Combinatorial Pattern Matching: 11th Annual Symposium, CPM 2000 Montreal, Canada, June 21–23, 2000 Proceedings

434 Pages·2000·6.545 MB·English

by  Andrei Z. Broder (auth.), Raffaele Giancarlo, David Sankoff (eds.)

Lecture Notes in Computer Science 1848
Editedby G.Goos,J. Hartmanisand J.van Leeuwen
3
Berlin
Heidelberg
NewYork
Barcelona
HongKong
London
Milan
Paris
Singapore
Tokyo
Raffaele Giancarlo David Sankoff (Eds.)
Combinatorial
Pattern Matching
11th Annual Symposium, CPM 2000
Montreal, Canada, June 21-23, 2000
Proceedings
1 3
SeriesEditors
GerhardGoos,KarlsruheUniversity,Germany
JurisHartmanis,CornellUniversity,NY,USA
JanvanLeeuwen,UtrechtUniversity,TheNetherlands
VolumeEditors
RaffaeleGiancarlo
Universita`diePalermo
DipartimentodiMatematicaedApplicazioni
ViaArchirafi34,90123Palermo,Italy
E-mail:[email protected]
DavidSankoff
Universite´deMontre´al
Centrederecherchesmathe´matiques
CP6128succursaleCentre-Ville
Montre´al,Que´bec,CanadaH3C3J7
E-mail:[email protected]
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Combinatorialpatternmatching:11thannualsymposium;proceedings/
CPM2000,Montre´al,Canada,June21-23,2000.RaffaeleGiancarlo;
DavidSankoff(ed.).-Berlin;Heidelberg;NewYork;Barcelona;
HongKong;London;Milan;Paris;Singapore;Tokyo:Springer,2000
(Lecturenotesincomputerscience;Vol.1848)
ISBN3-540-67633-3
CRSubjectClassification(1998):F.2.2,I.5.4,I.5.0,I.7.3,H.3.3,E.4,G.2.1
ISSN0302-9743
ISBN3-540-67633-3Springer-VerlagBerlinHeidelbergNewYork
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Foreword
Thepapers contained inthisvolumewere presented atthe 11thAnnualSympo-
siumon CombinatorialPattern Matching,held June 21-23,2000 at the Univer-
sit(cid:19)e de Montr(cid:19)eal. They were selected from 44 abstracts submitted in response
to the call for papers. In addition,there were invited lectures by Andrei Broder
(AltaVista),Fernando Pereira (AT&T Research Labs), and Ian H. Witten (Uni-
versity of Waikato).
The symposium was preceded by a two-day summer school set up to at-
tract and trainyoungresearchers. The lecturers at the school were Greg Butler,
ClementLam,andGusGrahne:BLAST!Howdoyousearchsequencedatabases?,
DavidBryant:Phylogeny,Ra(cid:11)aeleGiancarlo:Algorithmicaspectsofspeechrecog-
nition, Nadia El-Mabrouk: Genome rearrangement, Laxmi Parida: Flexible-
pattern discovery, and Ian H. Witten: Adaptive text mining: inferring structure
from sequences.
Combinatorial Pattern Matching (CPM) addresses issues of searching and
matching strings and more complicated patterns such as trees, regular expres-
sions graphs, point sets, and arrays. The goal is to derive non-trivial combina-
torial properties of such structures and to exploit these properties in order to
achieve superior performance for the corresponding computationalproblems.
Over recent years a steady flow of high-qualityresearch on this subject has
changed a sparse set of isolated results into a fully-fledged area of algorithmics.
This area is continuing to grow even further due to the increasing demand for
speed and e(cid:14)ciency that comes from important and rapidly expanding appli-
cations such as the World Wide Web, computational biology, and multimedia
systems,involvingrequirements forinformationretrieval,datacompression,and
patternrecognition.TheobjectiveoftheannualCPMgatheringsistoprovidean
international forum for research in combinatorial pattern matching and related
applications.
The (cid:12)rst ten meetings were held in Paris (1990), London (1991), Tucson
(1992),Padova (1993),Asilomar (1994), Helsinki (1995), Laguna Beach (1996),
Aahrus(1997),Piscataway(1998),andWarwick(1999).Afterthe(cid:12)rstmeeting,a
selectionofpapersappearedasaspecialissueofTheoreticalComputerSciencein
Volume92.The proceedings ofthe thirdtotenth meetings appeared as volumes
644,684, 807,937, 1075,1264, 1448,and 1645 of the Springer LNCS series.
The general organizationand orientationofCPM conferences is coordinated
by a steering committee composed of:
Alberto Apostolico,
Zvi Galil,
University of Padova
Columbia University
& Purdue University
Udi Manber,
MaximeCrochemore,
Yahoo! Inc.
Universit(cid:19)e de Marne-la-Vall(cid:19)ee
VI Foreword
The program committee of CPM 2000 consisted of:
Gad Landau,
Amihood Amir, University of Haifa
Bar Ilan University & Polytechnic University
Bonnie Berger, Wojciech Rytter,
MIT University of Warsaw
Byron Dom, & University of Liverpool
IBM Almaden Marie-France Sagot,
Ra(cid:11)aele Giancarlo,Co-chair, Institut Pasteur
University of Palermo Cenk Sahinalp,
Dan Gus(cid:12)eld, Case Western Reserve University
University of California, Davis DavidSanko(cid:11), Co-chair,
Monika Henzinger, Universit(cid:19)e de Montr(cid:19)eal
Google, Inc. Jim Storer,
John Kececioglu, Brandeis University
University of Georgia Esko Ukkonen,
University of Helsinki
The local organizing committee, all from the Universit(cid:19)e de Montr(cid:19)eal,
consisted of:
Nadia El-Mabrouk David Sanko(cid:11)
Louis Pelletier SylvainViart
The conference was supported by the Centre de recherches math(cid:19)ema-
tiques of the Universit(cid:19)e de Montr(cid:19)eal, in the context of a thematic year on
Mathematical Methods in Biologyand Medecine (2000-2001).
April 2000 Ra(cid:11)aele Giancarlo
David Sanko(cid:11)
Foreword VII
List of Reviewers
O. Arbel P. Ferragina R. Sprugnoli
D. Brown R. Grossi M. Sciortino
D. Bryant R. Kumar D. Shapira
C. Constantinescu A. Malinowski J. Sharp
C. Cormode D. Modha L. Stockmeyer
K. Diks M. Nykanen
F. Ergun W. Plandowski
R.Fagin A. Piccolboni
Table of Contents
Invited Lectures
Identifyingand Filtering Near-Duplicate Documents:::::::::::::::::::: 1
Andrei Z. Broder
Machine Learning for E(cid:14)cient Natural-Language Processing::::::::::::: 11
Fernando Pereira
Browsing around a DigitalLibrary: Todayand Tomorrow ::::::::::::::: 12
Ian H. Witten
Summer School Lectures
AlgorithmicAspects of Speech Recognition:A Synopsis::::::::::::::::: 27
Adam L. Buchsbaum and Ra(cid:11)aele Giancarlo
Some Results on Flexible-Pattern Discovery ::::::::::::::::::::::::::: 33
Laxmi Parida
Contributed Papers
Explainingand ControllingAmbiguityin Dynamic Programming :::::::: 46
Robert Giegerich
A Dynamic Edit Distance Table ::::::::::::::::::::::::::::::::::::: 60
Sung-Ryul Kim and Kunsoo Park
Parametric Multiple Sequence Alignment and Phylogeny Construction:::: 69
David Ferna(cid:19)ndez-Baca, Timo Seppa¨la¨inen, and Giora Slutzki
TsukubaBB:ABranchandBoundAlgorithmforLocalMultipleSequence
Alignment :::::::::::::::::::::::::::::::::::::::::::::::::::::::: 84
Paul Horton
A Polynomial Time Approximation Scheme for the Closest Substring
Problem :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 99
Bin Ma
ApproximationAlgorithms for Hamming Clustering Problems :::::::::::108
Leszek Ga(cid:24)sieniec, Jesper Jansson, and Andrzej Lingas
Approximatingthe MaximumIsomorphic Agreement Subtree Is Hard ::::119
Paola Bonizzoni, Gianluca Della Vedova, and Giancarlo Mauri
X Table of Contents
A Faster and Unifying Algorithm for Comparing Trees :::::::::::::::::129
Ming-Yang Kao, Tak-Wah Lam, Wing-Kin Sung, and Hing-Fung Ting
Incomplete Directed Perfect Phylogeny :::::::::::::::::::::::::::::::143
Itsik Pe’er, Ron Shamir, and Roded Sharan
The Longest Common Subsequence Problem for Arc-Annotated Sequences 154
Tao Jiang, Guo-Hui Lin, Bin Ma, and Kaizhong Zhang
Boyer-Moore String Matching over Ziv-Lempel Compressed Text:::::::::166
Gonzalo Navarro and Jorma Tarhio
A Boyer-Moore Type Algorithm for Compressed Pattern Matching :::::::181
Yusuke Shibata, Tetsuya Matsumoto, Masayuki Takeda,
Ayumi Shinohara, and Setsuo Arikawa
Approximate String Matching over Ziv-Lempel Compressed Text:::::::::195
Juha Ka¨rkka¨inen, Gonzalo Navarro, and Esko Ukkonen
ImprovingStatic Compression Schemes by Alphabet Extension ::::::::::210
Shmuel T. Klein
Genome Rearrangement by Reversals and Insertions/Deletions of
Contiguous Segments:::::::::::::::::::::::::::::::::::::::::::::::222
Nadia El-Mabrouk
A Lower Bound for the Breakpoint Phylogeny Problem :::::::::::::::::235
David Bryant
Structural Properties and Tractability Results for Linear Synteny ::::::::248
David Liben-Nowell and Jon Kleinberg
Shift Error Detection in Standardized Exams::::::::::::::::::::::::::264
Steven Skiena and Pavel Sumazin
An Upper Bound for Number of Contacts in the HP-Model on the
Face-Centered-Cubic Lattice (FCC) ::::::::::::::::::::::::::::::::::277
Rolf Backofen
The CombinatorialPartitioning Method ::::::::::::::::::::::::::::::293
Matthew R. Nelson, Sharon L. Kardia, and Charles F. Sing
Compact Su(cid:14)x Array ::::::::::::::::::::::::::::::::::::::::::::::305
Veli Ma¨kinen
Linear Bidirectional On-Line Construction of A(cid:14)x Trees::::::::::::::::320
Moritz G. Maa(cid:25)
Using Su(cid:14)x Trees for Gapped Motif Discovery:::::::::::::::::::::::::335
Emily Rocke