT 2012",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "In this work, we explore a new type of flexible
shortest-path query, in which the query can be
dynamically parameterized to constrain the type of
edges that may be included in the resulting shortest
path (e.g., find the shortest path in a road network
that avoids toll roads and low overpasses, respective
of the specified vehicle height). We extend the
hierarchical preprocessing technique known as
Contraction Hierarchies to efficiently support such
flexible queries. We also present several effective
algorithmic optimizations for further improving the
overall scalability and query times of this approach,
including the addition of goal-directed search
techniques, search space pruning techniques, and
generalizing the constraints of the local search.
Experiments are presented for both the North American
and the European road networks, showcasing the general
effectiveness and scalability of our proposed
methodology to large-scale, real-world graphs.",
acknowledgement = ack-nhfb,
articleno = "1.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Abraham:2013:ARR,
author = "Ittai Abraham and Daniel Delling and Andrew V.
Goldberg and Renato F. Werneck",
title = "Alternative routes in road networks",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "18",
number = "1",
pages = "1.3:1--1.3:??",
month = dec,
year = "2013",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2444016.2444019",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon May 6 18:55:51 MDT 2013",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We study the problem of finding good alternative
routes in road networks. We look for routes that are
substantially different from the shortest path, have
small stretch, and are locally optimal. We formally
define the problem of finding alternative routes with a
single via vertex, develop efficient algorithms for it,
and evaluate them experimentally. Our algorithms are
efficient enough for practical use and compare
favorably with previous methods in both speed and
solution quality.",
acknowledgement = ack-nhfb,
articleno = "1.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Batz:2013:MTD,
author = "G. Veit Batz and Robert Geisberger and Peter Sanders
and Christian Vetter",
title = "Minimum time-dependent travel times with contraction
hierarchies",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "18",
number = "1",
pages = "1.4:1--1.4:??",
month = dec,
year = "2013",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2444016.2444020",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon May 6 18:55:51 MDT 2013",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Time-dependent road networks are represented as
weighted graphs, where the weight of an edge depends on
the time one passes through that edge. This way, we can
model periodic congestions during rush hour and similar
effects. In this work we deal with the special case
where edge weights are time-dependent travel times.
Namely, we consider two problems in this setting:
Earliest arrival queries ask for a minimum travel time
route for a start and a destination depending on a
given departure time. Travel time profile queries ask
for the travel time profile for a start, a destination,
and an interval of possible departure times. For an
instance representing the German road network, for
example, we can answer earliest arrival queries in less
than 1.5ms. For travel time profile queries, which are
much harder to answer, we need less than 40ms if the
interval of possible departure times has a width of 24
hours. For inexact travel time profiles with an allowed
error of about 1\% this even reduces to 3.2ms. The
underlying hierarchical representations of the road
network, which are variants of a time-dependent
contraction hierarchy (TCH), need less than 1GiB of
space and can be generated in about 30 minutes. As far
as we know, TCHs are currently the only method being
able to answer travel time profile queries efficiently.
Altogether, with TCHs, web servers with massive request
traffic are able to provide fast time-dependent
earliest arrival route planning and computation of
travel time profiles.",
acknowledgement = ack-nhfb,
articleno = "1.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Bonami:2013:BRC,
author = "Pierre Bonami and Jon Lee and Sven Leyffer and Andreas
W{\"a}chter",
title = "On branching rules for convex mixed-integer nonlinear
optimization",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "18",
number = "1",
pages = "2.6:1--2.6:??",
month = dec,
year = "2013",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2532568",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed May 21 14:36:03 MDT 2014",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Branch-and-Bound (B\&B) is perhaps the most
fundamental algorithm for the global solution of convex
Mixed-Integer Nonlinear Programming (MINLP) problems.
It is well-known that carrying out branching in a
nonsimplistic manner can greatly enhance the
practicality of B\&B in the context of Mixed-Integer
Linear Programming (MILP). No detailed study of
branching has heretofore been carried out for MINLP. In
this article, we study and identify useful
sophisticated branching methods for MINLP, including
novel approaches based on approximations of the
nonlinear relaxations by linear and quadratic
programs.",
acknowledgement = ack-nhfb,
articleno = "2.6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Canzar:2013:PDA,
author = "Stefan Canzar and Khaled Elbassioni and Juli{\'a}n
Mestre",
title = "A polynomial-delay algorithm for enumerating
approximate solutions to the interval constrained
coloring problem",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "18",
number = "1",
pages = "2.2:1--2.2:??",
month = dec,
year = "2013",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2444016.2493372",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed May 21 14:36:03 MDT 2014",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We study the interval constrained coloring problem, a
combinatorial problem arising in the interpretation of
data on protein structure emanating from experiments
based on hydrogen/deuterium exchange and mass
spectrometry. The problem captures the challenging task
of increasing the spatial resolution of experimental
data in order to get a better picture of the protein
structure. Since solutions proposed by any algorithmic
framework have to ultimately be verified by
biochemists, it is important to provide not just a
single solution, but a valuable set of candidate
solutions. Our contribution is a polynomial-delay,
polynomial-space algorithm for enumerating all exact
solutions plus further approximate solutions, which are
guaranteed to be within an absolute error of two of the
optimum within fragments of the protein, that is,
within sets of consecutive residues. Our experiments
indicate that the quality of the approximate solutions
is comparable to the optimal ones in terms of deviation
from the underlying true solution. In addition, the
experiments also confirm the effectiveness of the
method in reducing the delay between two consecutive
solutions considerably, compared to what it takes an
integer programming solver to produce the next exact
solution.",
acknowledgement = ack-nhfb,
articleno = "2.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Delort:2013:HDP,
author = "Charles Delort and Olivier Spanjaard",
title = "A hybrid dynamic programming approach to the
biobjective binary knapsack problem",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "18",
number = "1",
pages = "1.2:1--1.2:??",
month = dec,
year = "2013",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2444016.2444018",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed May 21 14:36:03 MDT 2014",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "This article is devoted to a study of the impact of
using bound sets in biobjective dynamic programming.
This notion, introduced by Villareal and Karwan [1981],
has been independently revisited by Ehrgott and
Gandibleux [2007], as well as by Sourd and Spanjaard
[2008]. The idea behind it is very general and can,
therefore, be adapted to a wide range of biobjective
combinatorial problems. We focus here on the
biobjective binary knapsack problem. We show that using
bound sets to perform a hybrid dynamic programming
procedure embedded in a two-phase method [Ulungu and
Teghem 1995] yields numerical results that outperform
previous dynamic programming approaches to the problem,
both in execution times and memory requirements.",
acknowledgement = ack-nhfb,
articleno = "1.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Ferraro-Petrillo:2013:DSR,
author = "Umberto Ferraro-Petrillo and Fabrizio Grandoni and
Giuseppe F. Italiano",
title = "Data structures resilient to memory faults: an
experimental study of dictionaries",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "18",
number = "1",
pages = "1.6:1--1.6:??",
month = dec,
year = "2013",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2444016.2444022",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon May 6 18:55:51 MDT 2013",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We address the problem of implementing data structures
resilient to memory faults, which may arbitrarily
corrupt memory locations. In this framework, we focus
on the implementation of dictionaries and perform a
thorough experimental study using a testbed that we
designed for this purpose. Our main discovery is that
the best-known (asymptotically optimal) resilient data
structures have very large space overheads. More
precisely, most of the space used by these data
structures is not due to key storage. This might not be
acceptable in practice, since resilient data structures
are meant for applications where a huge amount of data
(often of the order of terabytes) has to be stored.
Exploiting techniques developed in the context of
resilient (static) sorting and searching, in
combination with some new ideas, we designed and
engineered an alternative implementation, which, while
still guaranteeing optimal asymptotic time and space
bounds, performs much better in terms of memory without
compromising the time efficiency.",
acknowledgement = ack-nhfb,
articleno = "1.6",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Festa:2013:FSI,
author = "Paola Festa",
title = "Foreword to the special issue {SEA 2010}",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "18",
number = "1",
pages = "1.1:1--1.1:??",
month = dec,
year = "2013",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2444016.2444017",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed May 21 14:36:03 MDT 2014",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
acknowledgement = ack-nhfb,
articleno = "1.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Gog:2013:CST,
author = "Simon Gog and Enno Ohlebusch",
title = "Compressed suffix trees: Efficient computation and
storage of {LCP}-values",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "18",
number = "1",
pages = "2.1:1--2.1:??",
month = dec,
year = "2013",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2444016.2461327",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed May 21 14:36:03 MDT 2014",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "The suffix tree is a very important data structure in
string processing, but typical implementations suffer
from huge space consumption. In large-scale
applications, compressed suffix trees (CSTs) are
therefore used instead. A CST consists of three
(compressed) components: the suffix array, the longest
common prefix (LCP)-array and data structures for
simulating navigational operations on the suffix tree.
The LCP-array stores the lengths of the LCPs of
lexicographically adjacent suffixes, and it can be
computed in linear time. In this article, we present a
new LCP-array construction algorithm that is fast and
very space efficient. In practice, our algorithm
outperforms alternative algorithms. Moreover, we
introduce a new compressed representation of
LCP-arrays.",
acknowledgement = ack-nhfb,
articleno = "2.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Gorke:2013:DGC,
author = "Robert G{\"o}rke and Pascal Maillard and Andrea Schumm
and Christian Staudt and Dorothea Wagner",
title = "Dynamic graph clustering combining modularity and
smoothness",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "18",
number = "1",
pages = "1.5:1--1.5:??",
month = dec,
year = "2013",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2444016.2444021",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Mon May 6 18:55:51 MDT 2013",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Maximizing the quality index modularity has become one
of the primary methods for identifying the clustering
structure within a graph. Since many contemporary
networks are not static but evolve over time,
traditional static approaches can be inappropriate for
specific tasks. In this work, we pioneer the NP-hard
problem of online dynamic modularity maximization. We
develop scalable dynamizations of the currently fastest
and the most widespread static heuristics and engineer
a heuristic dynamization of an optimal static
algorithm. Our algorithms efficiently maintain a
modularity -based clustering of a graph for which
dynamic changes arrive as a stream. For our quickest
heuristic we prove a tight bound on its number of
operations. In an experimental evaluation on both a
real-world dynamic network and on dynamic clustered
random graphs, we show that the dynamic maintenance of
a clustering of a changing graph yields higher
modularity than recomputation, guarantees much smoother
clustering dynamics, and requires much lower runtimes.
We conclude with giving sound recommendations for the
choice of an algorithm.",
acknowledgement = ack-nhfb,
articleno = "1.5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Hofri:2013:OSS,
author = "Micha Hofri",
title = "Optimal selection and sorting via dynamic
programming",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "18",
number = "1",
pages = "2.3:1--2.3:??",
month = dec,
year = "2013",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2444016.2493373",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed May 21 14:36:03 MDT 2014",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We show how to find optimal algorithms for the
selection of one or more order statistics over a small
set of numbers, and as an extreme case, complete
sorting. The criterion is using the smallest number of
comparisons; separate derivations are performed for
minimization on the average (over all permutations) or
in the worst case. When the computational process
establishes the optimal values, it also generates
C-language functions that implement policies which
achieve those optimal values. The search for the
algorithms is driven by a Markov decision process, and
the program provides the optimality proof as well.",
acknowledgement = ack-nhfb,
articleno = "2.3",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Kouri:2013:FRM,
author = "Tina M. Kouri and Dinesh P. Mehta",
title = "Faster reaction mapping through improved naming
techniques",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "18",
number = "1",
pages = "2.5:1--2.5:??",
month = dec,
year = "2013",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2532569",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed May 21 14:36:03 MDT 2014",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Automated reaction mapping is an important tool in
cheminformatics where it may be used to classify
reactions or validate reaction mechanisms. The reaction
mapping problem is known to be NP-Hard and may be
formulated as an optimization problem. In this article,
we present four algorithms that continue to obtain
optimal solutions to this problem, but with
significantly improved runtimes over the previous
Constructive Count Vector (CCV) algorithm. Our
algorithmic improvements include (i) the use of a fast
(but not 100\% accurate) canonical labeling algorithm,
(ii) name reuse (i.e., storing intermediate results
rather than recomputing), and (iii) an incremental
approach to canonical name computation. The time to map
the reactions from the Kegg/Ligand database previously
took over 2 days using CCV, but now it takes fewer than
4 hours to complete. Experimental results on chemical
reaction databases demonstrate our 2-CCV FDN MS
algorithm usually performs over fifteen times faster
than previous automated reaction mapping algorithms.",
acknowledgement = ack-nhfb,
articleno = "2.5",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Kouzinopoulos:2013:EOT,
author = "Charalampos S. Kouzinopoulos and Konstantinos G.
Margaritis",
title = "Exact online two-dimensional pattern matching using
multiple pattern matching algorithms",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "18",
number = "1",
pages = "2.4:1--2.4:??",
month = dec,
year = "2013",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2513148",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed May 21 14:36:03 MDT 2014",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "Baker and Bird and Baeza-Yates and Regnier are two of
the most efficient and widely used algorithms for exact
online two-dimensional pattern matching. Both use the
automaton of the Aho--Corasick multiple pattern
matching algorithm to locate all the occurrences of a
two-dimensional pattern in a two-dimensional input
string, a data structure that is considered by many as
inefficient, especially when used to process long
patterns or data using large alphabet sizes. This
article presents variants of the Baker and Bird and the
Baeza-Yates and Regnier algorithms that use the data
structures of the Set Horspool, Wu-Manber, Set Backward
Oracle Matching, and SOG multiple pattern matching
algorithms in place of the automaton of Aho--Corasick
and evaluates their performance experimentally in terms
of preprocessing and searching time.",
acknowledgement = ack-nhfb,
articleno = "2.4",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Doerr:2014:RRP,
author = "Benjamin Doerr and Magnus Wahlstr{\"o}m",
title = "Randomized Rounding in the Presence of a Cardinality
Constraint",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "19",
number = "1",
pages = "1.2:1--1.2:??",
month = may,
year = "2014",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2594409",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed May 21 14:36:05 MDT 2014",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We consider the problem of generating randomized
roundings that satisfy a single cardinality constraint
and admit Chernoff-type large deviation bounds for
weighted sums of the variables. That this can be done
efficiently was proven by Srinivasan [2001], a
different approach was later given by the first author
[Doerr 2006]. In this work, we (a) present an improved
version of the bitwise derandomization given by Doerr,
(b) give the first derandomization of Srinivasan's
tree-based randomized approach and prove its
correctness, and (c) experimentally compare the
resulting algorithms. Our experiments show that adding
a single cardinality constraint typically reduces the
rounding errors and only moderately increases the
running times. In general, our derandomization of the
tree-based approach is superior to the derandomized
bitwise one, while the two randomized versions produce
very similar rounding errors. When implementing the
derandomized tree-based approach, however, the choice
of the tree is important.",
acknowledgement = ack-nhfb,
articleno = "1.2",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
@Article{Gonzalez:2014:LCS,
author = "Rodrigo Gonz{\'a}lez and Gonzalo Navarro and
H{\'e}ctor Ferrada",
title = "Locally Compressed Suffix Arrays",
journal = j-ACM-J-EXP-ALGORITHMICS,
volume = "19",
number = "1",
pages = "1.1:1--1.1:??",
month = may,
year = "2014",
CODEN = "????",
DOI = "http://dx.doi.org/10.1145/2594408",
ISSN = "1084-6654",
ISSN-L = "1084-6654",
bibdate = "Wed May 21 14:36:05 MDT 2014",
bibsource = "http://portal.acm.org/;
http://www.math.utah.edu/pub/tex/bib/datacompression.bib;
http://www.math.utah.edu/pub/tex/bib/jea.bib",
abstract = "We introduce a compression technique for suffix
arrays. It is sensitive to the compressibility of the
text and local, meaning that random portions of the
suffix array can be decompressed by accessing mostly
contiguous memory areas. This makes decompression very
fast, especially when various contiguous cells must be
accessed. Our main technical contributions are the
following. First, we show that runs of consecutive
values that are known to appear in function $ \Psi (i)
= A^{-1} [A[i] + 1] $ of suffix arrays $A$ of
compressible texts also show up as repetitions in the
differential suffix array $ A'[i] = A[i] - A [i - 1]$.
Second, we use Re-Pair, a grammar-based compressor, to
compress the differential suffix array, and upper bound
its compression ratio in terms of the number of runs.
Third, we show how to compact the space used by the
grammar rules by up to 50\%, while still permitting
direct access to the rules. Fourth, we develop specific
variants of Re-Pair that work using knowledge of $ \Psi
$, and use much less space than the general Re-Pair
compressor, while achieving almost the same compression
ratios. Fifth, we implement the scheme and compare it
exhaustively with previous work, including the first
implementations of previous theoretical proposals.",
acknowledgement = ack-nhfb,
articleno = "1.1",
fjournal = "Journal of Experimental Algorithmics (JEA)",
journal-URL = "http://portal.acm.org/browse_dl.cfm?idx=J430",
}
%% [21-May-2014] Check for additional papers from in-progress issue v19n1.