{"id":"https://openalex.org/W7171571569","doi":"https://doi.org/10.1145/3807503.3819571","title":"GenoME-SL: Genomic-LLM Fused Mechanism Explanation Framework for Synthetic Lethality","display_name":"GenoME-SL: Genomic-LLM Fused Mechanism Explanation Framework for Synthetic Lethality","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7171571569","doi":"https://doi.org/10.1145/3807503.3819571"},"language":null,"primary_location":{"id":"doi:10.1145/3807503.3819571","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819571","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3807503.3819571","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111296955","display_name":"Xueheng Lv","orcid":null},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xueheng Lv","raw_affiliation_strings":["School of Information Science and Technology, ShanghaiTech University, Shanghai, China"],"raw_orcid":"https://orcid.org/0009-0003-7611-651X","affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, ShanghaiTech University, Shanghai, China","institution_ids":["https://openalex.org/I30809798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058225167","display_name":"\u51af\u8d3b\u82d7","orcid":null},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yimiao Feng","raw_affiliation_strings":["School of Information Science and Technology, ShanghaiTech University, Shanghai, China and Lingang Laboratory, Shanghai, China"],"raw_orcid":"https://orcid.org/0009-0004-8389-2223","affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, ShanghaiTech University, Shanghai, China and Lingang Laboratory, Shanghai, China","institution_ids":["https://openalex.org/I30809798"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014529529","display_name":"Jie Zheng","orcid":"https://orcid.org/0000-0001-6774-9786"},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Zheng","raw_affiliation_strings":["School of Information Science and Technology, ShanghaiTech University, Shanghai, China and Shanghai Engineering Research Center of Intelligent Vision and Imaging, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0001-6774-9786","affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, ShanghaiTech University, Shanghai, China and Shanghai Engineering Research Center of Intelligent Vision and Imaging, Shanghai, China","institution_ids":["https://openalex.org/I30809798"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I30809798"],"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":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/synthetic-lethality","display_name":"Synthetic lethality","score":0.5467000007629395},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.5378999710083008},{"id":"https://openalex.org/keywords/lethality","display_name":"Lethality","score":0.5300999879837036},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.21870000660419464}],"concepts":[{"id":"https://openalex.org/C2778502085","wikidata":"https://www.wikidata.org/wiki/Q7662767","display_name":"Synthetic lethality","level":4,"score":0.5467000007629395},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.5378999710083008},{"id":"https://openalex.org/C20379349","wikidata":"https://www.wikidata.org/wiki/Q1720706","display_name":"Lethality","level":2,"score":0.5300999879837036},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4607999920845032},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38510000705718994},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2526000142097473},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.24490000307559967},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.23330000042915344},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.21870000660419464},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.20469999313354492}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3807503.3819571","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819571","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3807503.3819571","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819571","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W2064102777","https://openalex.org/W2123588904","https://openalex.org/W2962784628","https://openalex.org/W2983649157","https://openalex.org/W4225820450","https://openalex.org/W4360612299","https://openalex.org/W4382630911","https://openalex.org/W4389265672","https://openalex.org/W4403479110","https://openalex.org/W4403572618","https://openalex.org/W4403789768","https://openalex.org/W4404821554","https://openalex.org/W4416960790","https://openalex.org/W7131823714"],"related_works":[],"abstract_inverted_index":{"Synthetic":[0],"lethality":[1],"(SL)":[2],"offers":[3],"a":[4,98,160,181],"promising":[5,182],"strategy":[6],"for":[7,68,108,184],"precision":[8],"cancer":[9],"therapy":[10],"by":[11,120],"selectively":[12],"targeting":[13],"cancer-specific":[14],"genetic":[15,89],"interactions.":[16,45,90,189],"Although":[17],"high-throughput":[18],"screening":[19],"and":[20,40,53,75,78,123,126,131,151],"computational":[21],"methods":[22],"have":[23],"identified":[24],"numerous":[25],"candidate":[26],"SL":[27,69,109,188],"gene":[28],"pairs,":[29],"understanding":[30],"their":[31],"underlying":[32],"molecular":[33],"mechanisms":[34],"remains":[35],"challenging,":[36],"limiting":[37],"the":[38,58,80,145],"prioritization":[39],"practical":[41],"use":[42],"of":[43,60,82,187],"predicted":[44],"Recent":[46],"advances":[47],"in":[48,163],"large":[49],"language":[50],"models":[51,56,105],"(LLMs)":[52],"genomic":[54,83,103,174],"foundation":[55,104],"enable":[57],"integration":[59],"heterogeneous":[61],"biological":[62],"information.":[63],"However,":[64],"existing":[65],"LLM-based":[66],"approaches":[67],"interpretation":[70,186],"rely":[71],"mainly":[72],"on":[73,144],"textual":[74],"structured":[76,150],"knowledge":[77,132],"lack":[79],"incorporation":[81],"sequence":[84,175],"features,":[85],"which":[86],"often":[87],"underlie":[88],"To":[91],"address":[92],"this":[93],"limitation,":[94],"we":[95],"propose":[96],"GenoME-SL,":[97,142],"cross-modal":[99,114],"framework":[100],"that":[101,141,172],"integrates":[102],"with":[106,177],"LLMs":[107],"mechanism":[110],"interpretation.":[111],"GenoME-SL":[112],"performs":[113],"pre-alignment":[115],"via":[116],"contrastive":[117],"learning,":[118,125],"followed":[119],"supervised":[121],"fine-tuning":[122],"reinforcement":[124],"further":[127],"incorporates":[128],"biomedical":[129],"literature":[130],"graphs":[133],"through":[134],"retrieval-augmented":[135],"generation":[136],"(RAG).":[137],"Experimental":[138],"results":[139,170],"show":[140],"built":[143],"Qwen3-4B":[146],"backbone,":[147],"produces":[148],"more":[149],"biologically":[152],"informative":[153],"explanations":[154],"than":[155],"several":[156],"LLM":[157],"baselines,":[158],"achieving":[159],"21.1%":[161],"improvement":[162],"Feature":[164],"Matching":[165],"Ratio":[166],"over":[167],"GPT-5.":[168],"These":[169],"suggest":[171],"integrating":[173],"representations":[176],"language-model":[178],"reasoning":[179],"provides":[180],"approach":[183],"mechanism-aware":[185]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-07-29T00:00:00"}
