{"id":"https://openalex.org/W7155564574","doi":"https://doi.org/10.48550/arxiv.2604.21690","title":"Evaluating Post-hoc Explanations of the Transformer-based Genome Language Model DNABERT-2","display_name":"Evaluating Post-hoc Explanations of the Transformer-based Genome Language Model DNABERT-2","publication_year":2026,"publication_date":"2026-04-23","ids":{"openalex":"https://openalex.org/W7155564574","doi":"https://doi.org/10.48550/arxiv.2604.21690"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2604.21690","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.21690","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2604.21690","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041536802","display_name":"Isabel Kurth","orcid":"https://orcid.org/0000-0003-0607-0467"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Kurth, Isabel","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5095851441","display_name":"Paulo Yanez Sarmiento","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sarmiento, Paulo Yanez","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5005996110","display_name":"Bernhard Y. Renard","orcid":"https://orcid.org/0000-0003-4589-9809"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Renard, Bernhard Y.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5041536802"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.17829999327659607,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.17829999327659607,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11948","display_name":"Machine Learning in Materials Science","score":0.13210000097751617,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12026","display_name":"Explainable Artificial Intelligence (XAI)","score":0.10369999706745148,"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/relevance","display_name":"Relevance (law)","score":0.6345999836921692},{"id":"https://openalex.org/keywords/comparability","display_name":"Comparability","score":0.5307999849319458},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4674000144004822},{"id":"https://openalex.org/keywords/security-token","display_name":"Security token","score":0.42829999327659607},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.3833000063896179},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.3402000069618225},{"id":"https://openalex.org/keywords/inheritance","display_name":"Inheritance (genetic algorithm)","score":0.33500000834465027},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.3328999876976013}],"concepts":[{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.6345999836921692},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6051999926567078},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5328999757766724},{"id":"https://openalex.org/C197947376","wikidata":"https://www.wikidata.org/wiki/Q5155608","display_name":"Comparability","level":2,"score":0.5307999849319458},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4674000144004822},{"id":"https://openalex.org/C48145219","wikidata":"https://www.wikidata.org/wiki/Q1335365","display_name":"Security token","level":2,"score":0.42829999327659607},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4034000039100647},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3833000063896179},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.3402000069618225},{"id":"https://openalex.org/C2780902518","wikidata":"https://www.wikidata.org/wiki/Q6033780","display_name":"Inheritance (genetic algorithm)","level":3,"score":0.33500000834465027},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.3328999876976013},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.326200008392334},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.3179999887943268},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.30630001425743103},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.30550000071525574},{"id":"https://openalex.org/C12725497","wikidata":"https://www.wikidata.org/wiki/Q810247","display_name":"Baseline (sea)","level":2,"score":0.303600013256073},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.302700012922287},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.30070000886917114},{"id":"https://openalex.org/C64357122","wikidata":"https://www.wikidata.org/wiki/Q1149766","display_name":"Causality (physics)","level":2,"score":0.27950000762939453},{"id":"https://openalex.org/C150899416","wikidata":"https://www.wikidata.org/wiki/Q1820378","display_name":"Transfer of learning","level":2,"score":0.2721000015735626},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.2705000042915344},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26080000400543213},{"id":"https://openalex.org/C44291984","wikidata":"https://www.wikidata.org/wiki/Q1074173","display_name":"Question answering","level":2,"score":0.2547000050544739}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2604.21690","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.21690","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2604.21690","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.21690","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Explaining":[0],"deep":[1],"neural":[2,25],"network":[3],"predictions":[4],"on":[5,95],"genome":[6,36,48],"sequences":[7],"enables":[8],"biological":[9,127,137],"insight":[10],"and":[11,69,86,112,147],"hypothesis":[12],"generation-often":[13],"of":[14,23,61,93,110,145,151],"greater":[15],"interest":[16],"than":[17],"predictive":[18],"performance":[19],"alone.":[20],"While":[21],"explanations":[22,83,109,123],"convolutional":[24],"networks":[26],"(CNNs)":[27],"have":[28],"been":[29],"shown":[30],"to":[31,44,65,72,81,125,142],"capture":[32],"relevant":[33],"patterns":[34],"in":[35],"sequences,":[37],"it":[38,71],"is":[39],"unclear":[40],"whether":[41],"this":[42,54],"transfers":[43],"more":[45],"expressive":[46],"Transformer-based":[47],"language":[49],"models":[50],"(gLMs).":[51],"To":[52],"answer":[53],"question,":[55],"we":[56,78,102],"adapt":[57],"AttnLRP,":[58],"an":[59,104],"extension":[60],"layer-wise":[62],"relevance":[63,152],"propagation":[64],"the":[66,73,91,108,143,149],"attention":[67],"mechanism,":[68],"apply":[70],"state-of-the-art":[74],"gLM":[75],"DNABERT-2.":[76],"Thereby,":[77],"propose":[79],"strategies":[80],"transfer":[82],"from":[84],"token":[85],"nucleotide":[87],"level.":[88],"We":[89],"evaluate":[90],"adaption":[92],"AttnLRP":[94,120],"genomic":[96],"datasets":[97],"using":[98],"multiple":[99],"metrics.":[100],"Further,":[101],"provide":[103],"extensive":[105],"comparison":[106],"between":[107],"DNABERT-2":[111],"a":[113],"baseline":[114],"CNN.":[115],"Our":[116],"results":[117],"demonstrate":[118],"that":[119],"yields":[121],"reliable":[122],"corresponding":[124],"known":[126],"patterns.":[128],"Hence,":[129],"like":[130],"CNNs,":[131],"gLMs":[132,146],"can":[133],"also":[134],"help":[135],"derive":[136],"insights.":[138],"This":[139],"work":[140],"contributes":[141],"explainability":[144],"addresses":[148],"comparability":[150],"attributions":[153],"across":[154],"different":[155],"architectures.":[156]},"counts_by_year":[],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2026-04-25T00:00:00"}