{"id":"https://openalex.org/W7171543994","doi":"https://doi.org/10.1145/3807503.3820007","title":"Translating Deep Multi-Omic Latent Spaces into LLM-Synthesized Mechanistic Hypotheses","display_name":"Translating Deep Multi-Omic Latent Spaces into LLM-Synthesized Mechanistic Hypotheses","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7171543994","doi":"https://doi.org/10.1145/3807503.3820007"},"language":null,"primary_location":{"id":"doi:10.1145/3807503.3820007","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3820007","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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/10.1145/3807503.3820007","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075965877","display_name":"Neil Y. C. Lin","orcid":"https://orcid.org/0000-0002-8653-1894"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Neil Lin","raw_affiliation_strings":["University California Los Angeles, Los Angeles, USA"],"raw_orcid":"https://orcid.org/0000-0002-8653-1894","affiliations":[{"raw_affiliation_string":"University California Los Angeles, Los Angeles, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5075965877"],"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":"1","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.33559998869895935},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.29269999265670776},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.2888000011444092},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.2547000050544739},{"id":"https://openalex.org/keywords/perspective","display_name":"Perspective (graphical)","score":0.251800000667572}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4763000011444092},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46709999442100525},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.33559998869895935},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.29269999265670776},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.2888000011444092},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2572000026702881},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.2547000050544739},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.251800000667572},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.2506999969482422},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.24310000240802765}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3807503.3820007","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3820007","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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:10.1145/3807503.3820007","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3820007","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":3,"referenced_works":["https://openalex.org/W2606568412","https://openalex.org/W3005127469","https://openalex.org/W4285388094"],"related_works":[],"abstract_inverted_index":{"Neural":[0],"networks":[1],"can":[2],"effectively":[3],"model":[4],"high-dimensional":[5],"single-cell":[6,99],"multimodal":[7],"omics,":[8],"yet":[9],"their":[10],"opacity":[11],"hinders":[12],"translating":[13],"predictions":[14],"into":[15,69],"testable":[16],"biological":[17],"mechanisms.":[18],"We":[19,91],"introduce":[20],"Parsing":[21],"Integrated-gradients":[22],"and":[23],"Trees":[24],"to":[25,53,85,102],"Create":[26],"Hypotheses":[27],"(PITCH),":[28],"a":[29,44,96],"pipeline":[30],"bridging":[31],"mathematical":[32],"feature":[33],"attribution":[34],"with":[35],"LLM-driven":[36],"automated":[37],"hypothesis":[38],"generation.":[39],"The":[40],"framework":[41],"first":[42],"trains":[43],"Multilayer":[45],"Perceptron":[46],"before":[47],"calculating":[48],"Integrated":[49],"Gradients":[50],"for":[51],"regression":[52],"isolate":[54],"predictive":[55],"variables":[56],"across":[57],"multi-omic":[58],"manifolds.":[59],"A":[60],"decision":[61,71],"tree":[62],"classifier":[63],"then":[64],"distills":[65],"these":[66,76],"continuous":[67],"attributions":[68],"discrete":[70],"thresholds.":[72],"Finally,":[73],"by":[74],"employing":[75],"extracted":[77],"rules":[78,108],"as":[79],"structural":[80],"priors,":[81],"PITCH":[82],"constrains":[83],"LLMs":[84],"produce":[86],"context-specific,":[87],"literature-grounded":[88],"mechanistic":[89],"hypotheses.":[90],"demonstrate":[92],"this":[93],"approach":[94],"using":[95],"highly":[97],"multiplexed":[98],"signaling":[100],"dataset":[101],"systematically":[103],"derive":[104],"the":[105],"context-dependent":[106],"mechanobiological":[107],"governing":[109],"EGF-induced":[110],"MAPK":[111],"activation.":[112]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-07-29T00:00:00"}
