{"id":"https://openalex.org/W4384819947","doi":"https://doi.org/10.1186/s12859-023-05411-z","title":"Leveraging pre-trained language models for mining microbiome-disease relationships","display_name":"Leveraging pre-trained language models for mining microbiome-disease relationships","publication_year":2023,"publication_date":"2023-07-19","ids":{"openalex":"https://openalex.org/W4384819947","doi":"https://doi.org/10.1186/s12859-023-05411-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/37468830"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05411-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05411-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05411-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05411-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111155252","display_name":"Nikitha Karkera","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nikitha Karkera","raw_affiliation_strings":["SBX Corporation, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SBX Corporation, Tokyo, Japan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019437628","display_name":"Sathwik Acharya","orcid":"https://orcid.org/0000-0002-0023-8516"},"institutions":[{"id":"https://openalex.org/I4210118579","display_name":"Systems Biology Institute","ror":"https://ror.org/02c7akf81","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210118579"]},{"id":"https://openalex.org/I196608512","display_name":"PES University","ror":"https://ror.org/05m169e78","country_code":"IN","type":"education","lineage":["https://openalex.org/I196608512"]}],"countries":["IN","JP"],"is_corresponding":false,"raw_author_name":"Sathwik Acharya","raw_affiliation_strings":["PES University, Bengaluru, India","The Systems Biology Institute, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"PES University, Bengaluru, India","institution_ids":["https://openalex.org/I196608512"]},{"raw_affiliation_string":"The Systems Biology Institute, Tokyo, Japan","institution_ids":["https://openalex.org/I4210118579"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070784871","display_name":"Sucheendra K. Palaniappan","orcid":"https://orcid.org/0000-0002-2829-2311"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Sucheendra K. Palaniappan","raw_affiliation_strings":["Iom Bioworks Pvt Ltd., Bengaluru, India. sucheendra@sbi.jp","SBX Corporation, Tokyo, Japan. sucheendra@sbi.jp","The Systems Biology Institute, Tokyo, Japan. sucheendra@sbi.jp","Iom Bioworks Pvt Ltd., Bengaluru, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iom Bioworks Pvt Ltd., Bengaluru, India. sucheendra@sbi.jp","institution_ids":[]},{"raw_affiliation_string":"SBX Corporation, Tokyo, Japan. sucheendra@sbi.jp","institution_ids":[]},{"raw_affiliation_string":"The Systems Biology Institute, Tokyo, Japan. sucheendra@sbi.jp","institution_ids":[]},{"raw_affiliation_string":"Iom Bioworks Pvt Ltd., Bengaluru, India","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5070784871"],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":5.9302,"has_fulltext":true,"cited_by_count":40,"citation_normalized_percentile":{"value":0.96865938,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"24","issue":"1","first_page":"290","last_page":"290"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.14640000462532043,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.14640000462532043,"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/T10028","display_name":"Topic Modeling","score":0.12460000067949295,"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"}},{"id":"https://openalex.org/T13702","display_name":"Machine Learning in Healthcare","score":0.12430000305175781,"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/computer-science","display_name":"Computer science","score":0.7604420781135559},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6450428366661072},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.6410491466522217},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.5804967284202576},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5567092895507812},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.5535460710525513},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.5364388227462769},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5322574973106384},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5192039608955383},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.5056092739105225},{"id":"https://openalex.org/keywords/human-microbiome-project","display_name":"Human Microbiome Project","score":0.4940531551837921},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.45937642455101013},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.43743693828582764},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.4259836673736572},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.4115406274795532},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.2827598452568054},{"id":"https://openalex.org/keywords/human-microbiome","display_name":"Human microbiome","score":0.2611921429634094},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.24447080492973328},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.165569007396698},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09225919842720032}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7604420781135559},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6450428366661072},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.6410491466522217},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.5804967284202576},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5567092895507812},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.5535460710525513},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.5364388227462769},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5322574973106384},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5192039608955383},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.5056092739105225},{"id":"https://openalex.org/C190944805","wikidata":"https://www.wikidata.org/wiki/Q3922751","display_name":"Human Microbiome Project","level":4,"score":0.4940531551837921},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.45937642455101013},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.43743693828582764},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.4259836673736572},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.4115406274795532},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.2827598452568054},{"id":"https://openalex.org/C91478284","wikidata":"https://www.wikidata.org/wiki/Q6623796","display_name":"Human microbiome","level":3,"score":0.2611921429634094},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.24447080492973328},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.165569007396698},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09225919842720032},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"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/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006304","descriptor_name":"Health Status","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006304","descriptor_name":"Health Status","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006304","descriptor_name":"Health Status","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006304","descriptor_name":"Health Status","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":"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":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","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":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-023-05411-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05411-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05411-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37468830","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37468830","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10357883","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10357883","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10357883/pdf/12859_2023_Article_5411.pdf","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:95ddf55cfb614127afd69f8b6bf0f373","is_oa":true,"landing_page_url":"https://doaj.org/article/95ddf55cfb614127afd69f8b6bf0f373","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-19 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05411-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05411-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05411-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.7599999904632568}],"awards":[{"id":"https://openalex.org/G1510026529","display_name":null,"funder_award_id":"N62909-21-1-2032","funder_id":"https://openalex.org/F4320338298","funder_display_name":"Office of Naval Research Global"}],"funders":[{"id":"https://openalex.org/F4320337345","display_name":"Office of Naval Research","ror":"https://ror.org/00rk2pe57"},{"id":"https://openalex.org/F4320338298","display_name":"Office of Naval Research Global","ror":"https://ror.org/00rk2pe57"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4384819947.pdf"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1981276685","https://openalex.org/W2012606594","https://openalex.org/W2099320393","https://openalex.org/W2116846792","https://openalex.org/W2322763599","https://openalex.org/W2431459199","https://openalex.org/W2765928324","https://openalex.org/W2776589520","https://openalex.org/W2807176368","https://openalex.org/W2911489562","https://openalex.org/W2914431807","https://openalex.org/W2916981547","https://openalex.org/W2950173838","https://openalex.org/W2963716420","https://openalex.org/W2972021296","https://openalex.org/W2979072963","https://openalex.org/W2979826702","https://openalex.org/W3004227146","https://openalex.org/W3033077186","https://openalex.org/W3036061157","https://openalex.org/W3046375318","https://openalex.org/W3097354806","https://openalex.org/W3104578551","https://openalex.org/W3119962804","https://openalex.org/W3132948971","https://openalex.org/W3157142061","https://openalex.org/W3160638507","https://openalex.org/W3170383918","https://openalex.org/W3170949898","https://openalex.org/W3179076314","https://openalex.org/W3211263674","https://openalex.org/W4205340501","https://openalex.org/W4221153690","https://openalex.org/W4255502791","https://openalex.org/W4286322052","https://openalex.org/W4293727927","https://openalex.org/W4297253404","https://openalex.org/W4304116809","https://openalex.org/W4306728852","https://openalex.org/W4318624508","https://openalex.org/W4365511667","https://openalex.org/W6601298480","https://openalex.org/W6702248584","https://openalex.org/W6778883912","https://openalex.org/W6837901829"],"related_works":["https://openalex.org/W2134429551","https://openalex.org/W2064314529","https://openalex.org/W2548624545","https://openalex.org/W2916255597","https://openalex.org/W3095980030","https://openalex.org/W2352298027","https://openalex.org/W4319940250","https://openalex.org/W3004288456","https://openalex.org/W4379379356","https://openalex.org/W2572241437"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,40],"growing":[2],"recognition":[3],"of":[4,45,110,119,154,172,182],"the":[5,19,105,111,114,151,179],"microbiome's":[6],"impact":[7],"on":[8],"human":[9],"health":[10],"and":[11,24,43,137,143,162,170,201],"well-being":[12],"has":[13],"prompted":[14],"extensive":[15],"research":[16],"into":[17],"discovering":[18],"links":[20],"between":[21],"microbiome":[22],"dysbiosis":[23],"disease":[25],"(healthy)":[26],"states.":[27],"However,":[28],"this":[29,85,103,186],"valuable":[30],"information":[31],"is":[32],"scattered":[33],"in":[34,54],"unstructured":[35],"form":[36],"within":[37,95],"biomedical":[38,81],"literature.":[39,82],"structured":[41],"extraction":[42],"qualification":[44],"microbe-disease":[46,78],"interactions":[47,218],"are":[48],"important.":[49],"In":[50,84,102],"parallel,":[51],"recent":[52],"advancements":[53],"deep-learning-based":[55],"natural":[56],"language":[57,74,93,121,127,191],"processing":[58],"algorithms":[59],"have":[60],"revolutionized":[61],"language-related":[62],"tasks":[63],"such":[64],"as":[65,194],"ours.":[66],"This":[67],"study":[68,187],"aims":[69],"to":[70,76,178,206],"leverage":[71],"state-of-the-art":[72,152,208],"deep-learning":[73],"models":[75,94,106,128,157,192],"extract":[77],"relationships":[79],"from":[80,219],"RESULTS:":[83],"study,":[86],"we":[87,124],"first":[88],"evaluate":[89,144],"multiple":[90,126],"pre-trained":[91,190],"large":[92],"a":[96],"zero-shot":[97],"or":[98],"few-shot":[99],"learning":[100],"context.":[101],"setting,":[104],"performed":[107],"poorly":[108],"out":[109],"box,":[112],"emphasizing":[113],"need":[115],"for":[116,215],"domain-specific":[117],"fine-tuning":[118],"these":[120,155],"models.":[122],"Subsequently,":[123],"fine-tune":[125],"(specifically,":[129],"GPT-3,":[130,160],"BioGPT,":[131],"BioMedLM,":[132,161],"BERT,":[133],"BioMegatron,":[134],"PubMedBERT,":[135],"BioClinicalBERT,":[136],"BioLinkBERT)":[138],"using":[139],"labeled":[140],"training":[141,213],"data":[142,214],"their":[145],"performance.":[146],"Our":[147],"experimental":[148],"results":[149,209],"demonstrate":[150],"performance":[153],"fine-tuned":[156,198],"(":[158],"specifically":[159],"BioLinkBERT),":[163],"achieving":[164],"an":[165],"average":[166],"F1":[167],"score,":[168],"precision,":[169],"recall":[171],"over":[173],"[Formula:":[174],"see":[175],"text]":[176],"compared":[177],"previous":[180],"best":[181],"0.74.":[183],"CONCLUSION:":[184],"Overall,":[185],"establishes":[188],"that":[189],"excel":[193],"transfer":[195],"learners":[196],"when":[197],"with":[199,211],"domain":[200],"problem-specific":[202],"data,":[203],"enabling":[204],"them":[205],"achieve":[207],"even":[210],"limited":[212],"extracting":[216],"microbiome-disease":[217],"scientific":[220],"publications.":[221]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":22}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}