{"id":"https://openalex.org/W4392781760","doi":"https://doi.org/10.1145/3589335.3651572","title":"Thought Graph: Generating Thought Process for Biological Reasoning","display_name":"Thought Graph: Generating Thought Process for Biological Reasoning","publication_year":2024,"publication_date":"2024-05-12","ids":{"openalex":"https://openalex.org/W4392781760","doi":"https://doi.org/10.1145/3589335.3651572"},"language":"en","primary_location":{"id":"doi:10.1145/3589335.3651572","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3589335.3651572","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3589335.3651572","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Companion Proceedings of the ACM Web Conference 2024","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3589335.3651572","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010483978","display_name":"Chi-Yang Hsu","orcid":"https://orcid.org/0009-0007-8668-2901"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chi-Yang Hsu","raw_affiliation_strings":["University of Texas at Austin, Austin, TX, USA"],"raw_orcid":"https://orcid.org/0009-0007-8668-2901","affiliations":[{"raw_affiliation_string":"University of Texas at Austin, Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074989561","display_name":"Kyle Cox","orcid":"https://orcid.org/0009-0003-8248-0254"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyle Cox","raw_affiliation_strings":["University of Texas at Austin, Austin, TX, USA"],"raw_orcid":"https://orcid.org/0009-0003-8248-0254","affiliations":[{"raw_affiliation_string":"University of Texas at Austin, Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101834496","display_name":"Jiawei Xu","orcid":"https://orcid.org/0000-0003-4386-5277"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiawei Xu","raw_affiliation_strings":["University of Texas at Austin, Austin, Texas, USA"],"raw_orcid":"https://orcid.org/0000-0003-4386-5277","affiliations":[{"raw_affiliation_string":"University of Texas at Austin, Austin, Texas, USA","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101925382","display_name":"Zhen Tan","orcid":"https://orcid.org/0009-0006-9548-2330"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhen Tan","raw_affiliation_strings":["Arizona State University, Tempe, AZ, USA"],"raw_orcid":"https://orcid.org/0009-0006-9548-2330","affiliations":[{"raw_affiliation_string":"Arizona State University, Tempe, AZ, USA","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084521312","display_name":"Tianhua Zhai","orcid":"https://orcid.org/0009-0007-9712-9132"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tianhua Zhai","raw_affiliation_strings":["University of Pennsylvania, Philadelphia, Pennsylvania, USA"],"raw_orcid":"https://orcid.org/0009-0007-9712-9132","affiliations":[{"raw_affiliation_string":"University of Pennsylvania, Philadelphia, Pennsylvania, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077208479","display_name":"Mengzhou Hu","orcid":"https://orcid.org/0000-0002-1571-8029"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mengzhou Hu","raw_affiliation_strings":["University of California San Diego, La Jolla, California, USA"],"raw_orcid":"https://orcid.org/0000-0002-1571-8029","affiliations":[{"raw_affiliation_string":"University of California San Diego, La Jolla, California, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038117263","display_name":"Dexter Pratt","orcid":"https://orcid.org/0000-0002-1471-9513"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dexter Pratt","raw_affiliation_strings":["University of California San Diego, La Jolla, California, USA"],"raw_orcid":"https://orcid.org/0000-0002-1471-9513","affiliations":[{"raw_affiliation_string":"University of California San Diego, La Jolla, California, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103073431","display_name":"Tianlong Chen","orcid":"https://orcid.org/0000-0001-7774-8197"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tianlong Chen","raw_affiliation_strings":["The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA"],"raw_orcid":"https://orcid.org/0000-0001-7774-8197","affiliations":[{"raw_affiliation_string":"The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060639952","display_name":"Ziniu Hu","orcid":"https://orcid.org/0009-0007-8818-739X"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ziniu Hu","raw_affiliation_strings":["California Institute of Technology, Pasadena, California, USA"],"raw_orcid":"https://orcid.org/0009-0007-8818-739X","affiliations":[{"raw_affiliation_string":"California Institute of Technology, Pasadena, California, USA","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047170063","display_name":"Ying Ding","orcid":"https://orcid.org/0000-0003-2567-2009"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ying Ding","raw_affiliation_strings":["University of Texas at Austin, Austin, TX, USA"],"raw_orcid":"https://orcid.org/0000-0003-2567-2009","affiliations":[{"raw_affiliation_string":"University of Texas at Austin, Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"537","last_page":"540"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12805","display_name":"Cognitive Science and Mapping","score":0.9905999898910522,"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"}},"topics":[{"id":"https://openalex.org/T12805","display_name":"Cognitive Science and Mapping","score":0.9905999898910522,"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"}},{"id":"https://openalex.org/T13106","display_name":"Neuroscience, Education and Cognitive Function","score":0.9593999981880188,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13283","display_name":"Mental Health Research Topics","score":0.9437999725341797,"subfield":{"id":"https://openalex.org/subfields/3205","display_name":"Experimental and Cognitive Psychology"},"field":{"id":"https://openalex.org/fields/32","display_name":"Psychology"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6899892091751099},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.618824303150177},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.46588319540023804},{"id":"https://openalex.org/keywords/cognitive-science","display_name":"Cognitive science","score":0.4532420039176941},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3298313021659851},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3004332184791565},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2546716630458832},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.15103977918624878}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6899892091751099},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.618824303150177},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.46588319540023804},{"id":"https://openalex.org/C188147891","wikidata":"https://www.wikidata.org/wiki/Q147638","display_name":"Cognitive science","level":1,"score":0.4532420039176941},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3298313021659851},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3004332184791565},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2546716630458832},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.15103977918624878}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3589335.3651572","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3589335.3651572","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3589335.3651572","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Companion Proceedings of the ACM Web Conference 2024","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:2403.07144","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2403.07144","pdf_url":"https://arxiv.org/pdf/2403.07144","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"}],"best_oa_location":{"id":"doi:10.1145/3589335.3651572","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3589335.3651572","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3589335.3651572","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Companion Proceedings of the ACM Web Conference 2024","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5851915153","display_name":null,"funder_award_id":"NSF 2303038","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6503218615","display_name":"Collaborative Research: NSF-CSIRO: RESILIENCE: Graph Representation Learning for Fair Teaming in Crisis Response","funder_award_id":"2303038","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7695958241","display_name":null,"funder_award_id":"R01LM014306-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G885746081","display_name":"Proto-OKN Theme 1: DREAM-KG: Develop Dynamic, REsponsive, Adaptive, and Multifaceted Knowledge Graphs to address homelessness with Explainable AI","funder_award_id":"2333703","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8859862982","display_name":null,"funder_award_id":"R01LM014306","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4392781760.pdf"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W2103017472","https://openalex.org/W2130410032","https://openalex.org/W4318983406","https://openalex.org/W4393160302","https://openalex.org/W4401043168","https://openalex.org/W4402671983"],"related_works":["https://openalex.org/W3188962172","https://openalex.org/W2772917594","https://openalex.org/W4306742369","https://openalex.org/W4303457083","https://openalex.org/W2131146434","https://openalex.org/W2951359407","https://openalex.org/W4376623224","https://openalex.org/W3136979370","https://openalex.org/W2058170566","https://openalex.org/W2965396565"],"abstract_inverted_index":{"We":[0],"present":[1],"the":[2],"Thought":[3],"Graph":[4],"as":[5,18],"a":[6,37],"novel":[7],"framework":[8,29],"to":[9,21,35,57],"support":[10],"complex":[11],"reasoning":[12],"and":[13,48,72,76],"use":[14],"gene":[15,41],"set":[16],"analysis":[17,61],"an":[19],"example":[20],"uncover":[22],"semantic":[23],"relationships":[24],"between":[25],"biological":[26,69],"processes.":[27],"Our":[28,60],"stands":[30],"out":[31],"for":[32,74],"its":[33],"ability":[34],"provide":[36],"deeper":[38],"understanding":[39],"of":[40,68],"sets,":[42],"significantly":[43],"surpassing":[44],"GSEA":[45],"by":[46,51],"40.28%":[47],"LLM":[49],"baselines":[50],"5.38%":[52],"based":[53],"on":[54],"cosine":[55],"similarity":[56],"human":[58],"annotations.":[59],"further":[62],"provides":[63],"insights":[64],"into":[65],"future":[66],"directions":[67],"processes":[70],"naming,":[71],"implications":[73],"bioinformatics":[75],"precision":[77],"medicine.":[78]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
