{"id":"https://openalex.org/W7131637523","doi":"https://doi.org/10.1016/j.jbi.2026.105003","title":"Integrating histology and spatial transcriptomics via multimodal transformers and contrastive representation learning for accurate gene expression prediction","display_name":"Integrating histology and spatial transcriptomics via multimodal transformers and contrastive representation learning for accurate gene expression prediction","publication_year":2026,"publication_date":"2026-02-26","ids":{"openalex":"https://openalex.org/W7131637523","doi":"https://doi.org/10.1016/j.jbi.2026.105003","pmid":"https://pubmed.ncbi.nlm.nih.gov/41763376"},"language":"en","primary_location":{"id":"doi:10.1016/j.jbi.2026.105003","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.jbi.2026.105003","pdf_url":null,"source":{"id":"https://openalex.org/S11622463","display_name":"Journal of Biomedical Informatics","issn_l":"1532-0464","issn":["1532-0464","1532-0480"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Informatics","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/A5126945491","display_name":"Kai Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210092944","display_name":"Dalian University","ror":"https://ror.org/00g2ypp58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092944"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kai Wang","raw_affiliation_strings":["Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China","institution_ids":["https://openalex.org/I4210092944"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047308019","display_name":"Liuming Shi","orcid":null},"institutions":[{"id":"https://openalex.org/I4210092944","display_name":"Dalian University","ror":"https://ror.org/00g2ypp58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092944"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liuming Shi","raw_affiliation_strings":["Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China","institution_ids":["https://openalex.org/I4210092944"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126887702","display_name":"Xue Li","orcid":null},"institutions":[{"id":"https://openalex.org/I4210092944","display_name":"Dalian University","ror":"https://ror.org/00g2ypp58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092944"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xue Li","raw_affiliation_strings":["Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China","institution_ids":["https://openalex.org/I4210092944"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126902132","display_name":"Wei Li","orcid":null},"institutions":[{"id":"https://openalex.org/I877107187","display_name":"University of Roehampton","ror":"https://ror.org/043071f54","country_code":"GB","type":"education","lineage":["https://openalex.org/I877107187"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Wei Li","raw_affiliation_strings":["School of Computing, Engineering and the Built Environment (CEBE), University of Roehampton, London SW15 5PU, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, Engineering and the Built Environment (CEBE), University of Roehampton, London SW15 5PU, United Kingdom","institution_ids":["https://openalex.org/I877107187"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Bin Wang","orcid":"https://orcid.org/0000-0002-8800-000X"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]},{"id":"https://openalex.org/I4210092944","display_name":"Dalian University","ror":"https://ror.org/00g2ypp58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092944"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bin Wang","raw_affiliation_strings":["Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China. Electronic address: wangbin@dlu.edu.cn"],"raw_orcid":"https://orcid.org/0000-0002-8800-000X","affiliations":[{"raw_affiliation_string":"Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China. Electronic address: wangbin@dlu.edu.cn","institution_ids":["https://openalex.org/I27357992","https://openalex.org/I4210092944"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126859984","display_name":"Shihua Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shihua Zhou","raw_affiliation_strings":["Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China. Electronic address: zhoushihua@dlu.edu.cn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China. Electronic address: zhoushihua@dlu.edu.cn","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122937510","display_name":"Ben Cao","orcid":null},"institutions":[{"id":"https://openalex.org/I49332381","display_name":"University of Oklahoma Health Sciences Center","ror":"https://ror.org/0457zbj98","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I49332381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ben Cao","raw_affiliation_strings":["Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, 73104, USA. Electronic address: bencaocs@gmail.com"],"raw_orcid":"https://orcid.org/0000-0003-1503-6009","affiliations":[{"raw_affiliation_string":"Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, 73104, USA. Electronic address: bencaocs@gmail.com","institution_ids":["https://openalex.org/I49332381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5126919109","display_name":"Pan Zheng","orcid":null},"institutions":[{"id":"https://openalex.org/I185492890","display_name":"University of Canterbury","ror":"https://ror.org/03y7q9t39","country_code":"NZ","type":"education","lineage":["https://openalex.org/I185492890"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Pan Zheng","raw_affiliation_strings":["Department of Accounting and Information Systems, University of Canterbury, Christchurch 8140, New Zealand"],"raw_orcid":"https://orcid.org/0000-0002-6067-626X","affiliations":[{"raw_affiliation_string":"Department of Accounting and Information Systems, University of Canterbury, Christchurch 8140, New Zealand","institution_ids":["https://openalex.org/I185492890"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5122937510","https://openalex.org/A5126859984"],"corresponding_institution_ids":["https://openalex.org/I27357992","https://openalex.org/I4210092944","https://openalex.org/I49332381"],"apc_list":{"value":2980,"currency":"USD","value_usd":2980},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.42094946,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"176","issue":null,"first_page":"105003","last_page":"105003"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9049000144004822,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9049000144004822,"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/T10885","display_name":"Gene expression and cancer classification","score":0.05609999969601631,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.006200000178068876,"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/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5561000108718872},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.48750001192092896},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.4724999964237213},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.4004000127315521},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.3700999915599823},{"id":"https://openalex.org/keywords/transformation","display_name":"Transformation (genetics)","score":0.3682999908924103},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.35019999742507935},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.3319999873638153}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7414000034332275},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6837999820709229},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5561000108718872},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.48750001192092896},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.4724999964237213},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.4004000127315521},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38109999895095825},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.3700999915599823},{"id":"https://openalex.org/C204241405","wikidata":"https://www.wikidata.org/wiki/Q461499","display_name":"Transformation (genetics)","level":3,"score":0.3682999908924103},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.35019999742507935},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.3319999873638153},{"id":"https://openalex.org/C2779903281","wikidata":"https://www.wikidata.org/wiki/Q6888026","display_name":"Modalities","level":2,"score":0.321399986743927},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.31459999084472656},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.30140000581741333},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.29589998722076416},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.28839999437332153},{"id":"https://openalex.org/C75294576","wikidata":"https://www.wikidata.org/wiki/Q5165192","display_name":"Contextual image classification","level":3,"score":0.27300000190734863},{"id":"https://openalex.org/C28006648","wikidata":"https://www.wikidata.org/wiki/Q6934509","display_name":"Multi-task learning","level":3,"score":0.27239999175071716},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.27219998836517334},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.27059999108314514},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.2694999873638153},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.2621999979019165},{"id":"https://openalex.org/C166704113","wikidata":"https://www.wikidata.org/wiki/Q861092","display_name":"Image registration","level":3,"score":0.2590999901294708},{"id":"https://openalex.org/C152139883","wikidata":"https://www.wikidata.org/wiki/Q252973","display_name":"Mutual information","level":2,"score":0.25380000472068787}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1016/j.jbi.2026.105003","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.jbi.2026.105003","pdf_url":null,"source":{"id":"https://openalex.org/S11622463","display_name":"Journal of Biomedical Informatics","issn_l":"1532-0464","issn":["1532-0464","1532-0480"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Informatics","raw_type":"journal-article"},{"id":"pmid:41763376","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41763376","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":"Journal of biomedical informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1708588729","display_name":null,"funder_award_id":"2024-BS-267","funder_id":"https://openalex.org/F4320323086","funder_display_name":"Natural Science Foundation of Liaoning Province"},{"id":"https://openalex.org/G4201996127","display_name":null,"funder_award_id":"D23006","funder_id":"https://openalex.org/F4320336698","funder_display_name":"Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center)"},{"id":"https://openalex.org/G4457078305","display_name":null,"funder_award_id":"62572088","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G503759827","display_name":null,"funder_award_id":"LJ222411258005","funder_id":"https://openalex.org/F4320324560","funder_display_name":"Department of Education of Liaoning Province"},{"id":"https://openalex.org/G5664334659","display_name":null,"funder_award_id":"2024-MS-212","funder_id":"https://openalex.org/F4320323086","funder_display_name":"Natural Science Foundation of Liaoning Province"},{"id":"https://openalex.org/G6419423173","display_name":null,"funder_award_id":"62502063","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8507679141","display_name":null,"funder_award_id":"XLYC2403039","funder_id":"https://openalex.org/F4320324560","funder_display_name":"Department of Education of Liaoning Province"},{"id":"https://openalex.org/G8610243087","display_name":null,"funder_award_id":"62272079","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320323086","display_name":"Natural Science Foundation of Liaoning Province","ror":null},{"id":"https://openalex.org/F4320324560","display_name":"Department of Education of Liaoning Province","ror":"https://ror.org/0022v2454"},{"id":"https://openalex.org/F4320336698","display_name":"Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center)","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W2037555606","https://openalex.org/W2110065044","https://openalex.org/W2144796873","https://openalex.org/W2168056522","https://openalex.org/W2173265026","https://openalex.org/W2194775991","https://openalex.org/W2345356016","https://openalex.org/W2471536144","https://openalex.org/W2585175142","https://openalex.org/W2616282068","https://openalex.org/W2800392236","https://openalex.org/W2915848182","https://openalex.org/W2984472267","https://openalex.org/W3036882247","https://openalex.org/W3127422037","https://openalex.org/W3165120573","https://openalex.org/W3190202966","https://openalex.org/W4206931977","https://openalex.org/W4221095552","https://openalex.org/W4229033508","https://openalex.org/W4285803722","https://openalex.org/W4313424250","https://openalex.org/W4313584788","https://openalex.org/W4323037718","https://openalex.org/W4375858779","https://openalex.org/W4376114117","https://openalex.org/W4386053919","https://openalex.org/W4390661109","https://openalex.org/W4390885355","https://openalex.org/W4392126039","https://openalex.org/W4392230499","https://openalex.org/W4392874417","https://openalex.org/W4394806969","https://openalex.org/W4400324827","https://openalex.org/W4400420052","https://openalex.org/W4401450053","https://openalex.org/W4402138734","https://openalex.org/W4403394014","https://openalex.org/W4403853489","https://openalex.org/W4404849814","https://openalex.org/W4406198038","https://openalex.org/W4406870564","https://openalex.org/W4407032649","https://openalex.org/W4409040576","https://openalex.org/W4409190914","https://openalex.org/W4411079260","https://openalex.org/W4411695051","https://openalex.org/W4412030743","https://openalex.org/W4415436687","https://openalex.org/W7130542785"],"related_works":[],"abstract_inverted_index":null,"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2026-02-27T00:00:00"}
