{"id":"https://openalex.org/W3205207815","doi":"https://doi.org/10.1093/bioinformatics/btab718","title":"Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning","display_name":"Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning","publication_year":2021,"publication_date":"2021-10-16","ids":{"openalex":"https://openalex.org/W3205207815","doi":"https://doi.org/10.1093/bioinformatics/btab718","mag":"3205207815","pmid":"https://pubmed.ncbi.nlm.nih.gov/34664632"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab718","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab718","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5061677175","display_name":"Lujing Zheng","orcid":"https://orcid.org/0000-0002-8789-0995"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lujing Zheng","raw_affiliation_strings":["Department of Computer Science and Engineering, Shanghai Jiao Tong University , Shanghai 200240, China","SJTU Paris Elite Institute of Technology (SPEIT), Shanghai Jiao Tong University , Shanghai 200240, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Shanghai Jiao Tong University , Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"SJTU Paris Elite Institute of Technology (SPEIT), Shanghai Jiao Tong University , Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020612509","display_name":"Zhenhuan Liu","orcid":"https://orcid.org/0000-0001-9932-9225"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenhuan Liu","raw_affiliation_strings":["Department of Automation, Shanghai Jiao Tong University , Shanghai 200240, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Automation, Shanghai Jiao Tong University , Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100397381","display_name":"Yang Yang","orcid":"https://orcid.org/0000-0001-5720-773X"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210165726","display_name":"Shanghai Municipal Education Commission","ror":"https://ror.org/05tewj457","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210165456","https://openalex.org/I4210165726"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yang Yang","raw_affiliation_strings":["Department of Computer Science and Engineering, Shanghai Jiao Tong University , Shanghai 200240, China","Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering , Shanghai 200240, China"],"raw_orcid":"https://orcid.org/0000-0001-5720-773X","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Shanghai Jiao Tong University , Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering , Shanghai 200240, China","institution_ids":["https://openalex.org/I4210165726"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076024045","display_name":"Hong\u2010Bin Shen","orcid":"https://orcid.org/0000-0002-4029-3325"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hong-Bin Shen","raw_affiliation_strings":["Department of Automation, Shanghai Jiao Tong University , Shanghai 200240, China","Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai Jiao Tong University , Shanghai 200240, China"],"raw_orcid":"https://orcid.org/0000-0002-4029-3325","affiliations":[{"raw_affiliation_string":"Department of Automation, Shanghai Jiao Tong University , Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai Jiao Tong University , Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100397381"],"corresponding_institution_ids":["https://openalex.org/I183067930","https://openalex.org/I4210165726"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.7446,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.85344062,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"3","first_page":"746","last_page":"753"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.33090001344680786,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.33090001344680786,"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/T10691","display_name":"Retinal Development and Disorders","score":0.164000004529953,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.09989999979734421,"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/inference","display_name":"Inference","score":0.7559995651245117},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6672526597976685},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6669220924377441},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5900988578796387},{"id":"https://openalex.org/keywords/margin","display_name":"Margin (machine learning)","score":0.5871378779411316},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5714889168739319},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5496375560760498},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4841940701007843},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.453494668006897},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4510379433631897},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.43106067180633545},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4199380874633789},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.37545129656791687},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3709256649017334},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3287789821624756},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17050540447235107}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7559995651245117},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6672526597976685},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6669220924377441},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5900988578796387},{"id":"https://openalex.org/C774472","wikidata":"https://www.wikidata.org/wiki/Q6760393","display_name":"Margin (machine learning)","level":2,"score":0.5871378779411316},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5714889168739319},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5496375560760498},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4841940701007843},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.453494668006897},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4510379433631897},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.43106067180633545},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4199380874633789},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.37545129656791687},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3709256649017334},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3287789821624756},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17050540447235107},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.0},{"id":"https://openalex.org/C62649853","wikidata":"https://www.wikidata.org/wiki/Q199687","display_name":"Remote sensing","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab718","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab718","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34664632","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34664632","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G3365264765","display_name":null,"funder_award_id":"61972251","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6154466079","display_name":null,"funder_award_id":"61725302","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6731818881","display_name":null,"funder_award_id":"62073219","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W1560277551","https://openalex.org/W1939431494","https://openalex.org/W1994540622","https://openalex.org/W2001135470","https://openalex.org/W2003038417","https://openalex.org/W2029523792","https://openalex.org/W2044525257","https://openalex.org/W2058221907","https://openalex.org/W2064025098","https://openalex.org/W2065305645","https://openalex.org/W2098119224","https://openalex.org/W2114892387","https://openalex.org/W2116015974","https://openalex.org/W2116631863","https://openalex.org/W2121150592","https://openalex.org/W2122289311","https://openalex.org/W2125631472","https://openalex.org/W2126222502","https://openalex.org/W2127043599","https://openalex.org/W2129265801","https://openalex.org/W2133357122","https://openalex.org/W2144776166","https://openalex.org/W2155418475","https://openalex.org/W2156716434","https://openalex.org/W2158092584","https://openalex.org/W2161922735","https://openalex.org/W2162979438","https://openalex.org/W2167194725","https://openalex.org/W2168933277","https://openalex.org/W2169053773","https://openalex.org/W2315452447","https://openalex.org/W2748889255","https://openalex.org/W2889326414","https://openalex.org/W2912050044","https://openalex.org/W2974274234"],"related_works":["https://openalex.org/W3125011624","https://openalex.org/W1508631387","https://openalex.org/W2370917603","https://openalex.org/W2952760143","https://openalex.org/W2017776670","https://openalex.org/W2950199998","https://openalex.org/W2560421304","https://openalex.org/W2951387065","https://openalex.org/W4385727351","https://openalex.org/W4306798985"],"abstract_inverted_index":{"MOTIVATION:":[0],"Reverse":[1],"engineering":[2],"of":[3,20,33,67,158,183,190],"gene":[4,21,34,43,76,93,97],"regulatory":[5,22,94],"networks":[6],"(GRNs)":[7],"has":[8,24,58],"long":[9],"been":[10],"an":[11,134],"attractive":[12],"research":[13],"topic":[14],"in":[15,47],"system":[16],"biology.":[17],"Computational":[18],"prediction":[19],"interactions":[23,95],"remained":[25],"a":[26,88,107,151,177],"challenging":[27],"problem":[28],"due":[29],"to":[30,133,138,150],"the":[31,65,74,125,131,143,148,188],"complexity":[32],"expression":[35,44,56,77,98,126],"and":[36,54,61,111,128,155,161,172,185,194],"scarce":[37],"information":[38,63],"resources.":[39],"The":[40,102],"high-throughput":[41],"spatial":[42,55,75],"data,":[45],"like":[46],"situ":[48],"hybridization":[49],"images":[50,127],"that":[51,167],"exhibit":[52],"temporal":[53],"patterns,":[57],"provided":[59],"abundant":[60],"reliable":[62],"for":[64,72,91,124,187,204],"inference":[66],"GRNs.":[68],"However,":[69],"computational":[70],"tools":[71],"analyzing":[73],"data":[78,214],"are":[79,215],"highly":[80],"underdeveloped.":[81],"RESULTS:":[82],"In":[83],"this":[84],"study,":[85],"we":[86],"develop":[87],"new":[89],"method":[90,103,149],"identifying":[92],"from":[96],"images,":[99],"called":[100],"ConGRI.":[101],"is":[104],"featured":[105],"by":[106,176],"contrastive":[108],"learning":[109,174],"scheme":[110],"deep":[112,173],"Siamese":[113],"convolutional":[114],"neural":[115,136],"network":[116,137],"architecture,":[117],"which":[118,180],"automatically":[119],"learns":[120],"high-level":[121],"feature":[122],"embeddings":[123,132],"then":[129],"feeds":[130],"artificial":[135],"determine":[139],"whether":[140],"or":[141],"not":[142],"interaction":[144],"exists.":[145],"We":[146],"apply":[147],"Drosophila":[152,205],"embryogenesis":[153],"dataset":[154],"identify":[156],"GRNs":[157,189],"eye":[159,192,206],"development":[160,193],"mesoderm":[162,195],"development.":[163,207],"Experimental":[164],"results":[165],"show":[166],"ConGRI":[168],"outperforms":[169],"previous":[170],"traditional":[171],"methods":[175],"large":[178],"margin,":[179],"achieves":[181],"accuracies":[182],"76.7%":[184],"68.7%":[186],"early":[191],"development,":[196],"respectively.":[197],"It":[198],"also":[199],"reveals":[200],"some":[201],"master":[202],"regulators":[203],"AVAILABILITYAND":[208],"IMPLEMENTATION:":[209],"https://github.com/lugimzheng/ConGRI.":[210],"SUPPLEMENTARY":[211],"INFORMATION:":[212],"Supplementary":[213],"available":[216],"at":[217],"Bioinformatics":[218],"online.":[219]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}