Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics: 11th European Conference, EvoBIO 2013, Vienna, Austria, April 3-5, 2013. Proceedings PDF
Preview Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics: 11th European Conference, EvoBIO 2013, Vienna, Austria, April 3-5, 2013. Proceedings
Lecture Notes in Computer Science 7833 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 MaxPlanckInstituteforInformatics,Saarbruecken,Germany Leonardo Vanneschi William S. Bush Mario Giacobini (Eds.) Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics 11th European Conference, EvoBIO 2013 Vienna, Austria, April 3-5, 2013 Proceedings 1 3 VolumeEditors LeonardoVanneschi ISEGI,UniversidadeNovadeLisboa 1070-312Lisboa,Portugaland D.I.S.Co.,UniversityofMilano-Bicocca 20126Milan,Italy E-mail:[email protected] WilliamS.Bush VanderbiltUniversity CenterforHumanGeneticsResearch DepartmentofBiomedicalInformatics 519LightHall,Nashville,TN37232,USA E-mail:[email protected] MarioGiacobini UniversityofTorino DepartmentofVeterinarySciences andMolecularBiotechnologyCenter viaLeonardodaVinci44,10095Grugliasco(TO),Italy E-mail:[email protected] FrontcoverEvoStar2013logobyKevinSim,EdinburghNapierUniversity ISSN0302-9743 e-ISSN1611-3349 ISBN978-3-642-37188-2 e-ISBN978-3-642-37189-9 DOI10.1007/978-3-642-37189-9 SpringerHeidelbergDordrechtLondonNewYork LibraryofCongressControlNumber:2013933105 CRSubjectClassification(1998):J.3,H.2.8,I.2.6,F.2,F.1,G.2 LNCSSublibrary:SL1–TheoreticalComputerScienceandGeneralIssues ©Springer-VerlagBerlinHeidelberg2013 Thisworkissubjecttocopyright.Allrightsarereserved,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,re-useofillustrations,recitation,broadcasting, reproductiononmicrofilmsorinanyotherway,andstorageindatabanks.Duplicationofthispublication orpartsthereofispermittedonlyundertheprovisionsoftheGermanCopyrightLawofSeptember9,1965, inistcurrentversion,andpermissionforusemustalwaysbeobtainedfromSpringer.Violationsareliable toprosecutionundertheGermanCopyrightLaw. Theuseofgeneraldescriptivenames,registerednames,trademarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelaws andregulationsandthereforefreeforgeneraluse. Typesetting:Camera-readybyauthor,dataconversionbyScientificPublishingServices,Chennai,India Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface Computational biology is a wide and varied discipline, incorporating aspects of statistical analysis, data structure and algorithm design, machine learning, and mathematical modeling toward the processing and improved understand- ing of biological data. Experimentalists routinely generate new information on such a massive scale that computer science techniques are now becoming indis- pensable for translating the resulting data into new biological knowledge. As a consequence, biologists now face the challenges of algorithmic complexity and tractability,aswellascombinatorialexplosionwhenconductingevenbasicanal- yses. The goal of the 11th European Conference on Evolutionary Computation, Machine Learning, and Data Mining in Computational Biology (EvoBIO 2013) was to bring together experts across multiple fields to discuss new and novel methods for tackling complex biologicalproblems,andoften these experts draw inspiration from biological systems in order to produce solutions to biological problems. The 11th EvoBIO conference took place at the Vienna University of Tech- nology, Austria, during April 3–5, 2013. It was held jointly with the 16th Euro- pean Conference on Genetic Programming (EuroGP 2013), the 13th European Conference onEvolutionaryComputationin CombinatorialOptimization(Evo- COP 2013), the 11th European Conference on Evolutionary and Biologically Inspired Music, Sound, Art, and Design (EvoMUSART 2013), and the Euro- peanConferenceontheApplicationsofEvolutionaryComputation(EvoApplica- tions 2013).Collectively,these eventsareorganizedunder the name EVO*2013 (www.evostar.org).EvoBIO, held annually as a workshop since 2003, became a conferencein2007anditisnowthepremierEuropeaneventforthoseinterested in the interface between evolutionary computation, machine learning, and data miningincomputationalbiology.Allpapersintheseproceedingswerepresented at EvoBIO 2013 in oral or poster presentations, and were received in response to a call for papers soliciting a wide range of topics in the realm of biological data analysis and computational biology. First and foremost, we thank all the authors who spent time and effort to generatetheexcellentcontributionstothisbodyofwork.Wethankthemembers ofthe ProgramCommittee for their hardworkandexpert evaluationin review- ing the submitted papers. We also thank many members of the EVO* com- munity, whose tireless work ensures a smooth and successful conference event; Jennifer Willies from the Edinburgh Napier University, UK, for her unwaver- ing dedication as event coordinator, A. S¸ima Uyar from the Istanbul Technical University,Turkey,forarrangingexceptionalpublicityfortheEVO*events,and Kevin Sim from the EdinburghNapier University, UK, for his excellent work as webmaster. From the Algorithms and Data Structures Group of the Institute of Computer Graphics and Algorithms at the Vienna University of Technology, VI Preface we thank Doris Dicklberger and Gu¨nther Raidl for their excellent planning as local organizers and especially Bin Hu for his outstanding work as local Orga- nizing Committee Chair. We extend our gratitude to the Vienna University of Technologyforhostingourevent,andtoMarcSchoenauerfromINRIA,France, andtotheMyReviewteam@csregistry.orgforprovidingthepublicationmanage- mentsystemandtechnicalsupport.Lastbutnotleast,wethankoursponsoring organizations: the Algorithms and Data Structures Group at the Institute of ComputerGraphicsandAlgorithmsoftheViennaUniversityofTechnology,the Austrian Institute of Technology, and the Institute for Informatics and Digital Innovation at Edinburgh Napier University, UK. We hope you enjoy the excellent research articles included in this volume, and we invite you to contribute to EvoBIO 2014. April 2013 Leonardo Vanneschi William S. Bush Mario Giacobini Organization EvoBIO2013,togetherwithEuroGP2013,EvoCOP2013,EvoAPPLICATIONS 2013, and EvoMUSART 2013 was part of EVO* 2013, Europe’s premier co- located events in the field of evolutionary computing. Program Chairs Leonardo Vanneschi Universidade Nova de Lisboa, Portugal University of Milano-Bicocca, Milan, Italy William S. Bush Vanderbilt University in Nashville, TN, USA Mario Giacobini University of Torino, Italy Local Chair Bin Hu Vienna University of Technology, Austria Local Organizers Doris Dicklberger Vienna University of Technology, Austria Gu¨nther Raidl Vienna University of Technology, Austria Publicity Chair A. S¸ima Uyar Istanbul Technical University, Turkey Kevin Sim Edinburgh Napier University, UK Proceedings Chair Mario Giacobini University of Torino, Italy Steering Committee Elena Marchiori Radboud University, Nijmegen, The Netherlands Jason H. Moore Dartmouth Medical School in Lebanon, NH,USA Clara Pizzuti ICAR-CNR, Italy Marylyn Ritchie Vanderbilt University, USA VIII Organization Program Committee Wolfgang Banzhaf MemorialUniversityofNewfoundland,Canada Luigi Bertolotti University of Torino, Italy Jacek Blazewicz Poznan University of Technology, Poland Erik Boczko, Vanderbilt University, USA Jos´e Caldas INESC-ID Lisboa, Portugal Dominique Chu University of Kent, UK Ernesto Costa University of Coimbra, Portugal Federico Divina Pablo de Olavide University Seville, Spain Jitesh Dundas Edencore Technologies, USA Alex Freitas University of Kent, UK Rosalba Giugno University of Catania, Italy Casey Greene Dartmouth College, Hanover, USA Jin-Kao Hao University of Angers, France Tom Heskes Radboud University, Nijmegen, The Netherlands Ting Hu Dartmouth College, Hanover, USA Mehmet Koyuturk Case Western Reserve University, USA Michael Lones University of York, UK Penousal Machado University of Coimbra, Portugal Elena Marchiori Radboud University, Nijmegen, The Netherlands Andrew Martin University College London, UK Brett McKinney University of Tulsa, USA Jason H. Moore Dartmouth College, Hanover, USA Pablo Moscato The University of Newcastle, UK Alison Motsinger-Reif University of North Carolina Raleigh, USA Vincent Moulton University of East Anglia, UK Giuseppe Nicosia University of Catania, Italy Carlotta Orsenigo Politecnico di Milano, Italy Paolo Provero University of Torino, Italy Michael Raymer Wright State University, USA Marylyn Ritchie The Pennsylvania State University, USA Raul Giraldez Rojo Pablo de Olivade University, Spain Simona Rombo ICAR-CNR, Italy Marc Schoenauer LRI- Universit´e Paris-Sud, France Ugur Sezerman Sabanci University, Turkey Sara Silva INESC-ID Lisboa, Portugal Marc Smith Vassar College, USA El-Ghazali Talbi Univ. des Sciences et Technologies de Lille, France Stephen Turner University of Virginia, USA Organization IX Ryan Urbanowicz Dartmouth College, Hanover, USA Alfonso Urso ICAR-CNR, Italy Antoine van Kampen Universiteit van Amsterdam, The Netherlands Andreas Zell University of Tu¨bingen, Germany Zhongming Zhao Vanderbilt University, USA Jia Zhenyu University of California, USA Sponsoring Institutions – The Institute of Computer Graphics and Algorithms , Vienna University of Technology, Austria – The Austrian Institute of Technology – The Institute for Informatics and Digital Innovationg, Edinburgh Napier University, UK Table of Contents Oral Contributions Multiple Threshold Spatially Uniform ReliefF for the Genetic Analysis of Complex Human Diseases....................................... 1 Delaney Granizo-Mackenzie and Jason H. Moore Time-Point Specific Weighting Improves Coexpression Networks from Time-Course Experiments......................................... 11 Jie Tan, Gavin D. Grant, Michael L. Whitfield, and Casey S. Greene Inferring Human Phenotype Networks from Genome-Wide Genetic Associations..................................................... 23 Christian Darabos, Kinjal Desai, Richard Cowper-Sal.lari, Mario Giacobini, Britney E. Graham, Mathieu Lupien, and Jason H. Moore Knowledge-Constrained K-Medoids Clustering of Regulatory Rare Alleles for Burden Tests .......................................... 35 R. Michael Sivley, Alexandra E. Fish, and William S. Bush Feature Selection and Classification of High Dimensional Mass Spectrometry Data: A Genetic Programming Approach ............... 43 Soha Ahmed, Mengjie Zhang, and Lifeng Peng Structured Populations and the Maintenance of Sex .................. 56 Peter A. Whigham, Grant Dick, Alden Wright, and Hamish G. Spencer Hybrid Multiobjective Artificial Bee Colony with Differential Evolution Applied to Motif Finding ......................................... 68 David L. Gonza´lez-A´lvarez and Miguel A. Vega-Rodr´ıguez ACO-Based Bayesian Network Ensembles for the Hierarchical Classification of Ageing-Related Proteins............................ 80 Khalid M. Salama and Alex A. Freitas Dimensionality Reduction via Isomap with Lock-Step and Elastic Measures for Time Series Gene ExpressionClassification .............. 92 Carlotta Orsenigo and Carlo Vercellis Supervising Random Forest Using Attribute Interaction Networks...... 104 Qinxin Pan, Ting Hu, James D. Malley, Angeline S. Andrew, Margaret R. Karagas, and Jason H. Moore XII Table of Contents Poster Contributions Hybrid Genetic Algorithms for Stress Recognition in Reading.......... 117 Nandita Sharma and Tom Gedeon Optimal Use of Biological Expert Knowledge from Literature Mining in Ant Colony Optimization for Analysis of Epistasis in Human Disease ......................................................... 129 Arvis Sulovari, Jeff Kiralis, and Jason H. Moore A Multiobjective ProposalBased on the Firefly Algorithm for Inferring Phylogenies ..................................................... 141 Sergio Santander-Jim´enez and Miguel A. Vega-Rodr´ıguez Mining for Variability in the Coagulation Pathway: A Systems Biology Approach ....................................................... 153 Davide Castaldi, Daniele Maccagnola, Daniela Mari, and Francesco Archetti Improving the Performance of CGPANN for Breast Cancer Diagnosis Using Crossover and Radial Basis Functions......................... 165 Timmy Manning and Paul Walsh An Evolutionary Approach to Wetlands Design ...................... 177 Marco Gaudesi, Andrea Marion, Tommaso Musner, Giovanni Squillero, and Alberto Tonda Impact of Different Recombination Methods in a Mutation-Specific MOEA for a Biochemical Application .............................. 188 Susanne Rosenthal, Nail El-Sourani, and Markus Borschbach Cell–Based Metrics Improve the Detection of Gene-Gene Interactions Using Multifactor Dimensionality Reduction......................... 200 Jonathan M. Fisher, Peter Andrews, Jeff Kiralis, Nicholas A. Sinnott-Armstrong, and Jason H. Moore Emergence of Motifs in Model Gene Regulatory Networks............. 212 Marcin Zago´rski Author Index.................................................. 217
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