{"id":"https://openalex.org/W7171544240","doi":"https://doi.org/10.1145/3807503.3819455","title":"Interactive Visual Analytics for Generating and Exploring LLM-Predicted Protein-Protein Interactions","display_name":"Interactive Visual Analytics for Generating and Exploring LLM-Predicted Protein-Protein Interactions","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7171544240","doi":"https://doi.org/10.1145/3807503.3819455"},"language":null,"primary_location":{"id":"doi:10.1145/3807503.3819455","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819455","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/10.1145/3807503.3819455","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5133715243","display_name":"Allison Austin","orcid":null},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Allison Austin","raw_affiliation_strings":["University of California, Davis, Davis, California, USA"],"raw_orcid":"https://orcid.org/0009-0000-3611-5166","affiliations":[{"raw_affiliation_string":"University of California, Davis, Davis, California, USA","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063969469","display_name":"Fnu Shilpika","orcid":null},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fnu Shilpika","raw_affiliation_strings":["Argonne National Laboratory, Lemont, Illinois, USA"],"raw_orcid":"https://orcid.org/0000-0001-9338-2690","affiliations":[{"raw_affiliation_string":"Argonne National Laboratory, Lemont, Illinois, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114634740","display_name":"Aditya Tanikanti","orcid":"https://orcid.org/0000-0002-5240-5064"},"institutions":[{"id":"https://openalex.org/I2801935854","display_name":"SLAC National Accelerator Laboratory","ror":"https://ror.org/05gzmn429","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I2801935854","https://openalex.org/I39565521","https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aditya Tanikanti","raw_affiliation_strings":["Argonne National Laboratory, Lemont, Illinois, USA and SLAC National Accelerator Laboratory, Menlo Park, California, USA"],"raw_orcid":"https://orcid.org/0000-0002-5240-5064","affiliations":[{"raw_affiliation_string":"Argonne National Laboratory, Lemont, Illinois, USA and SLAC National Accelerator Laboratory, Menlo Park, California, USA","institution_ids":["https://openalex.org/I2801935854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075500139","display_name":"Venkatram Vishwanath","orcid":"https://orcid.org/0000-0001-7248-6116"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Venkatram Vishwanath","raw_affiliation_strings":["Argonne National Laboratory, Lemont, Illinois, USA"],"raw_orcid":"https://orcid.org/0000-0001-7248-6116","affiliations":[{"raw_affiliation_string":"Argonne National Laboratory, Lemont, Illinois, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010928934","display_name":"Michael E. Papka","orcid":"https://orcid.org/0000-0002-6418-5767"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Papka","raw_affiliation_strings":["Argonne National Laboratory, Lemont, Illinois, USA and University of Illinois at Chicago, Chicago, Illinois, USA"],"raw_orcid":"https://orcid.org/0000-0002-6418-5767","affiliations":[{"raw_affiliation_string":"Argonne National Laboratory, Lemont, Illinois, USA and University of Illinois at Chicago, Chicago, Illinois, USA","institution_ids":["https://openalex.org/I1282105669","https://openalex.org/I39422238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037161857","display_name":"Kwan\u2010Liu Ma","orcid":"https://orcid.org/0000-0001-8086-0366"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kwan-Liu Ma","raw_affiliation_strings":["University of California, Davis, Davis, California, USA"],"raw_orcid":"https://orcid.org/0000-0001-8086-0366","affiliations":[{"raw_affiliation_string":"University of California, Davis, Davis, California, USA","institution_ids":["https://openalex.org/I84218800"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"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":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/visual-analytics","display_name":"Visual analytics","score":0.628600001335144},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.39660000801086426},{"id":"https://openalex.org/keywords/analytics","display_name":"Analytics","score":0.3797999918460846},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.3450999855995178},{"id":"https://openalex.org/keywords/information-visualization","display_name":"Information visualization","score":0.3343999981880188},{"id":"https://openalex.org/keywords/interactive-visual-analysis","display_name":"Interactive visual analysis","score":0.32030001282691956},{"id":"https://openalex.org/keywords/cultural-analytics","display_name":"Cultural analytics","score":0.287200003862381}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6801000237464905},{"id":"https://openalex.org/C59732488","wikidata":"https://www.wikidata.org/wiki/Q2528440","display_name":"Visual analytics","level":3,"score":0.628600001335144},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.4602000117301941},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.39660000801086426},{"id":"https://openalex.org/C79158427","wikidata":"https://www.wikidata.org/wiki/Q485396","display_name":"Analytics","level":2,"score":0.3797999918460846},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.3450999855995178},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33709999918937683},{"id":"https://openalex.org/C185578843","wikidata":"https://www.wikidata.org/wiki/Q10609775","display_name":"Information visualization","level":3,"score":0.3343999981880188},{"id":"https://openalex.org/C99740376","wikidata":"https://www.wikidata.org/wiki/Q17092520","display_name":"Interactive visual analysis","level":4,"score":0.32030001282691956},{"id":"https://openalex.org/C545860419","wikidata":"https://www.wikidata.org/wiki/Q5193251","display_name":"Cultural analytics","level":5,"score":0.287200003862381},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.2777000069618225},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.26820001006126404},{"id":"https://openalex.org/C64073096","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Interactive visualization","level":3,"score":0.26429998874664307},{"id":"https://openalex.org/C175801342","wikidata":"https://www.wikidata.org/wiki/Q1988917","display_name":"Data analysis","level":2,"score":0.2632000148296356},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.2603999972343445},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.2547000050544739},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.25040000677108765}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3807503.3819455","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819455","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:10.1145/3807503.3819455","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819455","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1990315216","https://openalex.org/W2016012447","https://openalex.org/W2016958746","https://openalex.org/W2042301222","https://openalex.org/W2103017472","https://openalex.org/W2107556275","https://openalex.org/W2113654464","https://openalex.org/W2125910575","https://openalex.org/W2159675211","https://openalex.org/W2403400382","https://openalex.org/W2534390616","https://openalex.org/W3003605616","https://openalex.org/W3096568637","https://openalex.org/W3107527779","https://openalex.org/W3159719254","https://openalex.org/W3165240900","https://openalex.org/W3199468887","https://openalex.org/W4214887964","https://openalex.org/W4220788548","https://openalex.org/W4220851257","https://openalex.org/W4220991280","https://openalex.org/W4309485183","https://openalex.org/W4366603484","https://openalex.org/W4399157241","https://openalex.org/W4399167256","https://openalex.org/W4402528490","https://openalex.org/W4402670977","https://openalex.org/W4403479110","https://openalex.org/W4410049544","https://openalex.org/W4410138743","https://openalex.org/W4410497420","https://openalex.org/W4415648205"],"related_works":[],"abstract_inverted_index":{"Protein-protein":[0],"interactions":[1,58],"(PPIs)":[2],"are":[3,59],"fundamental":[4],"to":[5,63,88],"understanding":[6],"cellular":[7],"function":[8],"and":[9,75,93,121,141],"disease":[10],"mechanisms.":[11],"While":[12],"large":[13],"language":[14],"models":[15],"(LLMs)":[16],"show":[17],"significant":[18],"promise":[19],"in":[20],"predicting":[21],"novel":[22,115],"interacting":[23],"proteins,":[24],"large-scale":[25],"evaluation":[26,94],"of":[27,95],"these":[28,54],"predictions":[29,37,116],"remains":[30],"a":[31,83,99],"challenge.":[32],"Validation":[33],"typically":[34],"requires":[35],"cross-referencing":[36],"against":[38],"molecular":[39],"databases,":[40],"which":[41],"often":[42],"omit":[43],"biologically":[44],"plausible":[45],"but":[46],"formally":[47],"untested":[48],"interactions.":[49],"Current":[50],"workflows":[51],"for":[52,150],"exploring":[53],"\"hidden\"":[55],"or":[56],"predicted":[57],"fragmented,":[60],"requiring":[61],"researchers":[62],"combine":[64],"text-based":[65],"LLM":[66,135],"outputs":[67],"with":[68,137],"separate":[69],"structural":[70],"viewers,":[71],"sequence":[72],"alignment":[73],"tools,":[74],"network":[76],"visualizations.":[77],"In":[78],"this":[79],"paper,":[80],"we":[81],"present":[82,104],"visual":[84],"analytics":[85],"system":[86,145],"designed":[87],"support":[89],"real-time":[90],"generation,":[91],"exploration,":[92],"LLM-generated":[96],"PPIs":[97],"within":[98],"single,":[100],"integrated":[101],"environment.":[102],"We":[103],"two":[105],"use":[106],"cases":[107],"centered":[108],"on":[109],"the":[110],"PDCD1":[111],"(PD-1)":[112],"axis,":[113],"identifying":[114],"across":[117],"multiple":[118],"evidence":[119],"channels":[120],"successfully":[122],"distinguishing":[123],"between":[124],"functionally-associated":[125],"protein":[126],"clusters":[127],"from":[128],"direct":[129],"physical":[130],"interactors.":[131],"By":[132],"unifying":[133],"rapid":[134],"inference":[136],"rigorous":[138],"biological":[139,154],"scoring":[140],"high-performance":[142],"visualization,":[143],"our":[144],"provides":[146],"an":[147],"end-to-end":[148],"framework":[149],"interpreting":[151],"large-scale,":[152],"AI-generated":[153],"networks.":[155]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-07-29T00:00:00"}