Computational Intelligence Methods for Bioinformatics and Biostatistics: 17th International Meeting, CIBB 2021 Virtual Event, November 15–17, 2021 Revised Selected Papers PDF
Preview Computational Intelligence Methods for Bioinformatics and Biostatistics: 17th International Meeting, CIBB 2021 Virtual Event, November 15–17, 2021 Revised Selected Papers
Davide Chicco · Angelo Facchiano · Erica Tavazzi · Enrico Longato · Martina Vettoretti · Anna Bernasconi · Simone Avesani · Paolo Cazzaniga (Eds.) Computational Intelligence Methods 3 8 for Bioinformatics 4 3 1 BI and Biostatistics N L 17th International Meeting, CIBB 2021 Virtual Event, November 15–17, 2021 Revised Selected Papers 123 Lecture Notes in Bioinformatics 13483 Subseries of Lecture Notes in Computer Science SeriesEditors SorinIstrail BrownUniversity,Providence,RI,USA PavelPevzner UniversityofCalifornia,SanDiego,CA,USA MichaelWaterman UniversityofSouthernCalifornia,LosAngeles,CA,USA EditorialBoardMembers SørenBrunak TechnicalUniversityofDenmark,KongensLyngby,Denmark MikhailS.Gelfand IITP,ResearchandTrainingCenteronBioinformatics,Moscow,Russia ThomasLengauer MaxPlanckInstituteforInformatics,Saarbrücken,Germany SatoruMiyano UniversityofTokyo,Tokyo,Japan EugeneMyers MaxPlanckInstituteofMolecularCellBiologyandGenetics,Dresden,Germany Marie-FranceSagot UniversitéLyon1,Villeurbanne,France DavidSankoff UniversityofOttawa,Ottawa,Canada RonShamir TelAvivUniversity,RamatAviv,TelAviv,Israel TerrySpeed WalterandElizaHallInstituteofMedicalResearch,Melbourne,VIC,Australia MartinVingron MaxPlanckInstituteforMolecularGenetics,Berlin,Germany W.EricWong UniversityofTexasatDallas,Richardson,TX,USA Moreinformationaboutthissubseriesathttps://link.springer.com/bookseries/5381 · · Davide Chicco Angelo Facchiano · · Erica Tavazzi Enrico Longato · · Martina Vettoretti Anna Bernasconi · Simone Avesani Paolo Cazzaniga (Eds.) Computational Intelligence Methods for Bioinformatics and Biostatistics 17th International Meeting, CIBB 2021 Virtual Event, November 15–17, 2021 Revised Selected Papers Editors DavideChicco AngeloFacchiano UniversityofToronto ConsiglioNazionaledelleRicerche Toronto,ON,Canada Avellino,Italy EricaTavazzi EnricoLongato UniversitàdiPadova UniversitàdiPadova Padua,Italy Padua,Italy MartinaVettoretti AnnaBernasconi UniversitàdiPadova PolitecnicodiMilano Padua,Italy Milan,Italy SimoneAvesani PaoloCazzaniga UniversitàdiVerona UniversitàdiBergamo Verona,Italy Bergamo,Italy ISSN 0302-9743 ISSN 1611-3349 (electronic) LectureNotesinBioinformatics ISBN 978-3-031-20836-2 ISBN 978-3-031-20837-9 (eBook) https://doi.org/10.1007/978-3-031-20837-9 LNCSSublibrary:SL8–Bioinformatics ©TheEditor(s)(ifapplicable)andTheAuthor(s),underexclusivelicense toSpringerNatureSwitzerlandAG2022 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodologynow knownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookare believedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictionalclaimsin publishedmapsandinstitutionalaffiliations. ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSwitzerlandAG Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Preface This volume contains selected scientific papers of the 17th edition of the Interna- tional Meeting on Computational Intelligence Methods for Bioinformatics and Bio- statistics (CIBB 2021), which was the first online edition since its foundation. This scientificconferencegatheredscientists,researchers,scholars,andstudentsworkingon computationalintelligence,bioinformatics,biostatistics,andmedicalinformaticsfrom allovertheworld.Morethaninthepreviouseditions,thevirtualformatofthisCIBB 2021 allowed the participation of attendees from all habited continents of the planet, creating a unique transdisciplinary and international forum to discuss new challenges andtrendsincomputationalbiology,biostatistics,andhealthinformatics. Theconferenceprogramincludedonlyoralpresentations,amongwhichcutting-edge plenary keynote lectures were given by five preeminent keynote scientific speakers: Karsten Borgwardt (ETH Zürich, Switzerland) who talked about machine learning applied to data of patients in the intensive care unit, Ombretta Melaiu (Ospedale PediatricoBambinoGesù,Italy)whotalkedaboutapplicationofcomputationalstatistics andmachinelearningtobioinformaticsdataofpatientswithneuroblastoma,AndréM. Carrington(OttawaHospitalandRegionImagingAssociates,Canada)whopresenteda new partial ROC AUC measure, Jacques Balayla (McGill University, Canada) who introduced the prevalence threshold metric, and Dmytro Fishman (Tartu Ülikool, Estonia)whopresentedtheDOMErecommendationsforvalidationofmachinelearning results. Moreover, our conference included two invited talks regarding themes functional to scientific research: Stefano Tonzani (lead editor at iScience, Cell Press, USA) presented some current editorial trends and challenges of modern scientific journals, whileOlafWolkenhauer (UniversitätRostock,Germany) gaveatalkaboutsuccessful grant writing. We organized the conference program with a main conference track, including short papers dealing with heterogeneous open problems at the forefront of currentresearch,andfourspecialsessionsonspecificthemes:ArtificialIntelligenceand StatisticalMethodsforNeurodegenerativeDiseases(incollaborationwiththeHorizon 2020BRAINTEASERproject),ModelingandSimulationMethodsforComputational Biology and Systems Medicine, Towards Standardizing Machine Learning in Life Sciences:theFAIRPrinciplesandtheDOMERecommendations(incollaborationwith theELIXIREuropeMachineLearningFocusGroup),andMachineLearninginHealth- careInformaticsandMedicalBiology.Moreinformationabouttheprogramisavailable ontheconferencewebsiteathttp://www.isa.cnr.it/cibb2021/orhttps://davidechicco.git hub.io/cibb2021/index.html. The organization of the CIBB 2021 conference was supported by the IEEE Italy Section, the Italian chapter of the IEEE Computational Intelligence Society, and the ItalianchapteroftheIEEESystems,Man,andCyberneticsSociety. The conference was held online on the WeConf.eu platform, during November 15–17,2021,thankstothesynergisticeffortofthegeneralchairs,theadvisoryboard, vi Preface the Program Committee, and the technical chairs. The conference was attended by approximately150uniqueparticipantspersessiononaverage. Followingtheprinciplesforopenscience,weinvitedtheauthorsofallshortpapers toreleasetheirmanuscriptsaspreprintsonpreprintwebservers(bioRxiv,medRxiv,and arXiv), to publish their software code on software code repositories (GitHub, GitLab, SourceForge,orothers),andtoopenlyreleasetheirdatasetsonlineonpublicdatarepos- itories (FigShare, Zenodo, Kaggle, University of California Irvine Machine Learning Repository,orothers),tomaketheircomputationalanalysesreproducibleandtheirdata reusable. Forauthorship,weinvitedtheCIBBauthorstofollowtheauthorshipguidelinesof theInternationalCommitteeofMedicalJournalEditors(ICMJE),asrecommendedby theUniversityofTorontoFacultyofMedicine. Atotalof68shortpapersweresubmittedforconsiderationtoCIBB2021and,after aroundofreviewshandledbythemembersoftheProgramCommittee,51shortpapers wereacceptedforanoralpresentation.Aftertheconference,theauthorsofallaccepted shortpaperswereinvitedtosubmitanextendedversionoftheirmanuscripttoasupple- mentoftwoscientificjournals(BMCBioinformaticsorBMCMedicalInformaticsand DecisionMaking)ortothisSpringerLNBIvolume.Thisvolumereceived26submitted chapters,andeachchapterreceivedthreeindependentreviews;eventually19chapters wereacceptedforpublication. The editors warmly thank the conference participants, the authors, the keynote speakers,theProgramCommitteemembers,theadvisoryboarddelegateRobertoTagli- aferri,thereviewers,theCIBB2019generalchairPaoloCazzaniga,thespecialsessions’ organizers, and anyone involved for their contributions to the success of CIBB 2021. Theeditorswouldliketosendaspecialthankyoutothegeneralchairsandorganizers ofallthepreviousCIBBconferenceeditions,fromCIBB2004toCIBB2019:theirhard work,devotion,andpatiencebuiltthefoundationsforCIBB2021andforallthefuture conferenceeditions(“IfIhaveseenfurtheritisbystandingontheshouldersofgiants”, IsaacNewton). September2022 DavideChicco AngeloFacchiano Organization GeneralChairs DavideChicco UniversityofToronto,Canada AngeloFacchiano ConsiglioNazionaledelleRicerche,Italy MargheritaMutarelli ConsiglioNazionaledelleRicerche,Italy ProgramCommitteeChairs DavideChicco UniversityofToronto,Canada AngeloFacchiano ConsiglioNazionaledelleRicerche,Italy EnricoLongato UniversitàdiPadova,Italy EricaTavazzi UniversitàdiPadova,Italy MartinaVettoretti UniversitàdiPadova,Italy SimoneAvesani UniversitàdiVerona,Italy AnnaBernasconi PolitecnicodiMilano,Italy PaoloCazzaniga UniversitàdiBergamo,Italy ProgramCommittee AbbasAlameer KuwaitUniversity,Kuwait AlessandroGuazzo UniversitàdiPadova,Italy AlessiaColonna UniversitàdiPadova,Italy AndreaTangherloni UniversitàdiBergamo,Italy ArnoutVanMessem UniversitédeLiège,Belgium BayuAdhiTama UniversityofMaryland,USA BenjaminHuremagic KatholiekeUniversiteitLeuven,Belgium BinhNguyen VictoriaUniversityofWellington,NewZealand BurraVenkataDurgaKumar XiamenUniversity,Malaysia ChiaraRoversi UniversitàdiPadova,Italy ChristophFriedrich FachhochschuleDortmund,Germany ClaudiaMengoni UniversitàdiVerona,Italy DanieleMariaPapetti UniversitàdiMilano-Bicocca,Italy EleonoraAuletta UniversidadedeLisboa,Portugal EmanuelWeitschek UniNettuno,Italy EugenioDelPrete IstitutoTelethondiGeneticaeMedicina,Italy EvaViesi UniversitàdiVerona,Italy FrancescaMarturano IstitutoOncologicoVeneto,Italy viii Organization GabrielCerono UniversityofCalifornia,SanFrancisco,USA GiacomoBaruzzo UniversitàdiPadova,Italy GiovanniBirolo UniversitàdiTorino,Italy GiuseppeAgapito UniversitàMagnaGraeciadiCatanzaro,Italy HugoLópezFernández UniversidadedeVigo,Spain IsottaTrescato UniversitàdiPadova,Italy IulianCiocoiu UniversitateaTehnica˘ GheorgheAsachidinIas¸i, Romania KarinVerspoor RMITUniversity,Australia LauraVeschetti UniversitàdiVerona,Italy MarcioDorn UniversidadeFederaldoRioGrandedoSul, Brazil MarcoNobile UniversitàCa’FoscariVenezia,Italy MarcoPansera ConsiglioNazionaledelleRicerche,Italy MarzioPennisi UniversitàdelPiemonteOrientale,Italy MikeleMilia UniversitàdiPadova,Italy MirkoTreccani UniversitàdiVerona,Italy PietroBosoni UniversitàdiPavia,Italy RobertoDiMarco UniversitàdiVerona,Italy SimoneRiva UniversityofOxford,UK SimoneSpolaor TechnischeUniversiteitEindhoven, TheNetherlands StefanoMaestri UniversitàdiCamerino,Italy TatianaLatychevskaia PaulScherrerInstitute,Switzerland UmbertoPerron HumanTechnopole,Italy VincenzoBonnici UniversitàdiParma,Italy WilliamYuan HarvardMedicalSchool,USA YoungroLee SeoulNationalUniversity,SouthKorea Reviewers AlessandroPalombit Corsmed,Sweden AlessandroStefanini UniversitàdiPisa,Italy AlessiaPaglialonga ConsiglioNazionaledelleRicerche,Italy AlexGraudenzi ConsiglioNazionaledelleRicerche,Italy AlfredoVellido UniversitatPolitècnicadeCatalunya,Spain AndreaBracciali UniversityofStirling,UK AndreiaS.Martins UniversidadedeLisboa,Portugal AndreyRzhetsky UniversityofChicago,USA AngeloCiaramella UniversitàdiNapoliParthenope,Italy AngeloFacchiano ConsiglioNazionaledelleRicerche,Italy AnjanySekuboyina TechnischeUniversitätMünchen,Germany AnnaBernasconi PolitecnicodiMilano,Italy Organization ix AnnamariaCarissimo ConsiglioNazionaledelleRicerche,Italy AntoninoStaiano UniversitàdiNapoliParthenope,Italy AriefGusnanto UniversityofLeeds,UK ArturAkbarov UniversityofManchester,UK BarbaraPes UniversitàdiCagliari,Italy BenoitLiquet MacquarieUniversity,Australia BerardinoDeBari RéseauHospitalierNeuchâtelois,Switzerland BudMishra NewYorkUniversity,USA CarlosPeña SwissInstituteofBioinformatics,Switzerland ChiaraDamiani UniversitàdiMilano-Bicocca,Italy ChristianBlum ConsejoSuperiordeInvestigacionesCientíficas, Spain ChristophFriedrich FachhochschuleDortmund,Germany ClaudiaAngelini ConsiglioNazionaledelleRicerche,Italy ClaudioAngione TeessideUniversity,UK DanielaBesozzi UniversitàdiMilano-Bicocca,Italy DanieleMariaPapetti UniversitàdiMilano-Bicocca,Italy DanielePala UniversitàdiPavia,Italy DaniloRiccio QueenMaryUniversityofLondon,UK DavideChicco UniversityofToronto,Canada EleniKariki ManchesterUniversityNationalHealthService FoundationTrust,UK EleonoraCiceri MediaClinicsItalia,Italy ElisaFerrari UniversitàdiPisa,Italy EmanuelaMerelli UniversitàdiCamerino,Italy EmmanuelIfeachor UniversityofPlymouth,UK EnricoFormenti UniversitéCôted’Azur,France EnricoLongato UniversitàdiPadova,Italy EricaSilvestri UniversitàdiPadova,Italy EricaTavazzi UniversitàdiPadova,Italy FernandoLuísFerreira UniversidadeNovadeLisboa,Portugal FilippoGeraci ConsiglioNazionaledelleRicerche,Italy FilippoUtro IBM,USA FrancescoNapolitano UniversitàdelSannio,Italy GiacomoCappon UniversitàdiPadova,Italy GiancarloMauri UniversitàdiMilano-Bicocca,Italy GillesBernot UniversitéCôted’Azur,France GiosuèLoBosco UniversitàdiPalermo,Italy GiuseppeJurman FondazioneBrunoKessler,Italy GlenMartin UniversityofManchester,UK GunnarKlau Heinrich-Heine-UniversitätDüsseldorf,Germany HelenaAidos UniversidadedeLisboa,Portugal
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