{"id":"https://openalex.org/W7161677068","doi":"https://doi.org/10.1109/tvcg.2026.3694805","title":"Chat Modeling: Interaction-Enhanced Agent Framework for Visualizing Literature-Grounded Biological Structures","display_name":"Chat Modeling: Interaction-Enhanced Agent Framework for Visualizing Literature-Grounded Biological Structures","publication_year":2026,"publication_date":"2026-05-19","ids":{"openalex":"https://openalex.org/W7161677068","doi":"https://doi.org/10.1109/tvcg.2026.3694805","pmid":"https://pubmed.ncbi.nlm.nih.gov/42154686"},"language":"en","primary_location":{"id":"doi:10.1109/tvcg.2026.3694805","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tvcg.2026.3694805","pdf_url":null,"source":{"id":"https://openalex.org/S84775595","display_name":"IEEE Transactions on Visualization and Computer Graphics","issn_l":"1077-2626","issn":["1077-2626","1941-0506","2160-9306"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Visualization and Computer Graphics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002662014","display_name":"Donggang Jia","orcid":"https://orcid.org/0000-0002-1358-8718"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Donggang Jia","raw_affiliation_strings":["Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia"],"raw_orcid":"https://orcid.org/0000-0002-1358-8718","affiliations":[{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068526974","display_name":"Yunhai Wang","orcid":"https://orcid.org/0000-0003-0059-6580"},"institutions":[{"id":"https://openalex.org/I78988378","display_name":"Renmin University of China","ror":"https://ror.org/041pakw92","country_code":"CN","type":"education","lineage":["https://openalex.org/I78988378"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yunhai Wang","raw_affiliation_strings":["School of Information, Renmin University of China, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0003-0059-6580","affiliations":[{"raw_affiliation_string":"School of Information, Renmin University of China, Beijing, China","institution_ids":["https://openalex.org/I78988378"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022294742","display_name":"Ivan Viola","orcid":"https://orcid.org/0000-0003-4248-6574"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Ivan Viola","raw_affiliation_strings":["Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia"],"raw_orcid":"https://orcid.org/0000-0003-4248-6574","affiliations":[{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.58525511,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"32","issue":"8","first_page":"7453","last_page":"7467"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.49380001425743103,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.49380001425743103,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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/T10799","display_name":"Data Visualization and Analytics","score":0.11330000311136246,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/T11986","display_name":"Scientific Computing and Data Management","score":0.061000000685453415,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6089000105857849},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.47850000858306885},{"id":"https://openalex.org/keywords/information-visualization","display_name":"Information visualization","score":0.33250001072883606},{"id":"https://openalex.org/keywords/multi-agent-system","display_name":"Multi-agent system","score":0.28130000829696655},{"id":"https://openalex.org/keywords/collaborative-software","display_name":"Collaborative software","score":0.27469998598098755}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8342999815940857},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6089000105857849},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.4921000003814697},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.47850000858306885},{"id":"https://openalex.org/C185578843","wikidata":"https://www.wikidata.org/wiki/Q10609775","display_name":"Information visualization","level":3,"score":0.33250001072883606},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2978000044822693},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2946000099182129},{"id":"https://openalex.org/C41550386","wikidata":"https://www.wikidata.org/wiki/Q529909","display_name":"Multi-agent system","level":2,"score":0.28130000829696655},{"id":"https://openalex.org/C554579003","wikidata":"https://www.wikidata.org/wiki/Q474157","display_name":"Collaborative software","level":2,"score":0.27469998598098755},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.2694000005722046},{"id":"https://openalex.org/C198439703","wikidata":"https://www.wikidata.org/wiki/Q1461602","display_name":"Computer-supported cooperative work","level":3,"score":0.2671000063419342},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.25949999690055847}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tvcg.2026.3694805","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tvcg.2026.3694805","pdf_url":null,"source":{"id":"https://openalex.org/S84775595","display_name":"IEEE Transactions on Visualization and Computer Graphics","issn_l":"1077-2626","issn":["1077-2626","1941-0506","2160-9306"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Visualization and Computer Graphics","raw_type":"journal-article"},{"id":"pmid:42154686","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42154686","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE transactions on visualization and computer graphics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G287846484","display_name":null,"funder_award_id":"BAS/1/1680-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Bioscientists":[0],"frequently":[1],"seek":[2],"to":[3,149,171],"visualize":[4],"the":[5,15,38,58,80,86,107,138,187,216],"biological":[6,21,31],"systems":[7],"they":[8],"have":[9],"empirically":[10],"characterized":[11],"and":[12,32,76,83,97,117,127,134,162,200,212],"reported":[13],"in":[14,85,92,106,223],"literature.":[16],"Realizing":[17],"such":[18,42,122,155],"visualizations":[19],"requires":[20],"structure":[22],"modeling,":[23],"an":[24],"inherently":[25],"complex":[26],"process":[27],"that":[28,56,111,131],"demands":[29],"both":[30],"geometric":[33],"understanding.":[34],"This":[35,166],"paper":[36],"addresses":[37],"problem":[39],"of":[40,60,79,189,218],"constructing":[41],"3D":[43,62,99,174],"models":[44],"for":[45,221],"visualization.":[46],"In":[47],"this":[48],"paper,":[49],"we":[50],"introduce":[51],"a":[52,93,145,195],"novel":[53,118],"agent":[54,109],"framework":[55,142],"mitigates":[57],"challenges":[59],"operating":[61],"modeling":[63,90,125,147,167,175,206],"software":[64],"by":[65],"transforming":[66],"user":[67,119,151,210],"inputs,":[68],"including":[69],"natural":[70],"language":[71],"descriptions,":[72],"research":[73],"publication":[74],"content,":[75],"textual":[77],"descriptions":[78],"existing":[81],"objects":[82],"structures":[84],"current":[87],"scene,":[88],"into":[89],"operations":[91],"structured":[94],"JSON":[95],"format":[96],"final":[98],"results.":[100],"The":[101,141,179],"major":[102],"technical":[103],"contribution":[104],"lies":[105],"collaborative":[108],"design":[110],"simultaneously":[112],"supports":[113],"model":[114],"planning,":[115],"execution,":[116],"interaction":[120,136],"design,":[121],"as":[123,156],"interactive":[124],"execution":[126],"dynamic":[128],"widget":[129],"generation":[130],"fuse":[132],"text":[133],"mouse":[135],"within":[137],"chat":[139],"window.":[140],"further":[143],"incorporates":[144],"customized":[146],"memory":[148,158,168],"enhance":[150],"interaction,":[152],"featuring":[153],"components":[154],"personalized":[157],"management,":[159],"feedback":[160],"collection,":[161],"skill":[163],"library":[164],"design.":[165],"is":[169],"leveraged":[170],"enable":[172],"improved":[173],"performance":[176],"over":[177],"time.":[178],"quantitative":[180],"evaluation":[181],"on":[182],"our":[183,190,219],"collected":[184],"dataset":[185],"showcases":[186],"effectiveness":[188],"framework.":[191],"We":[192],"also":[193],"develop":[194],"prototype":[196],"tool,":[197],"Chat":[198],"Modeling,":[199],"demonstrate":[201],"its":[202],"usage":[203],"through":[204],"two":[205],"case":[207],"studies.":[208],"Our":[209],"study":[211],"expert":[213],"interviews":[214],"highlight":[215],"potential":[217],"approach":[220],"use":[222],"scientific":[224],"workflows.":[225]},"counts_by_year":[],"updated_date":"2026-07-03T06:15:21.484131","created_date":"2026-05-20T00:00:00"}
