{"id":"https://openalex.org/W4410148659","doi":"https://doi.org/10.1371/journal.pcbi.1011353","title":"Learning a deep language model for microbiomes: The power of large scale unlabeled microbiome data","display_name":"Learning a deep language model for microbiomes: The power of large scale unlabeled microbiome data","publication_year":2025,"publication_date":"2025-05-07","ids":{"openalex":"https://openalex.org/W4410148659","doi":"https://doi.org/10.1371/journal.pcbi.1011353","pmid":"https://pubmed.ncbi.nlm.nih.gov/40334224"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011353","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011353","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1011353","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075188291","display_name":"Quintin Pope","orcid":"https://orcid.org/0009-0002-6014-9643"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Quintin Pope","raw_affiliation_strings":["School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon, United States of America"],"raw_orcid":"https://orcid.org/0009-0002-6014-9643","affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon, United States of America","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014393716","display_name":"Rohan Varma","orcid":"https://orcid.org/0000-0002-4635-7334"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rohan Varma","raw_affiliation_strings":["School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon, United States of America","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068423857","display_name":"Christine Tataru","orcid":"https://orcid.org/0000-0002-3869-2079"},"institutions":[{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christine Tataru","raw_affiliation_strings":["Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I1283280774"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002060091","display_name":"Maude M. David","orcid":"https://orcid.org/0000-0003-1561-418X"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maude M David","raw_affiliation_strings":["Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon, United States of America","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064053803","display_name":"Xiaoli Z. Fern","orcid":null},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoli Fern","raw_affiliation_strings":["School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon, United States of America","institution_ids":["https://openalex.org/I131249849"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5075188291"],"corresponding_institution_ids":["https://openalex.org/I131249849"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":9.1191,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.98275285,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"21","issue":"5","first_page":"e1011353","last_page":"e1011353"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9993000030517578,"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/T10066","display_name":"Gut microbiota and health","score":0.9993000030517578,"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/T11309","display_name":"Music and Audio Processing","score":0.9692999720573425,"subfield":{"id":"https://openalex.org/subfields/1711","display_name":"Signal Processing"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9664999842643738,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.648984432220459},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.596591055393219},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5534465909004211},{"id":"https://openalex.org/keywords/taxon","display_name":"Taxon","score":0.5172815322875977},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4822307527065277},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.45772653818130493},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.443737655878067},{"id":"https://openalex.org/keywords/predictive-power","display_name":"Predictive power","score":0.43006786704063416},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4297294318675995},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30311137437820435},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.26141417026519775},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22589901089668274}],"concepts":[{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.648984432220459},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.596591055393219},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5534465909004211},{"id":"https://openalex.org/C71640776","wikidata":"https://www.wikidata.org/wiki/Q16521","display_name":"Taxon","level":2,"score":0.5172815322875977},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4822307527065277},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.45772653818130493},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.443737655878067},{"id":"https://openalex.org/C2778136018","wikidata":"https://www.wikidata.org/wiki/Q10350689","display_name":"Predictive power","level":2,"score":0.43006786704063416},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4297294318675995},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30311137437820435},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.26141417026519775},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22589901089668274},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D043183","descriptor_name":"Irritable Bowel Syndrome","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D043183","descriptor_name":"Irritable Bowel Syndrome","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D043183","descriptor_name":"Irritable Bowel Syndrome","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1011353","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011353","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:40334224","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40334224","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1011353","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011353","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12058177","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12058177","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011353","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011353","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.7799999713897705,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G4321962480","display_name":null,"funder_award_id":"2025457","funder_id":"https://openalex.org/F4320337401","funder_display_name":"Division of Emerging Frontiers"}],"funders":[{"id":"https://openalex.org/F4320315389","display_name":"Open Philanthropy Project","ror":"https://ror.org/004d1k391"},{"id":"https://openalex.org/F4320337401","display_name":"Division of Emerging Frontiers","ror":"https://ror.org/01tnvpc68"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1666628340","https://openalex.org/W1849277567","https://openalex.org/W1974971448","https://openalex.org/W1977804070","https://openalex.org/W1978813754","https://openalex.org/W2005267105","https://openalex.org/W2056279562","https://openalex.org/W2085284704","https://openalex.org/W2088658556","https://openalex.org/W2095705004","https://openalex.org/W2096139589","https://openalex.org/W2097875133","https://openalex.org/W2101234009","https://openalex.org/W2122538988","https://openalex.org/W2187089797","https://openalex.org/W2250539671","https://openalex.org/W2337492846","https://openalex.org/W2401404581","https://openalex.org/W2588997555","https://openalex.org/W2603986758","https://openalex.org/W2770933704","https://openalex.org/W2794407684","https://openalex.org/W2797413896","https://openalex.org/W2805009121","https://openalex.org/W2896457183","https://openalex.org/W2947189704","https://openalex.org/W2949346354","https://openalex.org/W2949947154","https://openalex.org/W2963925437","https://openalex.org/W2989747508","https://openalex.org/W2995514860","https://openalex.org/W2996035354","https://openalex.org/W3003257820","https://openalex.org/W3003886759","https://openalex.org/W3014810983","https://openalex.org/W3023097186","https://openalex.org/W3106210592","https://openalex.org/W3127238141","https://openalex.org/W3146944767","https://openalex.org/W3177500196","https://openalex.org/W3183522126","https://openalex.org/W3207924272","https://openalex.org/W3213893926","https://openalex.org/W4205773061","https://openalex.org/W4283794074","https://openalex.org/W4287824654","https://openalex.org/W4294216483","https://openalex.org/W4308886201","https://openalex.org/W4385245566","https://openalex.org/W4386957668","https://openalex.org/W4402694371","https://openalex.org/W6675354045","https://openalex.org/W6739901393","https://openalex.org/W6892242122"],"related_works":["https://openalex.org/W2604155846","https://openalex.org/W4390658901","https://openalex.org/W3121185202","https://openalex.org/W4393043634","https://openalex.org/W4206185765","https://openalex.org/W2900546243","https://openalex.org/W3035180550","https://openalex.org/W1983943311","https://openalex.org/W4388834263","https://openalex.org/W3088497233"],"abstract_inverted_index":{"We":[0,102],"use":[1],"open":[2],"source":[3],"human":[4],"gut":[5],"microbiome":[6],"data":[7,136],"to":[8,37,66,71,111,134,174,184],"learn":[9],"a":[10,29,62,84,100,149],"microbial":[11,23,43,51,64,74,91],"\"language\"":[12,24],"model":[13,25,55,81,179],"by":[14,87],"adapting":[15],"techniques":[16],"from":[17,137],"Natural":[18],"Language":[19],"Processing":[20],"(NLP).":[21],"Our":[22],"is":[26],"trained":[27],"in":[28,50,76,93,114,141],"self-supervised":[30],"fashion":[31],"(i.e.,":[32],"without":[33],"additional":[34],"external":[35],"labels)":[36],"capture":[38],"the":[39,46,72,94,142,157,178],"interactions":[40,98],"among":[41],"different":[42,90],"taxa":[44,92],"and":[45,96,125,172],"common":[47],"compositional":[48],"patterns":[49],"communities.":[52],"The":[53,80],"learned":[54],"produces":[56],"contextualized":[57],"taxon":[58,65],"representations":[59],"that":[60,156],"allow":[61],"single":[63],"be":[67],"represented":[68],"differently":[69],"according":[70],"specific":[73],"environment":[75],"which":[77],"it":[78,128],"appears.":[79],"further":[82,154],"provides":[83],"sample":[85,95,107],"representation":[86,108],"collectively":[88],"interpreting":[89],"their":[97],"as":[99,119],"whole.":[101],"demonstrate":[103],"that,":[104],"while":[105],"our":[106],"performs":[109],"comparably":[110],"baseline":[112],"models":[113],"in-domain":[115],"prediction":[116],"tasks":[117],"such":[118,185],"predicting":[120],"Irritable":[121],"Bowel":[122],"Disease":[123],"(IBD)":[124],"diet":[126],"patterns,":[127],"significantly":[129],"outperforms":[130],"them":[131],"when":[132],"generalizing":[133],"test":[135],"independent":[138],"studies,":[139],"even":[140],"presence":[143],"of":[144,151],"substantial":[145],"distribution":[146],"shifts.":[147],"Through":[148],"variety":[150],"analyses,":[152],"we":[153],"show":[155],"pre-trained,":[158],"context-sensitive":[159],"embedding":[160],"captures":[161],"meaningful":[162],"biological":[163,170],"information,":[164],"including":[165],"taxonomic":[166],"relationships,":[167],"correlations":[168],"with":[169],"pathways,":[171],"relevance":[173],"IBD":[175],"expression,":[176],"despite":[177],"never":[180],"being":[181],"explicitly":[182],"exposed":[183],"signals.":[186]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":7}],"updated_date":"2026-04-28T14:05:53.105641","created_date":"2025-10-10T00:00:00"}
