{"id":"https://openalex.org/W4417200391","doi":"https://doi.org/10.1145/3765612.3767214","title":"An explainable approach to learning feature representations of omics data using optimal transport to improve phenotype stratification","display_name":"An explainable approach to learning feature representations of omics data using optimal transport to improve phenotype stratification","publication_year":2025,"publication_date":"2025-10-12","ids":{"openalex":"https://openalex.org/W4417200391","doi":"https://doi.org/10.1145/3765612.3767214"},"language":null,"primary_location":{"id":"doi:10.1145/3765612.3767214","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3765612.3767214","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3765612.3767214","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3765612.3767214","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093003470","display_name":"Nandini Amit Gadhia","orcid":"https://orcid.org/0009-0004-8233-1459"},"institutions":[{"id":"https://openalex.org/I146655781","display_name":"University of Liverpool","ror":"https://ror.org/04xs57h96","country_code":"GB","type":"education","lineage":["https://openalex.org/I146655781"]},{"id":"https://openalex.org/I162524378","display_name":"Science and Technology Facilities Council","ror":"https://ror.org/057g20z61","country_code":"GB","type":"government","lineage":["https://openalex.org/I162524378","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Nandini Amit Gadhia","raw_affiliation_strings":["Computer Science, University of Liverpool, Liverpool, United Kingdom","Hartree Centre, Science and Technology Facilities Council, Daresbury, United Kingdom"],"raw_orcid":"https://orcid.org/0009-0004-8233-1459","affiliations":[{"raw_affiliation_string":"Computer Science, University of Liverpool, Liverpool, United Kingdom","institution_ids":["https://openalex.org/I146655781"]},{"raw_affiliation_string":"Hartree Centre, Science and Technology Facilities Council, Daresbury, United Kingdom","institution_ids":["https://openalex.org/I162524378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105534157","display_name":"Soumyadip Ghosh","orcid":"https://orcid.org/0009-0005-1642-1891"},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Soumyadip Ghosh","raw_affiliation_strings":["IBM Research, Yorktown Heights, NY, USA"],"raw_orcid":"https://orcid.org/0009-0005-1642-1891","affiliations":[{"raw_affiliation_string":"IBM Research, Yorktown Heights, NY, USA","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078961975","display_name":"Ritesh Krishna","orcid":"https://orcid.org/0000-0002-5303-1412"},"institutions":[{"id":"https://openalex.org/I4210121844","display_name":"IBM (United Kingdom)","ror":"https://ror.org/02wat9f69","country_code":"GB","type":"company","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210121844"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ritesh Krishna","raw_affiliation_strings":["IBM Research, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-5303-1412","affiliations":[{"raw_affiliation_string":"IBM Research, London, United Kingdom","institution_ids":["https://openalex.org/I4210121844"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089006585","display_name":"Anh Nguyen","orcid":"https://orcid.org/0000-0002-1449-211X"},"institutions":[{"id":"https://openalex.org/I146655781","display_name":"University of Liverpool","ror":"https://ror.org/04xs57h96","country_code":"GB","type":"education","lineage":["https://openalex.org/I146655781"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Anh Nguyen","raw_affiliation_strings":["Computer Science, University of Liverpool, Liverpool, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-1449-211X","affiliations":[{"raw_affiliation_string":"Computer Science, University of Liverpool, Liverpool, United Kingdom","institution_ids":["https://openalex.org/I146655781"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033092397","display_name":"Michalis Smyrnakis","orcid":"https://orcid.org/0000-0003-1416-3727"},"institutions":[{"id":"https://openalex.org/I162524378","display_name":"Science and Technology Facilities Council","ror":"https://ror.org/057g20z61","country_code":"GB","type":"government","lineage":["https://openalex.org/I162524378","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Michalis Smyrnakis","raw_affiliation_strings":["Hartree Centre, Science and Technology Facilities Council, Daresbury, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0003-1416-3727","affiliations":[{"raw_affiliation_string":"Hartree Centre, Science and Technology Facilities Council, Daresbury, United Kingdom","institution_ids":["https://openalex.org/I162524378"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5093003470"],"corresponding_institution_ids":["https://openalex.org/I146655781","https://openalex.org/I162524378"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.33847548,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.24379999935626984,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.24379999935626984,"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/T10066","display_name":"Gut microbiota and health","score":0.12520000338554382,"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/T10885","display_name":"Gene expression and cancer classification","score":0.10729999840259552,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.9305999875068665},{"id":"https://openalex.org/keywords/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.4672999978065491},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.44670000672340393},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.4366999864578247},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4219000041484833},{"id":"https://openalex.org/keywords/stratification","display_name":"Stratification (seeds)","score":0.3763999938964844},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.36169999837875366},{"id":"https://openalex.org/keywords/risk-stratification","display_name":"Risk stratification","score":0.34439998865127563}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.9305999875068665},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5965999960899353},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5921000242233276},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5726000070571899},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.4672999978065491},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.44670000672340393},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.4366999864578247},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4219000041484833},{"id":"https://openalex.org/C192943249","wikidata":"https://www.wikidata.org/wiki/Q1893382","display_name":"Stratification (seeds)","level":5,"score":0.3763999938964844},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.36169999837875366},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36070001125335693},{"id":"https://openalex.org/C3020404979","wikidata":"https://www.wikidata.org/wiki/Q1058438","display_name":"Risk stratification","level":2,"score":0.34439998865127563},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.34380000829696655},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.3269999921321869},{"id":"https://openalex.org/C151201525","wikidata":"https://www.wikidata.org/wiki/Q177239","display_name":"Limit (mathematics)","level":2,"score":0.32659998536109924},{"id":"https://openalex.org/C2781170535","wikidata":"https://www.wikidata.org/wiki/Q30587856","display_name":"Noisy data","level":2,"score":0.3176000118255615},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.30959999561309814},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.298799991607666},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.27959999442100525},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.2782999873161316},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.27489998936653137},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.27149999141693115},{"id":"https://openalex.org/C2993807623","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genetic data","level":3,"score":0.25459998846054077},{"id":"https://openalex.org/C106934330","wikidata":"https://www.wikidata.org/wiki/Q1971873","display_name":"Trait","level":2,"score":0.2515999972820282},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.25099998712539673},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.2500999867916107}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3765612.3767214","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3765612.3767214","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3765612.3767214","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},{"id":"pmh:oai:purl.org/net/epubs:work/64777658","is_oa":false,"landing_page_url":"http://purl.org/net/epubs/work/64777658","pdf_url":null,"source":{"id":"https://openalex.org/S4306400334","display_name":"Science and Technology Facilities Council","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Paper In Conference Proceedings"}],"best_oa_location":{"id":"doi:10.1145/3765612.3767214","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3765612.3767214","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3765612.3767214","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334632","display_name":"Science and Technology Facilities Council","ror":"https://ror.org/057g20z61"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4417200391.pdf","grobid_xml":"https://content.openalex.org/works/W4417200391.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1622676895","https://openalex.org/W1973748132","https://openalex.org/W2004915807","https://openalex.org/W2026112119","https://openalex.org/W2098374857","https://openalex.org/W2334099820","https://openalex.org/W2769664962","https://openalex.org/W2793477525","https://openalex.org/W2805680509","https://openalex.org/W2903406988","https://openalex.org/W2911279170","https://openalex.org/W2951934944","https://openalex.org/W2964121744","https://openalex.org/W2967844557","https://openalex.org/W2997591727","https://openalex.org/W3004519953","https://openalex.org/W3026296114","https://openalex.org/W3034542787","https://openalex.org/W3111153674","https://openalex.org/W4206087897","https://openalex.org/W4224436908","https://openalex.org/W4233762729","https://openalex.org/W4280649077","https://openalex.org/W4285787895","https://openalex.org/W4295312788","https://openalex.org/W4391450968","https://openalex.org/W4399830007","https://openalex.org/W4401585036","https://openalex.org/W4404656292","https://openalex.org/W4416961035"],"related_works":[],"abstract_inverted_index":{"High-throughput":[0],"omics":[1],"data":[2,50],"offer":[3],"unprecedented":[4],"opportunities":[5],"to":[6,21],"advance":[7],"our":[8],"understanding":[9],"of":[10,39],"human":[11],"health":[12],"and":[13,26,35,58],"disease.":[14],"However,":[15],"their":[16,55],"analysis":[17],"remains":[18],"challenging":[19],"due":[20],"high":[22],"dimensionality,":[23],"noise,":[24],"heterogeneity,":[25],"sparsity\u2014factors":[27],"that":[28],"severely":[29],"limit":[30],"both":[31],"the":[32,36],"predictive":[33],"accuracy":[34],"biological":[37],"interpretability":[38],"conventional":[40],"machine":[41],"learning":[42],"approaches,":[43],"particularly":[44],"in":[45],"patient":[46],"stratification":[47],"tasks.":[48],"Microbiome":[49],"exemplify":[51],"these":[52],"challenges,":[53],"as":[54],"extreme":[56],"dimensionality":[57],"complex":[59],"structure":[60],"often":[61],"obscure":[62],"mechanistic":[63],"insights":[64],"into":[65],"disease":[66],"processes.":[67]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-12-10T00:00:00"}
