{"id":"https://openalex.org/W4390992353","doi":"https://doi.org/10.1109/bibm58861.2023.10385976","title":"Adapting Protein Language Models for Explainable Fine-Grained Evolutionary Pattern Discovery","display_name":"Adapting Protein Language Models for Explainable Fine-Grained Evolutionary Pattern Discovery","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390992353","doi":"https://doi.org/10.1109/bibm58861.2023.10385976"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385976","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385976","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/A5045156137","display_name":"Ashley Babjac","orcid":"https://orcid.org/0000-0002-0991-7726"},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ashley Babjac","raw_affiliation_strings":["University of Tennessee,Department of Computer Science,Knoxville,USA","Department of Computer Science, University of Tennessee, Knoxville, USA"],"affiliations":[{"raw_affiliation_string":"University of Tennessee,Department of Computer Science,Knoxville,USA","institution_ids":["https://openalex.org/I75027704"]},{"raw_affiliation_string":"Department of Computer Science, University of Tennessee, Knoxville, USA","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041142673","display_name":"Owen Queen","orcid":null},"institutions":[{"id":"https://openalex.org/I2801851002","display_name":"Harvard University Press","ror":"https://ror.org/006v7bf86","country_code":"US","type":"other","lineage":["https://openalex.org/I136199984","https://openalex.org/I2801851002"]},{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I33434090","display_name":"University of Massachusetts Boston","ror":"https://ror.org/04ydmy275","country_code":"US","type":"education","lineage":["https://openalex.org/I33434090"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Owen Queen","raw_affiliation_strings":["Harvard University,Department of Biomedical Informatics,Boston,USA","Department of Biomedical Informatics, Harvard University, Boston, USA"],"affiliations":[{"raw_affiliation_string":"Harvard University,Department of Biomedical Informatics,Boston,USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I111088046","https://openalex.org/I2801851002","https://openalex.org/I33434090"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard University, Boston, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093740447","display_name":"Shawn-Patrick Barhorst","orcid":null},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shawn-Patrick Barhorst","raw_affiliation_strings":["University of Tennessee,Department of Computer Science,Knoxville,USA","Department of Computer Science, University of Tennessee, Knoxville, USA"],"affiliations":[{"raw_affiliation_string":"University of Tennessee,Department of Computer Science,Knoxville,USA","institution_ids":["https://openalex.org/I75027704"]},{"raw_affiliation_string":"Department of Computer Science, University of Tennessee, Knoxville, USA","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065054478","display_name":"Kambiz Kalhor","orcid":null},"institutions":[{"id":"https://openalex.org/I2802706902","display_name":"Knoxville College","ror":"https://ror.org/02bxrp522","country_code":"US","type":"education","lineage":["https://openalex.org/I2802706902"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kambiz Kalhor","raw_affiliation_strings":["University of Tennessee,Department of Microbiology,Knoxville,USA","Department of Microbiology, University of Tennessee, Knoxville, USA"],"affiliations":[{"raw_affiliation_string":"University of Tennessee,Department of Microbiology,Knoxville,USA","institution_ids":["https://openalex.org/I75027704","https://openalex.org/I2802706902"]},{"raw_affiliation_string":"Department of Microbiology, University of Tennessee, Knoxville, USA","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040578598","display_name":"Andrew D. Steen","orcid":"https://orcid.org/0000-0003-4297-4332"},"institutions":[{"id":"https://openalex.org/I2802706902","display_name":"Knoxville College","ror":"https://ror.org/02bxrp522","country_code":"US","type":"education","lineage":["https://openalex.org/I2802706902"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew D. Steen","raw_affiliation_strings":["University of Tennessee,Department of Microbiology,Knoxville,USA","Department of Microbiology, University of Tennessee, Knoxville, USA"],"affiliations":[{"raw_affiliation_string":"University of Tennessee,Department of Microbiology,Knoxville,USA","institution_ids":["https://openalex.org/I75027704","https://openalex.org/I2802706902"]},{"raw_affiliation_string":"Department of Microbiology, University of Tennessee, Knoxville, USA","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019857186","display_name":"Scott Emrich","orcid":"https://orcid.org/0000-0002-5741-4517"},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott J. Emrich","raw_affiliation_strings":["University of Tennessee,Department of Computer Science,Knoxville,USA","Department of Computer Science, University of Tennessee, Knoxville, USA"],"affiliations":[{"raw_affiliation_string":"University of Tennessee,Department of Computer Science,Knoxville,USA","institution_ids":["https://openalex.org/I75027704"]},{"raw_affiliation_string":"Department of Computer Science, University of Tennessee, Knoxville, USA","institution_ids":["https://openalex.org/I75027704"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5045156137"],"corresponding_institution_ids":["https://openalex.org/I75027704"],"apc_list":null,"apc_paid":null,"fwci":0.3144,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.65492815,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"2609","last_page":"2616"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9939000010490417,"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":0.9939000010490417,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9894000291824341,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9858999848365784,"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/computer-science","display_name":"Computer science","score":0.6781090497970581},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5826904773712158},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5730529427528381},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.49874281883239746},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4466971755027771},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3628803491592407},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3442862629890442},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32421785593032837}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6781090497970581},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5826904773712158},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5730529427528381},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.49874281883239746},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4466971755027771},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3628803491592407},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3442862629890442},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32421785593032837},{"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/bibm58861.2023.10385976","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385976","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":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.5799999833106995}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1502478687","https://openalex.org/W1585607520","https://openalex.org/W1658117958","https://openalex.org/W2048697945","https://openalex.org/W2085522899","https://openalex.org/W2096451472","https://openalex.org/W2102461176","https://openalex.org/W2102612168","https://openalex.org/W2142073035","https://openalex.org/W2889326414","https://openalex.org/W2892113269","https://openalex.org/W2896457183","https://openalex.org/W2902995905","https://openalex.org/W2938517501","https://openalex.org/W2944851425","https://openalex.org/W2951433247","https://openalex.org/W2951500013","https://openalex.org/W2962778134","https://openalex.org/W2995744795","https://openalex.org/W3034765865","https://openalex.org/W3085380432","https://openalex.org/W3119872582","https://openalex.org/W3146944767","https://openalex.org/W3177828909","https://openalex.org/W3187251571","https://openalex.org/W3200988654","https://openalex.org/W4205192056","https://openalex.org/W4206950245","https://openalex.org/W4246413330","https://openalex.org/W4281719345","https://openalex.org/W4282960239","https://openalex.org/W4283815252","https://openalex.org/W4288066876","https://openalex.org/W4327550249","https://openalex.org/W4366163632","https://openalex.org/W4367598498","https://openalex.org/W4385245566","https://openalex.org/W4396578176","https://openalex.org/W6734194636","https://openalex.org/W6739901393","https://openalex.org/W6755207826","https://openalex.org/W6763868836","https://openalex.org/W6771550025","https://openalex.org/W6839093657","https://openalex.org/W6839106506","https://openalex.org/W6849932668"],"related_works":["https://openalex.org/W2081900870","https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2077542787","https://openalex.org/W2156434174","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W2070401501","https://openalex.org/W2121496884"],"abstract_inverted_index":{"Organisms":[0],"that":[1,13,148,170],"live":[2],"in":[3,46,84,119,158,163],"different":[4,7,73],"environments":[5,41,51,88],"face":[6],"evolutionary":[8,82],"pressures.":[9],"As":[10],"such,":[11],"organisms":[12],"have":[14,78],"more":[15,19],"successful":[16],"phenotypes":[17],"reproduce":[18],"frequently,":[20],"but":[21],"differing":[22],"selective":[23],"pressures":[24,83,96],"acting":[25],"at":[26],"the":[27,80],"organismal":[28],"level":[29],"can":[30,173],"influence":[31],"genes,":[32],"and":[33,91,113],"thus":[34],"proteins.":[35],"Understanding":[36],"how":[37],"proteins":[38,48,71,105],"adapt":[39],"across":[40],"may":[42],"therefore":[43],"be":[44,174],"useful":[45],"engineering":[47],"for":[49,135],"specific":[50],"as":[52,54,127],"well":[53],"to":[55,94,152],"improve":[56],"our":[57,120,136],"understanding":[58],"of":[59,86,103],"basic":[60],"biology.":[61],"In":[62],"this":[63],"work,":[64],"we":[65,129,168],"explicitly":[66],"compare":[67],"homologous":[68],"(read:":[69],"paired)":[70],"from":[72],"environments.":[74],"While":[75],"previous":[76],"studies":[77],"explored":[79],"relevant":[81,154],"one":[85],"these":[87,171],"[11],":[89],"[17]":[90],"genomic":[92],"responses":[93],"those":[95],"[1],":[97],"[28],":[98],"no":[99,117],"prior":[100],"computational":[101],"study":[102],"their":[104],"has":[106],"been":[107],"performed.":[108],"We":[109,145],"apply":[110],"ESM-2":[111,149],"[20]":[112],"although":[114],"there":[115],"is":[116,150],"signal":[118],"negative":[121],"control":[122],"(two":[123],"divergent":[124],"yeast":[125],"strains)":[126],"expected,":[128],"obtain":[130],"near":[131],"perfect":[132],"prediction":[133],"accuracy":[134],"selected":[137],"environmental":[138],"gradient\u2013the":[139],"well-established":[140],"subsurface":[141],"vs.":[142],"surface":[143],"biome.":[144],"further":[146],"show":[147],"able":[151],"capture":[153],"fine-grained":[155],"biological":[156],"patterns":[157],"its":[159,164],"embedding":[160],"space,":[161],"even":[162],"smallest":[165],"model.":[166],"Significantly,":[167],"demonstrate":[169],"embeddings":[172],"interpreted":[175],"using":[176,182],"a":[177],"novel":[178],"visualization":[179],"pipeline":[180],"built":[181],"explainable":[183],"AI":[184],"techniques.":[185]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-13T16:22:10.518609","created_date":"2025-10-10T00:00:00"}