{"id":"https://openalex.org/W4412454113","doi":"https://doi.org/10.1093/bioinformatics/btaf217","title":"Prediction of gene regulatory connections with joint single-cell foundation models and graph-based learning","display_name":"Prediction of gene regulatory connections with joint single-cell foundation models and graph-based learning","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412454113","doi":"https://doi.org/10.1093/bioinformatics/btaf217","pmid":"https://pubmed.ncbi.nlm.nih.gov/40662821"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf217","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf217","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i619/63745599/btaf217.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i619/63745599/btaf217.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107401847","display_name":"Sindhura Kommu","orcid":null},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sindhura Kommu","raw_affiliation_strings":["Department of Computer Science, Virginia Tech , Blacksburg, VA 24060,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech , Blacksburg, VA 24060,","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104668418","display_name":"Yizhi Wang","orcid":"https://orcid.org/0000-0001-9456-0743"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yizhi Wang","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Virginia Tech , Arlington, VA 22203,"],"raw_orcid":"https://orcid.org/0000-0001-9456-0743","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Virginia Tech , Arlington, VA 22203,","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100372002","display_name":"Yue Wang","orcid":"https://orcid.org/0000-0002-1788-1102"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yue Wang","raw_affiliation_strings":["Department of Electrical and Computer Engineering, Virginia Tech , Arlington, VA 22203,"],"raw_orcid":"https://orcid.org/0000-0002-1788-1102","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Virginia Tech , Arlington, VA 22203,","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100328989","display_name":"Xuan Wang","orcid":"https://orcid.org/0000-0002-1381-8958"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xuan Wang","raw_affiliation_strings":["Department of Computer Science, Virginia Tech , Blacksburg, VA 24060,"],"raw_orcid":"https://orcid.org/0000-0002-1381-8958","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech , Blacksburg, VA 24060,","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9736,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.75335027,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"41","issue":"Supplement_1","first_page":"i619","last_page":"i627"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9876999855041504,"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":0.9876999855041504,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.002899999963119626,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0019000000320374966,"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":0.7344093918800354},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6965811252593994},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6669430732727051},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.575283944606781},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.542356550693512},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.45747801661491394},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.44849610328674316},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4403461217880249},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32612115144729614},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20273837447166443},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1563170850276947},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.14569365978240967},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.10549241304397583}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7344093918800354},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6965811252593994},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6669430732727051},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.575283944606781},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.542356550693512},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.45747801661491394},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.44849610328674316},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4403461217880249},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32612115144729614},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20273837447166443},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1563170850276947},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14569365978240967},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.10549241304397583},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D000465","descriptor_name":"Algorithms","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":"D000465","descriptor_name":"Algorithms","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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},{"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},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf217","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf217","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i619/63745599/btaf217.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40662821","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40662821","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},{"id":"pmh:oai:pubmedcentral.nih.gov:12261397","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12261397","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf217","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf217","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i619/63745599/btaf217.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1184232923","display_name":null,"funder_award_id":"CA271891","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1494599793","display_name":null,"funder_award_id":"U19 NS123719","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G2721467841","display_name":null,"funder_award_id":"R01 HL111362","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G6049146910","display_name":null,"funder_award_id":"R01 MH110504","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G7435554953","display_name":null,"funder_award_id":"HL111362","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7480935274","display_name":null,"funder_award_id":"MH110504","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7895013820","display_name":null,"funder_award_id":"NS123719","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320307791","display_name":"Cisco Systems","ror":"https://ror.org/03yt1ez60"},{"id":"https://openalex.org/F4320312143","display_name":"National Centre for Supercomputing Applications","ror":"https://ror.org/03r10zj06"},{"id":"https://openalex.org/F4320317457","display_name":"Children's National Hospital","ror":"https://ror.org/03wa2q724"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412454113.pdf","grobid_xml":"https://content.openalex.org/works/W4412454113.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1175879704","https://openalex.org/W1964925945","https://openalex.org/W1967327758","https://openalex.org/W1968193820","https://openalex.org/W2061425021","https://openalex.org/W2076513103","https://openalex.org/W2107793443","https://openalex.org/W2112752664","https://openalex.org/W2118993986","https://openalex.org/W2134128560","https://openalex.org/W2259938310","https://openalex.org/W2612690371","https://openalex.org/W2901292166","https://openalex.org/W2949676527","https://openalex.org/W2951424836","https://openalex.org/W2952631022","https://openalex.org/W2996140569","https://openalex.org/W2997831639","https://openalex.org/W3193795275","https://openalex.org/W4290930137","https://openalex.org/W4294991206","https://openalex.org/W4297243391","https://openalex.org/W4378838672","https://openalex.org/W4388870182","https://openalex.org/W4392168151","https://openalex.org/W4399387478"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W2130974462","https://openalex.org/W2028665553","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],"Single-cell":[1],"RNA":[2],"sequencing":[3],"(scRNA-seq)":[4],"data":[5,39,58],"offers":[6],"unprecedented":[7],"opportunities":[8],"to":[9,71,108,151,183],"infer":[10],"gene":[11,86,95,106,189,210],"regulatory":[12,69,87,96,111,190,211],"networks":[13],"(GRNs)":[14],"at":[15,24,104,250],"a":[16,85,114,122,148,185,197],"fine-grained":[17],"resolution,":[18],"shedding":[19],"light":[20],"on":[21,67,164,224,238],"cellular":[22],"phenotypes":[23],"the":[25,29,94,105,235],"molecular":[26],"level.":[27],"However,":[28,113],"high":[30,76],"sparsity,":[31],"noise,":[32],"and":[33,45,74,135,144,168,199],"dropout":[34],"events":[35],"inherent":[36],"in":[37,52,78,138,141,218],"scRNA-seq":[38,166,226],"pose":[40],"significant":[41],"challenges":[42],"for":[43,188,209],"accurate":[44],"reliable":[46],"GRN":[47,79],"inference.":[48],"The":[49,245],"rapid":[50],"growth":[51],"experimentally":[53,133],"validated":[54],"transcription":[55],"factor-DNA":[56],"binding":[57,128],"has":[59],"enabled":[60],"supervised":[61,118],"machine":[62],"learning":[63,101,119,146,182,208],"methods,":[64],"which":[65,130],"rely":[66],"known":[68,126,169],"interactions":[70],"learn":[72],"patterns,":[73],"achieve":[75],"accuracy":[77],"inference":[80],"by":[81,100],"framing":[82],"it":[83],"as":[84,170],"link":[88,97,191,212],"prediction":[89,98],"task.":[90],"This":[91],"study":[92],"addresses":[93],"problem":[99],"vectorized":[102],"representations":[103],"level":[107],"predict":[109],"missing":[110],"interactions.":[112],"higher":[115],"performance":[116],"of":[117,125],"methods":[120,223,237],"requires":[121],"large":[123],"amount":[124],"TF-DNA":[127],"data,":[129],"is":[131,231,248],"often":[132],"expensive":[134],"therefore":[136],"limited":[137],"amount.":[139],"Advances":[140],"large-scale":[142,160],"pre-training":[143],"transfer":[145],"provide":[147],"transformative":[149],"opportunity":[150],"address":[152],"this":[153,156],"challenge.":[154],"In":[155],"study,":[157],"we":[158],"leverage":[159],"pre-trained":[161],"models,":[162],"trained":[163],"extensive":[165],"datasets":[167],"single-cell":[171],"foundation":[172,187],"models":[173,176],"(scFMs).":[174],"These":[175],"are":[177],"combined":[178],"with":[179,205,220],"joint":[180,206],"graph-based":[181,207],"establish":[184],"robust":[186,233],"prediction.":[192,213],"RESULTS:":[193],"We":[194],"propose":[195],"scRegNet,":[196],"novel":[198],"effective":[200],"framework":[201],"that":[202],"leverages":[203],"scFMs":[204],"scRegNet":[214,230],"achieves":[215],"state-of-the-art":[216],"results":[217],"comparison":[219],"nine":[221],"baseline":[222,236],"seven":[225],"benchmark":[227],"datasets.":[228],"Additionally,":[229],"more":[232],"than":[234],"noisy":[239],"training":[240],"data.":[241],"AVAILABILITY":[242],"AND":[243],"IMPLEMENTATION:":[244],"source":[246],"code":[247],"available":[249],"https://github.com/sindhura-cs/scRegNet.":[251]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
