Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics

259 Pages·2010·4.016 MB·English

by  Clara Pizzuti., Marylyn D. Ritchie., Mario Giacobini

Lecture Notes in Computer Science 6023
CommencedPublicationin1973
FoundingandFormerSeriesEditors:
GerhardGoos,JurisHartmanis,andJanvanLeeuwen
EditorialBoard
DavidHutchison
LancasterUniversity,UK
TakeoKanade
CarnegieMellonUniversity,Pittsburgh,PA,USA
JosefKittler
UniversityofSurrey,Guildford,UK
JonM.Kleinberg
CornellUniversity,Ithaca,NY,USA
AlfredKobsa
UniversityofCalifornia,Irvine,CA,USA
FriedemannMattern
ETHZurich,Switzerland
JohnC.Mitchell
StanfordUniversity,CA,USA
MoniNaor
WeizmannInstituteofScience,Rehovot,Israel
OscarNierstrasz
UniversityofBern,Switzerland
C.PanduRangan
IndianInstituteofTechnology,Madras,India
BernhardSteffen
TUDortmundUniversity,Germany
MadhuSudan
MicrosoftResearch,Cambridge,MA,USA
DemetriTerzopoulos
UniversityofCalifornia,LosAngeles,CA,USA
DougTygar
UniversityofCalifornia,Berkeley,CA,USA
GerhardWeikum
Max-PlanckInstituteofComputerScience,Saarbruecken,Germany
Clara Pizzuti Marylyn D. Ritchie
Mario Giacobini (Eds.)
Evolutionary Computation,
Machine Learning and
Data Mining in Bioinformatics
8th European Conference, EvoBIO 2010
Istanbul, Turkey, April 7-9, 2010
Proceedings
1 3
VolumeEditors
ClaraPizzuti
InstituteforHigh-PerformanceComputingandNetworking(ICAR)
ItalianNationalResearchCouncil(CNR)
ViaP.Bucci41C,87036Rende(CS),Italy
E-mail:[email protected]
MarylynD.Ritchie
VanderbiltUniversity,CenterforHumanGeneticsResearch
DepartmentofMolecularPhysiologyandBiophysics
519LightHall,Nashville,TN37232,USA
E-mail:[email protected]
MarioGiacobini
UniversityofTorino,MolecularBiotechnologyCenter
DepartmentofAnimalProductionEpidemiologyandEcology
ViaLeonardodaVinci44,10095Grugliasco(TO),Italy
E-mail:[email protected]
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LNCSSublibrary:SL1–TheoreticalComputerScienceandGeneralIssues
ISSN 0302-9743
ISBN-10 3-642-12210-8SpringerBerlinHeidelbergNewYork
ISBN-13 978-3-642-12210-1SpringerBerlinHeidelbergNewYork
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Preface
The field of bioinformatics has two main objectives: the creation and mainte-
nance of biological databases, and the discovery of knowledge from life sciences
datainordertounravelthemysteriesofbiologicalfunction,leadingtonewdrugs
andtherapiesforhumandisease.Lifesciencesdatacomeintheformofbiological
sequences, structures, pathways, or literature. One major aspect of discovering
biological knowledge is to search, predict, or model specific information in a
givendatasetin orderto generatenew interesting knowledge.Computer science
methods such as evolutionary computation, machine learning, and data mining
all have a great deal to offer the field of bioinformatics. The goalof the 8th Eu-
ropean Conference on EvolutionaryComputation, Machine Learning,and Data
Mining in Bioinformatics (EvoBIO2010)was to bring together experts in these
fields in order to discuss new and novelmethods for tackling complex biological
problems.
The 8th EvoBIO conference was held in Istanbul, Turkey during April 7–9,
2010attheIstanbulTechnicalUniversity.EvoBIO2010washeldjointlywiththe
13th European Conference on Genetic Programming (EuroGP 2010), the 10th
European Conference on Evolutionary Computation in Combinatorial Optimi-
sation (EvoCOP 2010), and the conference on the applications of evolutionary
computation,EvoApplications.Collectively,theconferencesareorganizedunder
the name Evo* (www.evostar.org). EvoBIO, held annually as a workshop since
2003, became a conference in 2007 and it is now the premiere European event
forthose interestedinthe interface betweenevolutionarycomputation,machine
learning, data mining, bioinformatics, and computational biology. All papers in
this book were presented at EvoBIO 2010 in oral or poster presentations and
respondedto a callfor papers that includedtopics ofinterestsuchas biomarker
discovery,cellsimulationandmodeling,ecologicalmodeling,fluxomics,genenet-
works,biotechnology,metabolomics,microarrayanalysis,phylogenetics,protein
interactions,proteomics, sequence analysis and alignment, and systems biology.
Atotalof40papersweresubmitted to the conferenceforpeer-review.Ofthose,
15 (37.5%) were accepted for oral presentation and 6 (15%) were accepted for
poster presentation. This result is in an overall acceptance rate of 21 (52.5%)
papers accepted for publication in the proceedings.
We would first and foremost like to thank all authors who have spent time
and effort to produce interesting contributions to this book. We would like to
acknowledgeMarioGiacobini,oftheUniversityofTorino,forhisthoroughwork
editing the EvoBIO 2010 volume. We would like to thank the members of the
Program Committee for their expert evaluation of the submitted papers, Jen-
nifer Willies from Edinburgh Napier University, for her unfaltering dedication
to the coordination of the event over the years, Stephen Dignum, University of
Essex, for his excellent work as the Publicity Chair, as well as Cecilia Di Chio,
VI Preface
University of Strathclyde, who assisted Stephen. We would also like to extend
specialthankstoS¸imaUyarfromIstanbulTechnicalUniversityforheroutstand-
ing work as the local organizer. Moreover,we would like to thank the following
personsandinstitutes:ComputerEngineeringDepartmentofIstanbulTechnical
University,Turkeyforlocalsupport,MarcSchoenauerINRIAinFranceandthe
MyReview team for providing the conference review management system and
efficient assistance.
Finally,wewanttoespeciallyacknowledgetheinvitedspeakerswhogavetwo
veryinterestingandinspirationaltalks:LucaCavalli-Sforza,ProfessorEmeritus
at the Stanford School of Medicine, and Kevin Warwick, Professor at the Uni-
versity of Reading.
Finally, we hope that you will consider contributing to EvoBIO 2011.
April 2010 Clara Pizzuti
Marylyn D. Ritchie
Organization
EvoBIO 2010, together with EuroGP 2010, EvoCOP 2010, and EvoAPPLICA-
TIONS2010,waspartofEVO*2010,Europe’spremierco-locatedeventsinthe
field of evolutionary computing.
Program Chairs
Clara Pizzuti Institute for High Performance Computing and Networking
National Research Council (ICAR-CNR), Italy
Marylyn D. RitchieVanderbilt University in Nashville, TN, USA
Local Chair
S¸ima Uyar Istanbul Technical University, Turkey
Publicity Chair
Stephen Dignum University of Essex, UK
Proceedings Chair
Mario Giacobini University of Torino, Italy
Steering Committee
David W. Corne Heriot-Watt University, Edinburgh, UK
Elena Marchiori Radboud University, Nijmegen, The Netherlands
Carlos Cotta University of Malaga, Spain
Jason H. Moore Dartmouth Medical School in Lebanon, NH, USA
Jagath C. RajapakseNanyang TechnologicalUniversity, Singapore
Program Committee
Jesus S. Aguilar-RuizPablo de Olavide University, Spain
Wolfgang Banzhaf Memorial University of Newfoundland, Canada
Jacek Blazewicz Poznan University of Technology, Poland
Erik Boczko Vanderbilt University, USA
William Bush Vanderbilt University, USA
VIII Organization
Zehra Catalpete Instanbul University, Turkey
Carlos Cotta University of Malaga, Spain
Federico Divina Pablo de Olavide University, Spain
Jitesh Dundas Edencore Technologies, USA
Todd Edwards Miami University, USA
Gary Fogel Natural Selection, Inc., USA
Raffaele Giancarlo University of Palermo, Italy
Rosalba Giugno University of Catania, Italy
Lutz Hamel University of Rhode Island, USA
Jin-Kao Hao University of Angers, France
Tom Heskes Radboud University Nijmegen, The Netherlands
Zhenyu Jia University of California, Irvine, USA
Mehmet Koyuturk Case Western Reserve University, USA
Natalio Krasnogor University of Nottingham, UK
Michael Lones University of York, UK
Bob MacCallum Imperial College London, UK
Daniel Marbach Ecole Polytechnique F´ed´erale de Lausanne, Switzerland
Elena Marchiori Radboud University, Nijmegen, The Netherlands
Andrew Martin University College London, UK
Brett McKinney University of Alabama, Birmingham, USA
Jason Moore Dartmouth College, USA
Pablo Moscato The University of Newcastle, Australia
Alison Motsinger-Reif North Carolina State University, USA
Vincent Moulton University of East Anglia, UK
See-Kiong Ng Institute for Infocomm Research, Singapore
Carlotta Orsenigo Politecnico di Milano, Italy
Clara Pizzuti ICAR-CNR, Italy
Michael Raymer Wright State University, USA
Marylyn Ritchie Vanderbilt University, USA
Raul Giraldez Rojo Pablo de Olavide University, Spain
Simona Rombo University of Calabria, Italy
Jem Rowland Aberystwyth University, UK
Marc Schoenauer University of Paris-Sud, France
Ugur Sezerman Sabanci University, Turkey
Marc L. Smith Vassar College, USA
El-Ghazali Talbi University des Sciences et Technologies de Lille, France
Tricia Thornton-WellsVanderbilt University, USA
Dave Trudgian University of Exeter, UK
Alfonso Urso ICAR-CNR, Italy
Antoine van Kampen University of Amsterdam, The Netherlands
Carlo Vercellis Politecnico di Milano, Italy
Tiffani Williams Texas A&M University, USA
Organization IX
Kai Ye Leiden Amsterdam Center for Drug
Research, The Netherlands
Andreas Zell University of Tu¨bingen, Germany
Zhongming ZhaoVanderbilt University, USA
Eckart Zitzler ETH Zurich, Switzerland
Blaz Zupan University of Ljubljana, Slovenia
Sponsoring Institutions
– Istanbul Technical University
– Microsoft
– Scientific and Technological Research Council of Turkey
– The Centre for Emergent Computing, Edinburgh Napier University, UK
Table of Contents
Variable Genetic Operator Search for the Molecular Docking
Problem ........................................................ 1
Salma Mesmoudi, Jorge Tavares, Laetitia Jourdan, and
El-Ghazali Talbi
Role of Centrality in Network-BasedPrioritization of Disease Genes .... 13
Sinan Erten and Mehmet Koyutu¨rk
ParallelMulti-Objective Approaches for Inferring Phylogenies ......... 26
Waldo Cancino, Laetitia Jourdan, El-Ghazali Talbi, and
Alexandre C.B. Delbem
An Evolutionary Model Based on Hill-Climbing Search Operators for
Protein Structure Prediction ...................................... 38
Camelia Chira, Dragos Horvath, and Dumitru Dumitrescu
Finding Gapped Motifs by a Novel Evolutionary Algorithm ........... 50
Chengwei Lei and Jianhua Ruan
Top-Down Induction of Phylogenetic Trees .......................... 62
Celine Vens, Eduardo Costa, and Hendrik Blockeel
A Model Free Method to Generate Human Genetics Datasets with
Complex Gene-Disease Relationships ............................... 74
Casey S. Greene, Daniel S. Himmelstein, and Jason H. Moore
Grammatical Evolution of Neural Networks for Discovering Epistasis
among Quantitative Trait Loci..................................... 86
Stephen D. Turner, Scott M. Dudek, and Marylyn D. Ritchie
Grammatical Evolution Decision Trees for Detecting Gene-Gene
Interactions ..................................................... 98
Sushamna Deodhar and Alison Motsinger-Reif
Identification of Individualized Feature Combinations for Survival
Prediction in Breast Cancer: A Comparison of Machine Learning
Techniques...................................................... 110
Leonardo Vanneschi, Antonella Farinaccio, Mario Giacobini,
Giancarlo Mauri, Marco Antoniotti, and Paolo Provero
Correlation–BasedScatter Search for Discovering Biclusters from Gene
Expression Data ................................................. 122
Juan A. Nepomuceno, Alicia Troncoso, and Jesu´s S. Aguilar–Ruiz