Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics: 11th European Conference, EvoBIO 2013, Vienna, Austria, April 3-5, 2013. Proceedings

226 Pages·2013·5.88 MB·English

by  Delaney Granizo-Mackenzie

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
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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,
[e-mail]ationmanage-
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