{"id":"https://openalex.org/W4390992158","doi":"https://doi.org/10.1109/bibm58861.2023.10386006","title":"pCCI: A machine learning patient-centric cell-cell interactions framework for cancer subtype classification","display_name":"pCCI: A machine learning patient-centric cell-cell interactions framework for cancer subtype classification","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390992158","doi":"https://doi.org/10.1109/bibm58861.2023.10386006"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10386006","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10386006","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076154269","display_name":"Pantelis Papageorgiou","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pantelis Papageorgiou","raw_affiliation_strings":["Deeplab,Athens,Greece","Deeplab, Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Deeplab,Athens,Greece","institution_ids":[]},{"raw_affiliation_string":"Deeplab, Athens, Greece","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050352797","display_name":"Aigli Korfiati","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Aigli Korfiati","raw_affiliation_strings":["Deeplab,Athens,Greece","Deeplab, Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Deeplab,Athens,Greece","institution_ids":[]},{"raw_affiliation_string":"Deeplab, Athens, Greece","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004426322","display_name":"Aristotelis Misios","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Aristotelis Misios","raw_affiliation_strings":["Deeplab,Athens,Greece","Deeplab, Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Deeplab,Athens,Greece","institution_ids":[]},{"raw_affiliation_string":"Deeplab, Athens, Greece","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082119404","display_name":"Aristidis G. Vrahatis","orcid":"https://orcid.org/0000-0003-1892-0000"},"institutions":[{"id":"https://openalex.org/I187792471","display_name":"Ionian University","ror":"https://ror.org/01xm4n520","country_code":"GR","type":"education","lineage":["https://openalex.org/I187792471"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Aristidis G. Vrahatis","raw_affiliation_strings":["Deeplab,Athens,Greece","Deeplab, Athens, Greece","Ionian University, Corfu, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Deeplab,Athens,Greece","institution_ids":[]},{"raw_affiliation_string":"Deeplab, Athens, Greece","institution_ids":[]},{"raw_affiliation_string":"Ionian University, Corfu, Greece","institution_ids":["https://openalex.org/I187792471"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029531579","display_name":"Alexandros A. Pittis","orcid":"https://orcid.org/0000-0003-4116-9972"},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Alexandros A. Pittis","raw_affiliation_strings":["Deeplab,Athens,Greece","Deeplab, Athens, Greece","National and Kapodistrian University of Athens, Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Deeplab,Athens,Greece","institution_ids":[]},{"raw_affiliation_string":"Deeplab, Athens, Greece","institution_ids":[]},{"raw_affiliation_string":"National and Kapodistrian University of Athens, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018574547","display_name":"Bogdan Tanas\u0103","orcid":"https://orcid.org/0000-0002-3797-8171"},"institutions":[{"id":"https://openalex.org/I157075465","display_name":"Bristol-Myers Squibb (Germany)","ror":"https://ror.org/032hfv632","country_code":"DE","type":"company","lineage":["https://openalex.org/I157075465","https://openalex.org/I4210091812"]},{"id":"https://openalex.org/I4210091812","display_name":"Bristol-Myers Squibb (United States)","ror":"https://ror.org/00gtmwv55","country_code":"US","type":"company","lineage":["https://openalex.org/I4210091812"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Bogdan Tanasa","raw_affiliation_strings":["Bristol Myers Squibb,Readwood City,CA,USA","Bristol Myers Squibb, Readwood City, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bristol Myers Squibb,Readwood City,CA,USA","institution_ids":["https://openalex.org/I157075465","https://openalex.org/I4210091812"]},{"raw_affiliation_string":"Bristol Myers Squibb, Readwood City, CA, USA","institution_ids":["https://openalex.org/I4210091812"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002539266","display_name":"Konstantinos Mavrommatis","orcid":"https://orcid.org/0000-0003-4549-385X"},"institutions":[{"id":"https://openalex.org/I4210091812","display_name":"Bristol-Myers Squibb (United States)","ror":"https://ror.org/00gtmwv55","country_code":"US","type":"company","lineage":["https://openalex.org/I4210091812"]},{"id":"https://openalex.org/I4210098725","display_name":"Bristol-Myers Squibb (France)","ror":"https://ror.org/013b57229","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210091812","https://openalex.org/I4210098725"]}],"countries":["FR","US"],"is_corresponding":false,"raw_author_name":"Konstantinos Mavrommatis","raw_affiliation_strings":["Bristol Myers Squibb,Boudry,NE,Switzerland","Bristol Myers Squibb, Boudry, NE, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bristol Myers Squibb,Boudry,NE,Switzerland","institution_ids":["https://openalex.org/I4210098725"]},{"raw_affiliation_string":"Bristol Myers Squibb, Boudry, NE, Switzerland","institution_ids":["https://openalex.org/I4210091812"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101409785","display_name":"Yilin Zhao","orcid":"https://orcid.org/0000-0002-3024-5784"},"institutions":[{"id":"https://openalex.org/I157075465","display_name":"Bristol-Myers Squibb (Germany)","ror":"https://ror.org/032hfv632","country_code":"DE","type":"company","lineage":["https://openalex.org/I157075465","https://openalex.org/I4210091812"]},{"id":"https://openalex.org/I4210091812","display_name":"Bristol-Myers Squibb (United States)","ror":"https://ror.org/00gtmwv55","country_code":"US","type":"company","lineage":["https://openalex.org/I4210091812"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Yilin Zhao","raw_affiliation_strings":["Bristol Myers Squibb,Readwood City,CA,USA","Bristol Myers Squibb, Readwood City, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bristol Myers Squibb,Readwood City,CA,USA","institution_ids":["https://openalex.org/I157075465","https://openalex.org/I4210091812"]},{"raw_affiliation_string":"Bristol Myers Squibb, Readwood City, CA, USA","institution_ids":["https://openalex.org/I4210091812"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086576990","display_name":"Tao Yang","orcid":"https://orcid.org/0000-0002-2705-6042"},"institutions":[{"id":"https://openalex.org/I168537998","display_name":"Eli Lilly (United States)","ror":"https://ror.org/01qat3289","country_code":"US","type":"company","lineage":["https://openalex.org/I168537998"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tao Yang","raw_affiliation_strings":["Prevail Therapeutics, a Wholly Owned Subsidiary of Eli Lilly and Company"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Prevail Therapeutics, a Wholly Owned Subsidiary of Eli Lilly and Company","institution_ids":["https://openalex.org/I168537998"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040922549","display_name":"Vassilis Pitsikalis","orcid":"https://orcid.org/0000-0002-1593-7491"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Vassilis Pitsikalis","raw_affiliation_strings":["Deeplab,Athens,Greece","Deeplab, Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Deeplab,Athens,Greece","institution_ids":[]},{"raw_affiliation_string":"Deeplab, Athens, Greece","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.34018231,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"910","last_page":"913"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10231","display_name":"Pancreatic and Hepatic Oncology Research","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6273293495178223},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5816649198532104},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5697193741798401},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5512508153915405},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5461848378181458},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.52892005443573},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.5014557838439941},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.48861581087112427},{"id":"https://openalex.org/keywords/carcinogenesis","display_name":"Carcinogenesis","score":0.4269787669181824},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3976306915283203},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20336753129959106},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.16604822874069214},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.0899718701839447}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6273293495178223},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5816649198532104},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5697193741798401},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5512508153915405},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5461848378181458},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.52892005443573},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5014557838439941},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.48861581087112427},{"id":"https://openalex.org/C555283112","wikidata":"https://www.wikidata.org/wiki/Q1637543","display_name":"Carcinogenesis","level":3,"score":0.4269787669181824},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3976306915283203},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20336753129959106},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.16604822874069214},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.0899718701839447},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10386006","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10386006","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.7699999809265137,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1497915798","https://openalex.org/W2054990133","https://openalex.org/W2146511318","https://openalex.org/W2900411771","https://openalex.org/W2908139053","https://openalex.org/W2991084017","https://openalex.org/W3007935255","https://openalex.org/W3012498554","https://openalex.org/W3092318937","https://openalex.org/W3138055079","https://openalex.org/W4210825082","https://openalex.org/W4220751358","https://openalex.org/W4221038504","https://openalex.org/W4281716326","https://openalex.org/W4283588821","https://openalex.org/W4295879679","https://openalex.org/W4306403570","https://openalex.org/W4306970977","https://openalex.org/W4313236841","https://openalex.org/W4393656670","https://openalex.org/W6757519749","https://openalex.org/W6862929370"],"related_works":["https://openalex.org/W1967821671","https://openalex.org/W3037187668","https://openalex.org/W3030842346","https://openalex.org/W1969795570","https://openalex.org/W2125789691","https://openalex.org/W2063781606","https://openalex.org/W4234772502","https://openalex.org/W4290263427","https://openalex.org/W4386564352","https://openalex.org/W2952668426"],"abstract_inverted_index":{"The":[0],"interaction":[1],"of":[2,20,29,37,60,97,112,114,136,182],"tumor":[3,23],"cells":[4],"with":[5],"their":[6],"environment":[7],"and":[8,22,40,91,157,186],"particularly":[9],"the":[10,26,35,70,105,110,125,153,172,180],"immune":[11],"system":[12],"is":[13,45],"increasingly":[14],"recognized":[15],"as":[16],"a":[17,41,49,80,134],"key":[18],"factor":[19],"tumorigenesis":[21],"progression.":[24],"However,":[25],"expression":[27,77],"levels":[28],"genes":[30],"alone":[31],"cannot":[32],"capture":[33],"directly":[34],"complexity":[36],"these":[38],"interactions,":[39],"more":[42],"elaborated":[43],"framework":[44],"necessary.":[46],"We":[47,145],"propose":[48,117],"new":[50],"cell-cell":[51],"interactions":[52,88],"(CCIs)":[53],"feature":[54,82,120],"space":[55,83,174],"based":[56],"on":[57],"scRNA-Seq":[58],"data":[59],"multiple":[61],"patient":[62,71],"samples":[63,142],"to":[64,123,152],"classify":[65],"cancers":[66],"into":[67,79,86,143],"subtypes":[68,160,185],"at":[69],"level.":[72],"Specifically,":[73],"we":[74,116],"transform":[75],"gene":[76],"profiles":[78],"redefined":[81],"that":[84,138,171],"takes":[85],"account":[87],"between":[89],"ligands":[90],"receptors":[92],"across":[93],"all":[94],"possible":[95],"pairs":[96],"cell":[98],"types":[99],"for":[100],"each":[101],"patient.":[102],"To":[103],"handle":[104],"ultrahigh":[106],"dimensionality":[107],"arising":[108],"from":[109],"hundreds":[111],"thousands":[113],"CCIs,":[115],"an":[118],"ensemble":[119],"selection":[121],"algorithm":[122],"prioritize":[124],"most":[126],"discriminatory":[127],"CCIs.":[128],"Our":[129,166],"machine":[130],"learning":[131],"pipeline":[132],"identifies":[133],"set":[135],"CCIs":[137],"accurately":[139],"classifies":[140],"cancer":[141,184],"subtypes.":[144],"apply":[146],"our":[147],"computational":[148],"framework,":[149],"named":[150],"pCCI,":[151],"Pancreatic":[154],"Ductal":[155],"Adenocarcinoma":[156],"Glioblastoma":[158],"Multiforme":[159],"classification,":[161],"achieving":[162],"high":[163],"classification":[164],"performance.":[165],"work":[167],"provides":[168],"compelling":[169],"evidence":[170],"CCI":[173],"can":[175],"successfully":[176],"reveal":[177],"differences":[178],"in":[179],"microenvironment":[181],"different":[183],"identify":[187],"novel":[188],"pharmacological":[189],"targets.":[190]},"counts_by_year":[],"updated_date":"2025-12-21T23:12:01.093139","created_date":"2025-10-10T00:00:00"}
