{"id":"https://openalex.org/W4391262644","doi":"https://doi.org/10.1145/3641284","title":"Deep Learning in Single-cell Analysis","display_name":"Deep Learning in Single-cell Analysis","publication_year":2024,"publication_date":"2024-01-26","ids":{"openalex":"https://openalex.org/W4391262644","doi":"https://doi.org/10.1145/3641284"},"language":"en","primary_location":{"id":"doi:10.1145/3641284","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3641284","pdf_url":null,"source":{"id":"https://openalex.org/S2492086750","display_name":"ACM Transactions on Intelligent Systems and Technology","issn_l":"2157-6904","issn":["2157-6904","2157-6912"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Intelligent Systems and Technology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071280526","display_name":"Dylan Molho","orcid":"https://orcid.org/0009-0008-9507-9693"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dylan Molho","raw_affiliation_strings":["Michigan State University, East Lansing, USA"],"affiliations":[{"raw_affiliation_string":"Michigan State University, East Lansing, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038387579","display_name":"Jiayuan Ding","orcid":"https://orcid.org/0000-0001-5783-0062"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiayuan Ding","raw_affiliation_strings":["Michigan State University, East Lansing, USA"],"affiliations":[{"raw_affiliation_string":"Michigan State University, East Lansing, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053741358","display_name":"Wenzhuo Tang","orcid":"https://orcid.org/0000-0002-7038-5765"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenzhuo Tang","raw_affiliation_strings":["Michigan State University, East Lansing, USA"],"affiliations":[{"raw_affiliation_string":"Michigan State University, East Lansing, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101427807","display_name":"Zhaoheng Li","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhaoheng Li","raw_affiliation_strings":["University of Washington, Seattle, USA"],"affiliations":[{"raw_affiliation_string":"University of Washington, Seattle, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I58610484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052257654","display_name":"Hongzhi Wen","orcid":"https://orcid.org/0000-0003-0775-8538"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hongzhi Wen","raw_affiliation_strings":["Michigan State University, East Lansing, USA"],"affiliations":[{"raw_affiliation_string":"Michigan State University, East Lansing, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100328544","display_name":"Yixin Wang","orcid":"https://orcid.org/0000-0002-8062-0765"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yixin Wang","raw_affiliation_strings":["Stanford University, Stanford, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University, Stanford, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040456043","display_name":"Julian Venegas","orcid":"https://orcid.org/0000-0001-8389-4131"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julian Venegas","raw_affiliation_strings":["Michigan State University, East Lansing, USA"],"affiliations":[{"raw_affiliation_string":"Michigan State University, East Lansing, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100758371","display_name":"Wei Jin","orcid":"https://orcid.org/0000-0002-5054-954X"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Jin","raw_affiliation_strings":["Emory University, Atlanta, USA"],"affiliations":[{"raw_affiliation_string":"Emory University, Atlanta, USA","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062057891","display_name":"Renming Liu","orcid":"https://orcid.org/0000-0002-6025-6492"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Renming Liu","raw_affiliation_strings":["Michigan State University, East Lansing, USA"],"affiliations":[{"raw_affiliation_string":"Michigan State University, East Lansing, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078927801","display_name":"Runze Su","orcid":"https://orcid.org/0000-0001-9631-3711"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Runze Su","raw_affiliation_strings":["Michigan State University, East Lansing, USA"],"affiliations":[{"raw_affiliation_string":"Michigan State University, East Lansing, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103238929","display_name":"Patrick Danaher","orcid":"https://orcid.org/0000-0002-2844-5883"},"institutions":[{"id":"https://openalex.org/I4210099129","display_name":"Nanostring Technologies (United States)","ror":"https://ror.org/00xzdzk88","country_code":"US","type":"company","lineage":["https://openalex.org/I4210099129"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patrick Danaher","raw_affiliation_strings":["NanoString Technologies, Seattle, USA"],"affiliations":[{"raw_affiliation_string":"NanoString Technologies, Seattle, USA","institution_ids":["https://openalex.org/I4210099129","https://openalex.org/I58610484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111589313","display_name":"Robert Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I1330063522","display_name":"Johnson & Johnson (United States)","ror":"https://ror.org/03qd7mz70","country_code":"US","type":"company","lineage":["https://openalex.org/I1330063522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Yang","raw_affiliation_strings":["Johnson &amp; Johnson, New Brunswick, USA"],"affiliations":[{"raw_affiliation_string":"Johnson &amp; Johnson, New Brunswick, USA","institution_ids":["https://openalex.org/I1330063522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012090861","display_name":"Yu L. Lei","orcid":"https://orcid.org/0000-0002-9868-9824"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu Leo Lei","raw_affiliation_strings":["University of Michigan, Ann Arbor, USA"],"affiliations":[{"raw_affiliation_string":"University of Michigan, Ann Arbor, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039712353","display_name":"Yuying Xie","orcid":"https://orcid.org/0000-0002-1049-2219"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuying Xie","raw_affiliation_strings":["Michigan State University, East Lansing, USA"],"affiliations":[{"raw_affiliation_string":"Michigan State University, East Lansing, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040639891","display_name":"Jiliang Tang","orcid":"https://orcid.org/0000-0001-7125-3898"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiliang Tang","raw_affiliation_strings":["Michigan State University, East Lansing, USA"],"affiliations":[{"raw_affiliation_string":"Michigan State University, East Lansing, USA","institution_ids":["https://openalex.org/I87216513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":15,"corresponding_author_ids":["https://openalex.org/A5071280526"],"corresponding_institution_ids":["https://openalex.org/I87216513"],"apc_list":null,"apc_paid":null,"fwci":4.6785,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.95574266,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"15","issue":"3","first_page":"1","last_page":"62"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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":1.0,"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":0.9991999864578247,"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/T11393","display_name":"Biosensors and Analytical Detection","score":0.9948999881744385,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.857873260974884},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.7807366251945496},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6876004934310913},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5386908054351807},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5064691305160522},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.479304701089859},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.45281970500946045}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.857873260974884},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.7807366251945496},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6876004934310913},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5386908054351807},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5064691305160522},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.479304701089859},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.45281970500946045},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"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/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3641284","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3641284","pdf_url":null,"source":{"id":"https://openalex.org/S2492086750","display_name":"ACM Transactions on Intelligent Systems and Technology","issn_l":"2157-6904","issn":["2157-6904","2157-6912"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Intelligent Systems and Technology","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2770860543","display_name":null,"funder_award_id":"UO1DE029255, R01DE026728, R01HL166508, and U01DE033330","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G877152271","display_name":null,"funder_award_id":"W911NF-21-1-0198","funder_id":"https://openalex.org/F4320338281","funder_display_name":"Army Research Office"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320338281","display_name":"Army Research Office","ror":"https://ror.org/05epdh915"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":367,"referenced_works":["https://openalex.org/W65738273","https://openalex.org/W70742678","https://openalex.org/W637153065","https://openalex.org/W1479753158","https://openalex.org/W1498436455","https://openalex.org/W1538131130","https://openalex.org/W1580018887","https://openalex.org/W1873848535","https://openalex.org/W1901129140","https://openalex.org/W1903029394","https://openalex.org/W1905036359","https://openalex.org/W1924770834","https://openalex.org/W1939689156","https://openalex.org/W1964963969","https://openalex.org/W1967327758","https://openalex.org/W1978486653","https://openalex.org/W1979594866","https://openalex.org/W1981233250","https://openalex.org/W1988391018","https://openalex.org/W1989762673","https://openalex.org/W1990523483","https://openalex.org/W1995341919","https://openalex.org/W1998871699","https://openalex.org/W1999478182","https://openalex.org/W2013571070","https://openalex.org/W2015255108","https://openalex.org/W2027061207","https://openalex.org/W2053129129","https://openalex.org/W2061567983","https://openalex.org/W2064675550","https://openalex.org/W2065340354","https://openalex.org/W2069143585","https://openalex.org/W2070339716","https://openalex.org/W2073307618","https://openalex.org/W2081098333","https://openalex.org/W2086187432","https://openalex.org/W2089923519","https://openalex.org/W2090461073","https://openalex.org/W2097455931","https://openalex.org/W2100383758","https://openalex.org/W2109890799","https://openalex.org/W2115108153","https://openalex.org/W2116341502","https://openalex.org/W2117757143","https://openalex.org/W2121469024","https://openalex.org/W2121901998","https://openalex.org/W2123273050","https://openalex.org/W2124260943","https://openalex.org/W2125310307","https://openalex.org/W2126537932","https://openalex.org/W2128227827","https://openalex.org/W2129872577","https://openalex.org/W2131681506","https://openalex.org/W2133811295","https://openalex.org/W2135937351","https://openalex.org/W2136680615","https://openalex.org/W2148489082","https://openalex.org/W2149573463","https://openalex.org/W2152656267","https://openalex.org/W2157150618","https://openalex.org/W2160041854","https://openalex.org/W2161160262","https://openalex.org/W2180374961","https://openalex.org/W2186615578","https://openalex.org/W2193067168","https://openalex.org/W2193667971","https://openalex.org/W2194775991","https://openalex.org/W2222000795","https://openalex.org/W2286667211","https://openalex.org/W2301358467","https://openalex.org/W2343237073","https://openalex.org/W2467628122","https://openalex.org/W2471536144","https://openalex.org/W2485836676","https://openalex.org/W2519887557","https://openalex.org/W2526262591","https://openalex.org/W2533012945","https://openalex.org/W2548342201","https://openalex.org/W2549518011","https://openalex.org/W2550179689","https://openalex.org/W2562003322","https://openalex.org/W2565639579","https://openalex.org/W2591733518","https://openalex.org/W2598326928","https://openalex.org/W2599879124","https://openalex.org/W2602582876","https://openalex.org/W2610509384","https://openalex.org/W2612519453","https://openalex.org/W2613282090","https://openalex.org/W2620296437","https://openalex.org/W2621109613","https://openalex.org/W2624431344","https://openalex.org/W2739492614","https://openalex.org/W2747545374","https://openalex.org/W2749963879","https://openalex.org/W2751468300","https://openalex.org/W2752378502","https://openalex.org/W2752426001","https://openalex.org/W2753908609","https://openalex.org/W2765407302","https://openalex.org/W2766736793","https://openalex.org/W2773348346","https://openalex.org/W2778345128","https://openalex.org/W2782146634","https://openalex.org/W2783406084","https://openalex.org/W2785264903","https://openalex.org/W2788242942","https://openalex.org/W2788348358","https://openalex.org/W2788592841","https://openalex.org/W2792647356","https://openalex.org/W2792693509","https://openalex.org/W2793965282","https://openalex.org/W2794083495","https://openalex.org/W2794521141","https://openalex.org/W2796170779","https://openalex.org/W2798122215","https://openalex.org/W2798368076","https://openalex.org/W2798559642","https://openalex.org/W2799796757","https://openalex.org/W2802349965","https://openalex.org/W2804460316","https://openalex.org/W2832881433","https://openalex.org/W2886347923","https://openalex.org/W2889236955","https://openalex.org/W2891826157","https://openalex.org/W2892341857","https://openalex.org/W2894687190","https://openalex.org/W2898718502","https://openalex.org/W2899235059","https://openalex.org/W2900510132","https://openalex.org/W2900569176","https://openalex.org/W2900614390","https://openalex.org/W2901586501","https://openalex.org/W2901677030","https://openalex.org/W2907514116","https://openalex.org/W2911964244","https://openalex.org/W2914568698","https://openalex.org/W2915848182","https://openalex.org/W2917457305","https://openalex.org/W2918342466","https://openalex.org/W2919779091","https://openalex.org/W2921092847","https://openalex.org/W2923300855","https://openalex.org/W2924067995","https://openalex.org/W2937917790","https://openalex.org/W2938910572","https://openalex.org/W2939093246","https://openalex.org/W2939939530","https://openalex.org/W2941148705","https://openalex.org/W2942380588","https://openalex.org/W2943401499","https://openalex.org/W2943865428","https://openalex.org/W2948978827","https://openalex.org/W2949148097","https://openalex.org/W2949177718","https://openalex.org/W2949236943","https://openalex.org/W2949238013","https://openalex.org/W2949637707","https://openalex.org/W2950030509","https://openalex.org/W2951381561","https://openalex.org/W2951444558","https://openalex.org/W2951506174","https://openalex.org/W2951699355","https://openalex.org/W2951737297","https://openalex.org/W2951876422","https://openalex.org/W2951914955","https://openalex.org/W2952303649","https://openalex.org/W2952602120","https://openalex.org/W2952650776","https://openalex.org/W2952935243","https://openalex.org/W2953036966","https://openalex.org/W2953405766","https://openalex.org/W2953866345","https://openalex.org/W2959295202","https://openalex.org/W2963037989","https://openalex.org/W2963150697","https://openalex.org/W2963803174","https://openalex.org/W2964015378","https://openalex.org/W2964227007","https://openalex.org/W2964643116","https://openalex.org/W2965552103","https://openalex.org/W2966415767","https://openalex.org/W2966569571","https://openalex.org/W2970971581","https://openalex.org/W2971398276","https://openalex.org/W2971653850","https://openalex.org/W2973034691","https://openalex.org/W2977512847","https://openalex.org/W2978426779","https://openalex.org/W2979301772","https://openalex.org/W2979482445","https://openalex.org/W2979670855","https://openalex.org/W2979911343","https://openalex.org/W2983968250","https://openalex.org/W2985765936","https://openalex.org/W2993905360","https://openalex.org/W2995410603","https://openalex.org/W2995430918","https://openalex.org/W2995942064","https://openalex.org/W2996489182","https://openalex.org/W2998334079","https://openalex.org/W2999977864","https://openalex.org/W3001485171","https://openalex.org/W3003185417","https://openalex.org/W3003802434","https://openalex.org/W3004512212","https://openalex.org/W3005127469","https://openalex.org/W3005494042","https://openalex.org/W3006533027","https://openalex.org/W3007573310","https://openalex.org/W3009370296","https://openalex.org/W3009560560","https://openalex.org/W3009609875","https://openalex.org/W3010560083","https://openalex.org/W3011667710","https://openalex.org/W3012788672","https://openalex.org/W3013151148","https://openalex.org/W3016020856","https://openalex.org/W3018990409","https://openalex.org/W3021272327","https://openalex.org/W3021920958","https://openalex.org/W3023701177","https://openalex.org/W3024842005","https://openalex.org/W3025113607","https://openalex.org/W3027051073","https://openalex.org/W3028505928","https://openalex.org/W3029148360","https://openalex.org/W3032266082","https://openalex.org/W3033148046","https://openalex.org/W3037216933","https://openalex.org/W3043558371","https://openalex.org/W3044352330","https://openalex.org/W3047081808","https://openalex.org/W3049025136","https://openalex.org/W3080555959","https://openalex.org/W3084900169","https://openalex.org/W3087223457","https://openalex.org/W3090605478","https://openalex.org/W3092493138","https://openalex.org/W3093046161","https://openalex.org/W3093858607","https://openalex.org/W3094091014","https://openalex.org/W3094217342","https://openalex.org/W3095848620","https://openalex.org/W3099768174","https://openalex.org/W3101369110","https://openalex.org/W3101592465","https://openalex.org/W3101697142","https://openalex.org/W3102434595","https://openalex.org/W3103358463","https://openalex.org/W3108118546","https://openalex.org/W3108591672","https://openalex.org/W3111521801","https://openalex.org/W3112563877","https://openalex.org/W3113310528","https://openalex.org/W3113863876","https://openalex.org/W3115781494","https://openalex.org/W3117771127","https://openalex.org/W3119379269","https://openalex.org/W3120224790","https://openalex.org/W3124346345","https://openalex.org/W3124439729","https://openalex.org/W3124814274","https://openalex.org/W3127011314","https://openalex.org/W3127422037","https://openalex.org/W3129476455","https://openalex.org/W3130453114","https://openalex.org/W3130814454","https://openalex.org/W3131450268","https://openalex.org/W3132715010","https://openalex.org/W3134482219","https://openalex.org/W3134897856","https://openalex.org/W3136021864","https://openalex.org/W3137285774","https://openalex.org/W3138479716","https://openalex.org/W3140605903","https://openalex.org/W3144696998","https://openalex.org/W3146817258","https://openalex.org/W3156830838","https://openalex.org/W3158466099","https://openalex.org/W3161009639","https://openalex.org/W3164692211","https://openalex.org/W3164736847","https://openalex.org/W3164839005","https://openalex.org/W3165062450","https://openalex.org/W3165120573","https://openalex.org/W3165519561","https://openalex.org/W3165800492","https://openalex.org/W3169098619","https://openalex.org/W3180540559","https://openalex.org/W3186021169","https://openalex.org/W3190202966","https://openalex.org/W3193570366","https://openalex.org/W3195383593","https://openalex.org/W3196890347","https://openalex.org/W3198628780","https://openalex.org/W3201237713","https://openalex.org/W3201518044","https://openalex.org/W3203148062","https://openalex.org/W3203731429","https://openalex.org/W3203976604","https://openalex.org/W3205339884","https://openalex.org/W3208967609","https://openalex.org/W3214280461","https://openalex.org/W3214596602","https://openalex.org/W3216323060","https://openalex.org/W4200129350","https://openalex.org/W4200138119","https://openalex.org/W4200581587","https://openalex.org/W4205281625","https://openalex.org/W4205514149","https://openalex.org/W4205530110","https://openalex.org/W4205559708","https://openalex.org/W4205817967","https://openalex.org/W4206199829","https://openalex.org/W4206304985","https://openalex.org/W4210242600","https://openalex.org/W4210247523","https://openalex.org/W4210443931","https://openalex.org/W4210829655","https://openalex.org/W4212836561","https://openalex.org/W4220765701","https://openalex.org/W4221042170","https://openalex.org/W4221065117","https://openalex.org/W4221125917","https://openalex.org/W4223570418","https://openalex.org/W4224009065","https://openalex.org/W4225148401","https://openalex.org/W4225272983","https://openalex.org/W4225278475","https://openalex.org/W4225535314","https://openalex.org/W4226218349","https://openalex.org/W4229033508","https://openalex.org/W4229035519","https://openalex.org/W4231145069","https://openalex.org/W4233721145","https://openalex.org/W4280596398","https://openalex.org/W4280598116","https://openalex.org/W4281716652","https://openalex.org/W4282983793","https://openalex.org/W4283585907","https://openalex.org/W4283689887","https://openalex.org/W4283815719","https://openalex.org/W4288419263","https://openalex.org/W4290154117","https://openalex.org/W4293649366","https://openalex.org/W4294558607","https://openalex.org/W4295312788","https://openalex.org/W4297969478","https://openalex.org/W4298884898","https://openalex.org/W4311415873","https://openalex.org/W4313386949","https://openalex.org/W4320013936","https://openalex.org/W4322832102","https://openalex.org/W4360942779","https://openalex.org/W4367602258","https://openalex.org/W4375955255","https://openalex.org/W4382877140","https://openalex.org/W4385955324","https://openalex.org/W6637618735","https://openalex.org/W6750469568","https://openalex.org/W6757078134","https://openalex.org/W6771982476","https://openalex.org/W6787007307","https://openalex.org/W6807645977","https://openalex.org/W6887772400","https://openalex.org/W7038994942"],"related_works":["https://openalex.org/W4375867731","https://openalex.org/W3037187668","https://openalex.org/W2611989081","https://openalex.org/W4234772502","https://openalex.org/W2731899572","https://openalex.org/W2380685755","https://openalex.org/W4230611425","https://openalex.org/W4294635752","https://openalex.org/W4304166257","https://openalex.org/W4380075502"],"abstract_inverted_index":{"Single-cell":[0],"technologies":[1,17,75],"are":[2,18,172],"revolutionizing":[3],"the":[4,88,98,126,150,181,185],"entire":[5],"field":[6],"of":[7,12,84,97,125],"biology.":[8],"The":[9],"large":[10],"volumes":[11],"data":[13,111],"generated":[14],"by":[15],"single-cell":[16,67,74,99,127],"high":[19],"dimensional,":[20],"sparse,":[21],"and":[22,24,37,76,142,156,160,164,169,184,198],"heterogeneous":[23],"have":[25],"complicated":[26],"dependency":[27],"structures,":[28],"making":[29],"analyses":[30],"using":[31],"conventional":[32],"machine":[33,52],"learning":[34,44,53,65,86,158,167],"approaches":[35],"challenging":[36],"impractical.":[38],"In":[39,55],"tackling":[40],"these":[41],"challenges,":[42],"deep":[43,64,85,91,157],"often":[45],"demonstrates":[46],"superior":[47],"performance":[48],"compared":[49],"to":[50,110],"traditional":[51],"methods.":[54],"this":[56],"work,":[57],"we":[58,148,179],"give":[59],"a":[60,194],"comprehensive":[61],"survey":[62,190],"on":[63,73],"in":[66,103,154],"analysis.":[68],"We":[69,93,116],"first":[70],"introduce":[71],"background":[72],"their":[77,162],"development,":[78],"as":[79,81,193],"well":[80],"fundamental":[82],"concepts":[83],"including":[87,130],"most":[89,151,186],"popular":[90,120],"architectures.":[92],"present":[94],"an":[95],"overview":[96],"analytic":[100],"pipeline":[101],"pursued":[102],"research":[104],"applications":[105],"while":[106],"noting":[107],"divergences":[108],"due":[109],"sources":[112],"or":[113],"specific":[114],"applications.":[115],"then":[117],"review":[118],"seven":[119],"tasks":[121],"spanning":[122],"different":[123],"stages":[124],"analysis":[128],"pipeline,":[129],"multimodal":[131],"integration,":[132],"imputation,":[133],"clustering,":[134],"spatial":[135],"domain":[136],"identification,":[137],"cell-type":[138,143],"deconvolution,":[139],"cell":[140],"segmentation,":[141],"annotation.":[144],"Under":[145],"each":[146,176],"task,":[147],"describe":[149],"recent":[152,187],"developments":[153],"classical":[155],"methods":[159],"discuss":[161,180],"advantages":[163],"disadvantages.":[165],"Deep":[166],"tools":[168],"benchmark":[170],"datasets":[171],"also":[173],"summarized":[174],"for":[175,196],"task.":[177],"Finally,":[178],"future":[182],"directions":[183],"challenges.":[188],"This":[189],"will":[191],"serve":[192],"reference":[195],"biologists":[197],"computer":[199],"scientists,":[200],"encouraging":[201],"collaborations.":[202]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
