{"id":"https://openalex.org/W7125782364","doi":"https://doi.org/10.3389/fbinf.2025.1715821","title":"Applications of AI to single-cell and spatial transcriptomics: current state-of-the-art and challenges","display_name":"Applications of AI to single-cell and spatial transcriptomics: current state-of-the-art and challenges","publication_year":2026,"publication_date":"2026-01-27","ids":{"openalex":"https://openalex.org/W7125782364","doi":"https://doi.org/10.3389/fbinf.2025.1715821","pmid":"https://pubmed.ncbi.nlm.nih.gov/41676376"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1715821","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1715821","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1715821/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1715821/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5123951204","display_name":"Boris Tchatchoua Ngassam","orcid":null},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Boris Tchatchoua Ngassam","raw_affiliation_strings":["Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123934120","display_name":"Huilin Niu","orcid":null},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Huilin Niu","raw_affiliation_strings":["Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123946807","display_name":"Sunny Pang","orcid":null},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Sunny Pang","raw_affiliation_strings":["Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123993393","display_name":"Valeryia Shydlouskaya","orcid":null},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Valeryia Shydlouskaya","raw_affiliation_strings":["Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124033603","display_name":"Tallulah S. Andrews","orcid":null},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Tallulah S. Andrews","raw_affiliation_strings":["Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario","Department of Computer Science, University of Western Ontario"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"Department of Computer Science, University of Western Ontario","institution_ids":["https://openalex.org/I125749732"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5124033603"],"corresponding_institution_ids":["https://openalex.org/I125749732"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.16968461,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":null,"first_page":"1715821","last_page":"1715821"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9993000030517578,"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":0.9993000030517578,"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/T12859","display_name":"Cell Image Analysis Techniques","score":9.999999747378752e-05,"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/T14427","display_name":"Environmental Monitoring and Data Management","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1907","display_name":"Geology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.4611999988555908},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.42010000348091125},{"id":"https://openalex.org/keywords/big-data","display_name":"Big data","score":0.40950000286102295},{"id":"https://openalex.org/keywords/data-exploration","display_name":"Data exploration","score":0.36000001430511475},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.35510000586509705},{"id":"https://openalex.org/keywords/applications-of-artificial-intelligence","display_name":"Applications of artificial intelligence","score":0.35499998927116394}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6399000287055969},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.48350000381469727},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.4611999988555908},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.436599999666214},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.42010000348091125},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4165000021457672},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.40950000286102295},{"id":"https://openalex.org/C2780977526","wikidata":"https://www.wikidata.org/wiki/Q42417149","display_name":"Data exploration","level":3,"score":0.36000001430511475},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.35510000586509705},{"id":"https://openalex.org/C157170001","wikidata":"https://www.wikidata.org/wiki/Q4781507","display_name":"Applications of artificial intelligence","level":2,"score":0.35499998927116394},{"id":"https://openalex.org/C148043351","wikidata":"https://www.wikidata.org/wiki/Q4456944","display_name":"Current (fluid)","level":2,"score":0.33660000562667847},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33489999175071716},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.3253999948501587},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.31200000643730164},{"id":"https://openalex.org/C64754055","wikidata":"https://www.wikidata.org/wiki/Q7574053","display_name":"Spatial contextual awareness","level":2,"score":0.2655999958515167},{"id":"https://openalex.org/C138827492","wikidata":"https://www.wikidata.org/wiki/Q6661985","display_name":"Data processing","level":2,"score":0.26489999890327454},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.25200000405311584}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2025.1715821","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1715821","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1715821/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41676376","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41676376","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:11694136","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12886477","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12886477","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12886477/","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":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1715821","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1715821","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1715821/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7125782364.pdf","grobid_xml":"https://content.openalex.org/works/W7125782364.grobid-xml"},"referenced_works_count":232,"referenced_works":["https://openalex.org/W1985987855","https://openalex.org/W2042789810","https://openalex.org/W2069089843","https://openalex.org/W2107665951","https://openalex.org/W2130430382","https://openalex.org/W2131681506","https://openalex.org/W2471536144","https://openalex.org/W2510850936","https://openalex.org/W2591733518","https://openalex.org/W2739329039","https://openalex.org/W2739492614","https://openalex.org/W2753908609","https://openalex.org/W2766437506","https://openalex.org/W2792693509","https://openalex.org/W2794480084","https://openalex.org/W2794521141","https://openalex.org/W2796170779","https://openalex.org/W2800392236","https://openalex.org/W2805619986","https://openalex.org/W2889236955","https://openalex.org/W2896457183","https://openalex.org/W2897249806","https://openalex.org/W2899348912","https://openalex.org/W2901677030","https://openalex.org/W2907783748","https://openalex.org/W2915848182","https://openalex.org/W2935703330","https://openalex.org/W2937917790","https://openalex.org/W2942108345","https://openalex.org/W2942610007","https://openalex.org/W2948978827","https://openalex.org/W2949177718","https://openalex.org/W2949237386","https://openalex.org/W2951381561","https://openalex.org/W2952001873","https://openalex.org/W2952240309","https://openalex.org/W2962897886","https://openalex.org/W2965552103","https://openalex.org/W2971048213","https://openalex.org/W2971653850","https://openalex.org/W2972926980","https://openalex.org/W2978541146","https://openalex.org/W2980495984","https://openalex.org/W2981024428","https://openalex.org/W2984472267","https://openalex.org/W2992151131","https://openalex.org/W2994000519","https://openalex.org/W2996140569","https://openalex.org/W3000145506","https://openalex.org/W3000350302","https://openalex.org/W3002417351","https://openalex.org/W3005127469","https://openalex.org/W3007935255","https://openalex.org/W3012498554","https://openalex.org/W3027051073","https://openalex.org/W3037216933","https://openalex.org/W3044352330","https://openalex.org/W3047141442","https://openalex.org/W3080162757","https://openalex.org/W3108118546","https://openalex.org/W3111521801","https://openalex.org/W3114078084","https://openalex.org/W3121168830","https://openalex.org/W3124439729","https://openalex.org/W3126492421","https://openalex.org/W3129866267","https://openalex.org/W3131634425","https://openalex.org/W3132357920","https://openalex.org/W3132661792","https://openalex.org/W3135168232","https://openalex.org/W3137285774","https://openalex.org/W3138479716","https://openalex.org/W3146944767","https://openalex.org/W3161009639","https://openalex.org/W3164839005","https://openalex.org/W3165120573","https://openalex.org/W3165190053","https://openalex.org/W3173845757","https://openalex.org/W3176693948","https://openalex.org/W3192169136","https://openalex.org/W3194520274","https://openalex.org/W3194730353","https://openalex.org/W3196650609","https://openalex.org/W3198628780","https://openalex.org/W3203588026","https://openalex.org/W3208940117","https://openalex.org/W3210860076","https://openalex.org/W3214596602","https://openalex.org/W3216323060","https://openalex.org/W4200581587","https://openalex.org/W4205206193","https://openalex.org/W4205817967","https://openalex.org/W4206092375","https://openalex.org/W4210583065","https://openalex.org/W4210683641","https://openalex.org/W4210712647","https://openalex.org/W4212836561","https://openalex.org/W4221092226","https://openalex.org/W4223964809","https://openalex.org/W4224470052","https://openalex.org/W4225278475","https://openalex.org/W4225591005","https://openalex.org/W4225598893","https://openalex.org/W4226192560","https://openalex.org/W4226206033","https://openalex.org/W4280533477","https://openalex.org/W4280631255","https://openalex.org/W4281618613","https://openalex.org/W4282963182","https://openalex.org/W4283579418","https://openalex.org/W4283704002","https://openalex.org/W4285013048","https://openalex.org/W4289745500","https://openalex.org/W4292121951","https://openalex.org/W4294631386","https://openalex.org/W4295880122","https://openalex.org/W4297162533","https://openalex.org/W4297243391","https://openalex.org/W4297733535","https://openalex.org/W4298289240","https://openalex.org/W4302362633","https://openalex.org/W4304140852","https://openalex.org/W4306406844","https://openalex.org/W4306742555","https://openalex.org/W4307953700","https://openalex.org/W4308834549","https://openalex.org/W4310437432","https://openalex.org/W4311404503","https://openalex.org/W4311415873","https://openalex.org/W4316096017","https://openalex.org/W4319049324","https://openalex.org/W4319604654","https://openalex.org/W4320487182","https://openalex.org/W4322738920","https://openalex.org/W4322754344","https://openalex.org/W4323926037","https://openalex.org/W4328048773","https://openalex.org/W4362521490","https://openalex.org/W4362521742","https://openalex.org/W4362701808","https://openalex.org/W4366526178","https://openalex.org/W4377121531","https://openalex.org/W4377157608","https://openalex.org/W4378212119","https://openalex.org/W4378838672","https://openalex.org/W4382632237","https://openalex.org/W4382877140","https://openalex.org/W4385163943","https://openalex.org/W4385245566","https://openalex.org/W4385350654","https://openalex.org/W4386692444","https://openalex.org/W4386709519","https://openalex.org/W4386791134","https://openalex.org/W4386801555","https://openalex.org/W4386923465","https://openalex.org/W4386983969","https://openalex.org/W4387906388","https://openalex.org/W4388374690","https://openalex.org/W4388899046","https://openalex.org/W4388997570","https://openalex.org/W4389135772","https://openalex.org/W4389943654","https://openalex.org/W4390066212","https://openalex.org/W4390531707","https://openalex.org/W4390639744","https://openalex.org/W4391262644","https://openalex.org/W4391886418","https://openalex.org/W4391915536","https://openalex.org/W4392168151","https://openalex.org/W4392868645","https://openalex.org/W4392874417","https://openalex.org/W4392899361","https://openalex.org/W4392947521","https://openalex.org/W4393055826","https://openalex.org/W4393153069","https://openalex.org/W4393392393","https://openalex.org/W4395010670","https://openalex.org/W4398240043","https://openalex.org/W4399141090","https://openalex.org/W4399387478","https://openalex.org/W4399389044","https://openalex.org/W4399830390","https://openalex.org/W4399892951","https://openalex.org/W4399970333","https://openalex.org/W4400045958","https://openalex.org/W4400152666","https://openalex.org/W4400674289","https://openalex.org/W4400801214","https://openalex.org/W4401332722","https://openalex.org/W4401412190","https://openalex.org/W4401450053","https://openalex.org/W4401914352","https://openalex.org/W4402135155","https://openalex.org/W4402348973","https://openalex.org/W4402827865","https://openalex.org/W4403146619","https://openalex.org/W4404356143","https://openalex.org/W4404400417","https://openalex.org/W4404566628","https://openalex.org/W4404566935","https://openalex.org/W4404860427","https://openalex.org/W4405021966","https://openalex.org/W4405096489","https://openalex.org/W4406023557","https://openalex.org/W4406221865","https://openalex.org/W4406298433","https://openalex.org/W4406844022","https://openalex.org/W4407053453","https://openalex.org/W4407360292","https://openalex.org/W4407869127","https://openalex.org/W4408033718","https://openalex.org/W4408069179","https://openalex.org/W4408738017","https://openalex.org/W4409356518","https://openalex.org/W4410153887","https://openalex.org/W4410245579","https://openalex.org/W4410368857","https://openalex.org/W4410521040","https://openalex.org/W4411200722","https://openalex.org/W4411279214","https://openalex.org/W4411670013","https://openalex.org/W4412072659","https://openalex.org/W4412152249","https://openalex.org/W4412702914","https://openalex.org/W4412815977","https://openalex.org/W4412867059","https://openalex.org/W4412869991","https://openalex.org/W4414380203","https://openalex.org/W4415101992","https://openalex.org/W4415306707","https://openalex.org/W4415428083","https://openalex.org/W6910634847"],"related_works":[],"abstract_inverted_index":{"Artificial":[0],"intelligence":[1],"(AI)":[2],"has":[3],"become":[4],"a":[5],"common":[6,70],"tool":[7],"for":[8,39,50,105,114],"bioinformatics,":[9],"with":[10],"hundreds":[11],"of":[12,24,34],"methods":[13],"published":[14],"in":[15],"recent":[16],"years.":[17],"Due":[18],"to":[19,61,102],"the":[20,35],"training":[21],"data":[22,77,79],"demands":[23],"deep-learning":[25],"algorithms,":[26],"high-throughput":[27],"single-cell":[28,51,91],"and":[29,52,56,89,92,108],"spatial":[30,53,93],"transcriptomics":[31,54,94],"is":[32,47],"one":[33],"most":[36],"popular":[37],"areas":[38],"these":[40,58],"applications.":[41],"Here":[42],"we":[43],"review":[44],"how":[45,57],"AI":[46],"being":[48],"used":[49],"analysis,":[55],"approaches":[59],"compare":[60],"alternative":[62],"statistical":[63],"or":[64],"heuristic-based":[65],"methods.":[66],"We":[67,96],"explored":[68],"10":[69],"analysis":[71],"tasks:":[72],"dimensionality":[73],"reduction,":[74],"cross-dataset":[75],"integration,":[76,88],"denoising,":[78],"augmentation,":[80],"deconvolution,":[81],"cell-cell":[82],"interactions,":[83],"transcriptional":[84],"velocity,":[85],"transcriptomic-chromatin":[86],"accessibility":[87],"integrating":[90],"modalities.":[95],"highlight":[97],"which":[98,109],"algorithms":[99],"are":[100,110],"likely":[101],"be":[103],"useful":[104],"discovery":[106],"researchers,":[107],"not":[111],"yet":[112],"ready":[113],"general":[115],"research":[116],"use.":[117]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2026-01-28T00:00:00"}
