{"id":"https://openalex.org/W7171550578","doi":"https://doi.org/10.1145/3807503.3819483","title":"BASIS: An LLM-Empowered Benchmark and Agent System for Inferring Synthetic Lethality","display_name":"BASIS: An LLM-Empowered Benchmark and Agent System for Inferring Synthetic Lethality","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7171550578","doi":"https://doi.org/10.1145/3807503.3819483"},"language":null,"primary_location":{"id":"doi:10.1145/3807503.3819483","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819483","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/10.1145/3807503.3819483","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044771057","display_name":"Yi Li","orcid":"https://orcid.org/0009-0008-9098-343X"},"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":"Yuanxian Li","raw_affiliation_strings":["School of Information Science and Technology, ShanghaiTech University, Shanghai, China"],"raw_orcid":"https://orcid.org/0009-0009-9809-1679","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/A5101613198","display_name":"Siyu Tao","orcid":"https://orcid.org/0009-0006-6655-2483"},"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":"Siyu Tao","raw_affiliation_strings":["School of Information Science and Technology, ShanghaiTech University, Shanghai, China and Lingang Laboratory, Shanghai, China"],"raw_orcid":"https://orcid.org/0009-0002-1139-487X","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":"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"],"raw_orcid":"https://orcid.org/0000-0001-6774-9786","affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, ShanghaiTech University, 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":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/lethality","display_name":"Lethality","score":0.6488999724388123},{"id":"https://openalex.org/keywords/synthetic-lethality","display_name":"Synthetic lethality","score":0.49059998989105225},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4853000044822693},{"id":"https://openalex.org/keywords/multi-agent-system","display_name":"Multi-agent system","score":0.43619999289512634},{"id":"https://openalex.org/keywords/agent-based-model","display_name":"Agent-based model","score":0.2653999924659729}],"concepts":[{"id":"https://openalex.org/C20379349","wikidata":"https://www.wikidata.org/wiki/Q1720706","display_name":"Lethality","level":2,"score":0.6488999724388123},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5874000191688538},{"id":"https://openalex.org/C2778502085","wikidata":"https://www.wikidata.org/wiki/Q7662767","display_name":"Synthetic lethality","level":4,"score":0.49059998989105225},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4853000044822693},{"id":"https://openalex.org/C41550386","wikidata":"https://www.wikidata.org/wiki/Q529909","display_name":"Multi-agent system","level":2,"score":0.43619999289512634},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3747999966144562},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.27410000562667847},{"id":"https://openalex.org/C2780873155","wikidata":"https://www.wikidata.org/wiki/Q392811","display_name":"Agent-based model","level":2,"score":0.2653999924659729},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2587999999523163},{"id":"https://openalex.org/C2775924081","wikidata":"https://www.wikidata.org/wiki/Q55608371","display_name":"Control (management)","level":2,"score":0.23520000278949738}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3807503.3819483","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819483","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:10.1145/3807503.3819483","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819483","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":23,"referenced_works":["https://openalex.org/W1895317372","https://openalex.org/W2149441684","https://openalex.org/W2347037915","https://openalex.org/W2597062310","https://openalex.org/W2704159227","https://openalex.org/W2741508285","https://openalex.org/W2963277165","https://openalex.org/W2990747402","https://openalex.org/W3161372396","https://openalex.org/W3181518724","https://openalex.org/W4294216483","https://openalex.org/W4309306035","https://openalex.org/W4378838672","https://openalex.org/W4385565351","https://openalex.org/W4392168151","https://openalex.org/W4403572618","https://openalex.org/W4404511387","https://openalex.org/W4409804355","https://openalex.org/W4410232400","https://openalex.org/W4412954363","https://openalex.org/W4414934086","https://openalex.org/W4416960790","https://openalex.org/W7131823714"],"related_works":[],"abstract_inverted_index":{"Synthetic":[0],"lethality":[1,205],"(SL)":[2],"has":[3],"emerged":[4],"as":[5],"a":[6,52,75,87,116,138,198],"clinically":[7],"validated":[8],"approach":[9],"to":[10,21,82,96,154],"identifying":[11],"anticancer":[12,67],"therapeutic":[13],"targets,":[14],"effectively":[15],"exposing":[16],"the":[17,160],"critical":[18,117],"vulnerabilities":[19],"unique":[20],"cancer":[22],"cells.":[23],"While":[24],"Large":[25],"Language":[26],"Models":[27],"(LLMs)":[28],"have":[29],"achieved":[30],"significant":[31],"progress":[32],"in":[33,38,62,177,184,211],"scientific":[34],"research,":[35],"their":[36,102],"reliability":[37],"reasoning":[39,107],"about":[40],"SL":[41,64],"gene":[42],"pairs":[43],"remains":[44],"unexplored.":[45],"To":[46,131],"fill":[47],"this":[48,133],"gap,":[49],"we":[50,135],"present":[51],"unified":[53],"framework,":[54],"named":[55],"BASIS,":[56],"for":[57,66,104],"evaluating":[58],"and":[59,182],"improving":[60],"LLMs":[61,85,120],"inferring":[63,127],"interactions":[65],"drug":[68],"target":[69],"discovery.":[70,206],"We":[71],"first":[72],"construct":[73],"SL-Bench,":[74],"systematic":[76,191],"benchmark":[77],"encompassing":[78],"seven":[79],"hierarchical":[80],"tasks,":[81],"rigorously":[83],"evaluate":[84],"across":[86],"spectrum":[88],"of":[89],"cognitive":[90],"demands":[91],"ranging":[92],"from":[93,122],"factual":[94],"recall":[95],"clinical":[97],"hypothesis":[98],"formulation,":[99],"thereby":[100],"probing":[101],"capacity":[103],"deep":[105],"mechanistic":[106],"over":[108],"shallow":[109],"statistical":[110],"correlations.":[111],"Our":[112],"benchmarking":[113],"study":[114],"revealed":[115],"limitation:":[118],"contemporary":[119],"suffer":[121],"substantial":[123],"logical":[124],"inconsistencies":[125],"when":[126,152],"intricate":[128],"biological":[129],"dependencies.":[130],"resolve":[132],"issue,":[134],"propose":[136],"SL-Agent,":[137],"neuro-symbolic":[139],"Solver-Verifier":[140],"architecture":[141],"that":[142],"integrates":[143],"GraphRAG":[144],"with":[145,169,193],"iterative":[146],"self-reflection,":[147],"demonstrating":[148],"consistent":[149],"performance":[150],"improvements":[151],"applied":[153],"various":[155],"base":[156],"models.":[157],"Notably,":[158],"on":[159],"most":[161],"challenging":[162],"task,":[163],"an":[164],"8B":[165],"open-source":[166],"model":[167],"equipped":[168],"SL-Agent":[170],"outperforms":[171],"leading":[172],"proprietary":[173],"models,":[174],"exceeding":[175],"GPT-5.2":[176],"accuracy":[178],"by":[179,186],"14.0":[180],"pp":[181],"Gemini-3-Pro":[183],"safety":[185],"28.0":[187],"pp.":[188],"By":[189],"unifying":[190],"evaluation":[192],"targeted":[194],"improvement,":[195],"BASIS":[196],"establishes":[197],"practical":[199],"path":[200],"toward":[201],"reliable,":[202],"AI-driven":[203],"synthetic":[204],"The":[207],"code":[208],"is":[209],"available":[210],"https://github.com/davidwushi1145/BASIS.":[212]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-07-29T00:00:00"}