{"id":"https://openalex.org/W3101592465","doi":"https://doi.org/10.1145/3388440.3412410","title":"Unsupervised manifold alignment for single-cell multi-omics data","display_name":"Unsupervised manifold alignment for single-cell multi-omics data","publication_year":2020,"publication_date":"2020-09-21","ids":{"openalex":"https://openalex.org/W3101592465","doi":"https://doi.org/10.1145/3388440.3412410","mag":"3101592465","pmid":"https://pubmed.ncbi.nlm.nih.gov/33954299"},"language":"en","primary_location":{"id":"doi:10.1145/3388440.3412410","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3388440.3412410","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8095090","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070578596","display_name":"Ritambhara Singh","orcid":"https://orcid.org/0000-0002-7523-160X"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ritambhara Singh","raw_affiliation_strings":["Department of Computer Science, Center for Computational Molecular, Biology, Brown University"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Center for Computational Molecular, Biology, Brown University","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009325417","display_name":"P\u0131nar Demet\u00e7i","orcid":"https://orcid.org/0000-0002-5644-0326"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pinar Demetci","raw_affiliation_strings":["Center for Computational Molecular, Biology, Brown University"],"affiliations":[{"raw_affiliation_string":"Center for Computational Molecular, Biology, Brown University","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086778001","display_name":"Giancarlo Bonora","orcid":"https://orcid.org/0000-0001-7558-3798"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Giancarlo Bonora","raw_affiliation_strings":["Department of Genome Sciences, University of Washington"],"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043115964","display_name":"Vijay Ramani","orcid":"https://orcid.org/0000-0003-3345-5960"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vijay Ramani","raw_affiliation_strings":["UC San Francisco"],"affiliations":[{"raw_affiliation_string":"UC San Francisco","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084731492","display_name":"Choli Lee","orcid":"https://orcid.org/0000-0002-8901-1835"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Choli Lee","raw_affiliation_strings":["Department of Genome Sciences, University of Washington"],"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101561465","display_name":"He Fang","orcid":"https://orcid.org/0000-0001-9036-8092"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"He Fang","raw_affiliation_strings":["Department of Pathology, University of Washington"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031973840","display_name":"Zhijun Duan","orcid":"https://orcid.org/0000-0002-8147-793X"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhijun Duan","raw_affiliation_strings":["Division of Hematology, University of Washington"],"affiliations":[{"raw_affiliation_string":"Division of Hematology, University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011158717","display_name":"Xinxian Deng","orcid":"https://orcid.org/0000-0002-5007-218X"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xinxian Deng","raw_affiliation_strings":["Department of Pathology, University of Washington"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083897996","display_name":"Jay Shendure","orcid":"https://orcid.org/0000-0002-1516-1865"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jay Shendure","raw_affiliation_strings":["Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington"],"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington","institution_ids":["https://openalex.org/I1344073410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067240879","display_name":"Christine M. Dist\u00e8che","orcid":"https://orcid.org/0000-0002-5433-495X"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christine Disteche","raw_affiliation_strings":["Department of Pathology, University of Washington"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057375933","display_name":"William Stafford Noble","orcid":"https://orcid.org/0000-0001-7283-4715"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William Stafford Noble","raw_affiliation_strings":["Department of Genome Sciences,University of Washington, Paul G. Allen School of Computer Science and Engineering, University of Washington"],"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences,University of Washington, Paul G. Allen School of Computer Science and Engineering, University of Washington","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5070578596"],"corresponding_institution_ids":["https://openalex.org/I27804330"],"apc_list":null,"apc_paid":null,"fwci":3.4201,"has_fulltext":false,"cited_by_count":59,"citation_normalized_percentile":{"value":0.93733663,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"2020","issue":null,"first_page":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9872000217437744,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.968500018119812,"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/computer-science","display_name":"Computer science","score":0.7568707466125488},{"id":"https://openalex.org/keywords/hyperparameter","display_name":"Hyperparameter","score":0.6619939208030701},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.43445849418640137},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38440853357315063},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3810771703720093},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3533325493335724},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14695021510124207}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7568707466125488},{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.6619939208030701},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.43445849418640137},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38440853357315063},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3810771703720093},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3533325493335724},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14695021510124207},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/3388440.3412410","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3388440.3412410","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},{"id":"pmid:33954299","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33954299","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":"ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8095090","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8095090","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ACM BCB","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8095090","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8095090","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ACM BCB","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1601740268","https://openalex.org/W1987971958","https://openalex.org/W2048444898","https://openalex.org/W2126438274","https://openalex.org/W2140348479","https://openalex.org/W2736547131","https://openalex.org/W2747545374","https://openalex.org/W2912390237","https://openalex.org/W2934716754","https://openalex.org/W2948469692","https://openalex.org/W2949177718","https://openalex.org/W2950030509","https://openalex.org/W2970971581","https://openalex.org/W2979911343","https://openalex.org/W3004086570","https://openalex.org/W3043558371","https://openalex.org/W4255865707"],"related_works":["https://openalex.org/W4295309597","https://openalex.org/W4210794429","https://openalex.org/W4223456145","https://openalex.org/W4309113015","https://openalex.org/W3199608561","https://openalex.org/W4283697347","https://openalex.org/W4295681619","https://openalex.org/W3014815208","https://openalex.org/W4298144215","https://openalex.org/W4375930479"],"abstract_inverted_index":{"Integrating":[0],"single-cell":[1,38,66,102,121,139,229],"measurements":[2,54],"that":[3,61,76,146,166,219],"capture":[4],"different":[5,35,105],"properties":[6],"of":[7,16,27,37,64,134,143,150,180,187,207],"the":[8,25,49,53,82,132,154,178,191,208,213,220],"genome":[9,17],"is":[10,21,90,128],"vital":[11],"to":[12,24,70,130,137,153,162,182,194,203,225],"extending":[13],"our":[14],"understanding":[15],"biology.":[18],"This":[19],"task":[20],"challenging":[22],"due":[23],"lack":[26,45],"a":[28,108,119,183,201],"shared":[29,110],"axis":[30],"across":[31],"datasets":[32,103,165],"obtained":[33],"from":[34,104],"types":[36],"experiments.":[39,230],"For":[40],"most":[41],"such":[42,91],"datasets,":[43],"we":[44,159,189],"corresponding":[46],"information":[47],"among":[48,81],"cells":[50,144],"(samples)":[51],"and":[52,118,169],"(features).":[55],"In":[56,156],"this":[57,135,157],"scenario,":[58],"unsupervised":[59,93],"algorithms":[60],"are":[62,68],"capable":[63],"aligning":[65],"experiments":[67,140],"critical":[69],"learning":[71],"an":[72,92],"<i>in":[73],"silico</i>":[74],"co-assay":[75],"can":[77,100,148],"help":[78],"draw":[79],"correspondences":[80],"cells.":[83,125,175],"Maximum":[84],"mean":[85],"discrepancy-based":[86],"manifold":[87],"alignment":[88],"(MMD-MA)":[89],"algorithm.":[94],"Without":[95],"requiring":[96],"correspondence":[97],"information,":[98],"it":[99,127,147],"align":[101,227],"modalities":[106],"in":[107,172],"common":[109],"latent":[111],"space,":[112],"showing":[113],"promising":[114],"results":[115],"on":[116,196],"simulations":[117],"small-scale":[120],"experiment":[122],"with":[123,141],"61":[124],"However,":[126],"essential":[129],"explore":[131],"applicability":[133],"method":[136,202],"larger":[138],"thousands":[142],"so":[145],"be":[149],"practical":[151],"interest":[152],"community.":[155],"paper,":[158],"apply":[160],"MMD-MA":[161,181,224],"two":[163],"recent":[164],"measure":[167],"transcriptome":[168],"chromatin":[170],"accessibility":[171],"~2000":[173],"single":[174],"To":[176],"scale":[177],"runtime":[179],"more":[184],"substantial":[185],"number":[186],"cells,":[188],"extend":[190],"original":[192],"implementation":[193],"run":[195],"GPUs.":[197],"We":[198,217],"also":[199],"introduce":[200],"automatically":[204],"select":[205],"one":[206],"user-defined":[209],"parameters,":[210],"thus":[211],"reducing":[212],"hyperparameter":[214],"search":[215],"space.":[216],"demonstrate":[218],"proposed":[221],"extensions":[222],"allow":[223],"accurately":[226],"state-of-the-art":[228]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":13}],"updated_date":"2026-03-12T08:34:05.389933","created_date":"2025-10-10T00:00:00"}