{"id":"https://openalex.org/W7126065224","doi":"https://doi.org/10.1109/bibm66473.2025.11356542","title":"GeneQuery: Generalized Gene Expression Prediction from Histology Images via Image-Gene QA","display_name":"GeneQuery: Generalized Gene Expression Prediction from Histology Images via Image-Gene QA","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126065224","doi":"https://doi.org/10.1109/bibm66473.2025.11356542"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356542","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356542","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5013848104","display_name":"Ying Xiong","orcid":"https://orcid.org/0000-0002-6270-5220"},"institutions":[{"id":"https://openalex.org/I4210113480","display_name":"Mohamed bin Zayed University of Artificial Intelligence","ror":"https://ror.org/0258gkt32","country_code":"AE","type":"education","lineage":["https://openalex.org/I4210113480"]}],"countries":["AE"],"is_corresponding":true,"raw_author_name":"Ying Xiong","raw_affiliation_strings":["Mohamed bin Zayed University of Artificial Intelligence,Abu Dhabi,United Arab Emirates"],"affiliations":[{"raw_affiliation_string":"Mohamed bin Zayed University of Artificial Intelligence,Abu Dhabi,United Arab Emirates","institution_ids":["https://openalex.org/I4210113480"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032961872","display_name":"Linjing Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Linjing Liu","raw_affiliation_strings":["The Chinese University of Hong Kong,Hong Kong,China"],"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong,Hong Kong,China","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100308531","display_name":"Yufei Cui","orcid":null},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Yufei Cui","raw_affiliation_strings":["McGill University,Montreal,Canada"],"affiliations":[{"raw_affiliation_string":"McGill University,Montreal,Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111341519","display_name":"Shangyu Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Shangyu Wu","raw_affiliation_strings":["City University of Hong Kong,Hong Kong,China"],"affiliations":[{"raw_affiliation_string":"City University of Hong Kong,Hong Kong,China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122937110","display_name":"Xue Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210113480","display_name":"Mohamed bin Zayed University of Artificial Intelligence","ror":"https://ror.org/0258gkt32","country_code":"AE","type":"education","lineage":["https://openalex.org/I4210113480"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Xue Liu","raw_affiliation_strings":["Mohamed bin Zayed University of Artificial Intelligence,Abu Dhabi,United Arab Emirates"],"affiliations":[{"raw_affiliation_string":"Mohamed bin Zayed University of Artificial Intelligence,Abu Dhabi,United Arab Emirates","institution_ids":["https://openalex.org/I4210113480"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124217752","display_name":"Antoni B. Chan","orcid":null},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Antoni B. Chan","raw_affiliation_strings":["City University of Hong Kong,Hong Kong,China"],"affiliations":[{"raw_affiliation_string":"City University of Hong Kong,Hong Kong,China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"last","author":{"id":null,"display_name":"Chun Jason Xue","orcid":null},"institutions":[{"id":"https://openalex.org/I4210113480","display_name":"Mohamed bin Zayed University of Artificial Intelligence","ror":"https://ror.org/0258gkt32","country_code":"AE","type":"education","lineage":["https://openalex.org/I4210113480"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Chun Jason Xue","raw_affiliation_strings":["Mohamed bin Zayed University of Artificial Intelligence,Abu Dhabi,United Arab Emirates"],"affiliations":[{"raw_affiliation_string":"Mohamed bin Zayed University of Artificial Intelligence,Abu Dhabi,United Arab Emirates","institution_ids":["https://openalex.org/I4210113480"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5013848104"],"corresponding_institution_ids":["https://openalex.org/I4210113480"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.81162874,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"5738","last_page":"5745"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.35120001435279846,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.35120001435279846,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10862","display_name":"AI in cancer detection","score":0.21539999544620514,"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/T10885","display_name":"Gene expression and cancer classification","score":0.13519999384880066,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/generality","display_name":"Generality","score":0.5652999877929688},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.5235000252723694},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4968000054359436},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4925000071525574},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4514999985694885},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4271000027656555},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.4092999994754791},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.37310001254081726}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6430000066757202},{"id":"https://openalex.org/C2780767217","wikidata":"https://www.wikidata.org/wiki/Q5532421","display_name":"Generality","level":2,"score":0.5652999877929688},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.5235000252723694},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5102999806404114},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4968000054359436},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4925000071525574},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4629000127315521},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4514999985694885},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4271000027656555},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4097999930381775},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.4092999994754791},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.37310001254081726},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.36410000920295715},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3580999970436096},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3499000072479248},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.3328000009059906},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.3249000012874603},{"id":"https://openalex.org/C141353440","wikidata":"https://www.wikidata.org/wiki/Q182221","display_name":"Fuse (electrical)","level":2,"score":0.3131999969482422},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.28360000252723694},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.2761000096797943},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.274399995803833},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.2709999978542328}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356542","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356542","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W2042789810","https://openalex.org/W2063575312","https://openalex.org/W2194775991","https://openalex.org/W2471536144","https://openalex.org/W2809368942","https://openalex.org/W2897249806","https://openalex.org/W2923300855","https://openalex.org/W2952383043","https://openalex.org/W3036882247","https://openalex.org/W3046305306","https://openalex.org/W3125011419","https://openalex.org/W4386741020","https://openalex.org/W4392947521","https://openalex.org/W4402660143","https://openalex.org/W4403365602"],"related_works":[],"abstract_inverted_index":{"Gene":[0],"expression":[1,30,76,107,176],"profiling":[2],"provides":[3],"profound":[4],"insights":[5],"into":[6],"molecular":[7],"mechanisms,":[8],"but":[9],"its":[10],"time-consuming":[11],"and":[12,43,87,96,101,120,131,198],"costly":[13],"nature":[14],"often":[15],"presents":[16,68],"significant":[17],"challenges.":[18],"Recent":[19],"advancements":[20],"have":[21],"utilized":[22],"histological":[23],"images":[24,98],"to":[25,72,111,125,135,150,168],"predict":[26],"spatially":[27],"resolved":[28],"gene":[29,33,44,75,92,106,118,139,152,175],"profiles.":[31],"The":[32],"prediction":[34,77,172],"problem":[35],"has":[36],"two":[37],"main":[38],"characteristics,":[39],"i.e.,":[40],"spatial":[41,52,114,129,184],"heterogeneity":[42],"interdependency.":[45],"Existing":[46],"works":[47],"only":[48],"focus":[49],"on":[50,183,196],"addressing":[51],"heterogeneity,":[53],"ignoring":[54],"the":[55,63,104,128,138,147,164,166,171,189,210],"importance":[56],"of":[57,143,173],"relationships":[58,153],"between":[59],"genes.":[60,200],"To":[61],"address":[62],"above":[64],"limitation,":[65],"this":[66,74],"paper":[67],"GeneQuery,":[69],"which":[70],"aims":[71],"solve":[73],"task":[78],"in":[79],"a":[80,132],"question-answering":[81],"(QA)":[82],"manner":[83],"for":[84,154],"better":[85],"generality":[86],"flexibility.":[88],"Specifically,":[89],"GeneQuery":[90,109,144,191,206],"takes":[91],"meta-information":[93],"as":[94,99],"queries":[95],"whole-slide":[97],"contexts":[100],"then":[102],"predicts":[103],"queried":[105],"values.":[108],"learns":[110],"dynamically":[112],"fuse":[113],"image":[115],"features":[116],"with":[117],"semantics,":[119],"uses":[121],"an":[122],"attention":[123,148],"mechanism":[124,149],"explicitly":[126],"capture":[127,137,151],"information":[130],"shared":[133],"regressor":[134],"implicitly":[136],"relationship.":[140],"A":[141],"variant":[142],"can":[145,207],"use":[146],"more":[155],"complex":[156],"tissue":[157,211],"cases.":[158],"This":[159],"QA-based":[160],"reformulation":[161],"also":[162,203],"grants":[163],"model":[165,179],"ability":[167],"generalize,":[169],"enabling":[170],"unseen":[174,199],"without":[177],"requiring":[178],"retraining.":[180],"Comprehensive":[181],"experiments":[182],"transcriptomics":[185],"datasets":[186],"show":[187],"that":[188,205],"proposed":[190],"outperforms":[192],"existing":[193],"state-of-the-art":[194],"methods":[195],"known":[197],"More":[201],"results":[202],"demonstrate":[204],"help":[208],"analyze":[209],"structure.":[212]},"counts_by_year":[],"updated_date":"2026-03-25T23:56:10.502304","created_date":"2026-01-30T00:00:00"}