Computational Intelligence Methods for Bioinformatics and Biostatistics: 17th International Meeting, CIBB 2021 Virtual Event, November 15–17, 2021 Revised Selected Papers

269 Pages·2022·20.711 MB·English

by  Davide Chicco, Angelo Facchiano, Erica Tavazzi, Enrico Longato, Martina Vettoretti, Anna Bernasconi, Simone Avesani, Paolo Cazzaniga

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
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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