{"id":"https://openalex.org/W4410786096","doi":"https://doi.org/10.1038/s43588-025-00809-6","title":"Interpretable niche-based cell\u2012cell communication inference using multi-view graph neural networks","display_name":"Interpretable niche-based cell\u2012cell communication inference using multi-view graph neural networks","publication_year":2025,"publication_date":"2025-05-27","ids":{"openalex":"https://openalex.org/W4410786096","doi":"https://doi.org/10.1038/s43588-025-00809-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/40425827"},"language":"en","primary_location":{"id":"doi:10.1038/s43588-025-00809-6","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-025-00809-6","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006909834","display_name":"Juntian Qi","orcid":"https://orcid.org/0000-0001-6753-9789"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210124606","display_name":"Institute of Genetics and Developmental Biology","ror":"https://ror.org/02aee5m12","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210124606"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Juntian Qi","raw_affiliation_strings":["Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China","State Key Laboratory of Gene Function and Modulation Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China","University of Chinese Academy of Sciences, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210124606","https://openalex.org/I19820366"]},{"raw_affiliation_string":"State Key Laboratory of Gene Function and Modulation Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100954380","display_name":"Zhengchao Luo","orcid":"https://orcid.org/0009-0005-4917-2967"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhengchao Luo","raw_affiliation_strings":["Department of Big Data and Biomedical AI, College of Future Technology, Peking University, Beijing, China"],"raw_orcid":"https://orcid.org/0009-0005-4917-2967","affiliations":[{"raw_affiliation_string":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University, Beijing, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042577846","display_name":"Chuan\u2010Yun Li","orcid":"https://orcid.org/0000-0002-8008-8430"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210124606","display_name":"Institute of Genetics and Developmental Biology","ror":"https://ror.org/02aee5m12","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210124606"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chuan-Yun Li","raw_affiliation_strings":["Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. chuanyunli@pku.edu.cn","State Key Laboratory of Gene Function and Modulation Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China. chuanyunli@pku.edu.cn","University of Chinese Academy of Sciences, Beijing, China. chuanyunli@pku.edu.cn"],"raw_orcid":"https://orcid.org/0000-0002-8008-8430","affiliations":[{"raw_affiliation_string":"Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. chuanyunli@pku.edu.cn","institution_ids":["https://openalex.org/I4210124606"]},{"raw_affiliation_string":"State Key Laboratory of Gene Function and Modulation Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China. chuanyunli@pku.edu.cn","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing, China. chuanyunli@pku.edu.cn","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084797829","display_name":"Jinzhuo Wang","orcid":"https://orcid.org/0000-0002-9464-4426"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jinzhuo Wang","raw_affiliation_strings":["Department of Big Data and Biomedical AI, College of Future Technology, Peking University, Beijing, China. wangjinzhuo@pku.edu.cn"],"raw_orcid":"https://orcid.org/0000-0002-9464-4426","affiliations":[{"raw_affiliation_string":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University, Beijing, China. wangjinzhuo@pku.edu.cn","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049503884","display_name":"Wanqiu Ding","orcid":"https://orcid.org/0000-0002-6650-8662"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wanqiu Ding","raw_affiliation_strings":["Bioinformatics Core Facility, College of Future Technology, Peking University, Beijing, China. dingwq@pku.edu.cn","State Key Laboratory of Gene Function and Modulation Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China. dingwq@pku.edu.cn"],"raw_orcid":"https://orcid.org/0000-0002-6650-8662","affiliations":[{"raw_affiliation_string":"Bioinformatics Core Facility, College of Future Technology, Peking University, Beijing, China. dingwq@pku.edu.cn","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"State Key Laboratory of Gene Function and Modulation Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China. dingwq@pku.edu.cn","institution_ids":["https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5042577846","https://openalex.org/A5049503884","https://openalex.org/A5084797829"],"corresponding_institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210124606","https://openalex.org/I4210165038"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":null,"fwci":3.3959,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.92267091,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"5","issue":"6","first_page":"444","last_page":"455"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13052","display_name":"Molecular Communication and Nanonetworks","score":0.9955999851226807,"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"}},"topics":[{"id":"https://openalex.org/T13052","display_name":"Molecular Communication and Nanonetworks","score":0.9955999851226807,"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"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9922000169754028,"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/T10862","display_name":"AI in cancer detection","score":0.9900000095367432,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6399856805801392},{"id":"https://openalex.org/keywords/niche","display_name":"Niche","score":0.6007882356643677},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5705388188362122},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.508683979511261},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.48082101345062256},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39950090646743774},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2980576455593109},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23329636454582214},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.11370691657066345}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6399856805801392},{"id":"https://openalex.org/C153991713","wikidata":"https://www.wikidata.org/wiki/Q17142856","display_name":"Niche","level":2,"score":0.6007882356643677},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5705388188362122},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.508683979511261},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.48082101345062256},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39950090646743774},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2980576455593109},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23329636454582214},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.11370691657066345}],"mesh":[{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1038/s43588-025-00809-6","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-025-00809-6","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},{"id":"pmid:40425827","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40425827","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":"Nature computational science","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":87,"referenced_works":["https://openalex.org/W1965498876","https://openalex.org/W1967532587","https://openalex.org/W1986241711","https://openalex.org/W1989480741","https://openalex.org/W1990776397","https://openalex.org/W1992885568","https://openalex.org/W2023527463","https://openalex.org/W2033296455","https://openalex.org/W2097749765","https://openalex.org/W2100068901","https://openalex.org/W2105389823","https://openalex.org/W2361876374","https://openalex.org/W2415341492","https://openalex.org/W2471536144","https://openalex.org/W2557833574","https://openalex.org/W2616922646","https://openalex.org/W2771542157","https://openalex.org/W2781034938","https://openalex.org/W2789788869","https://openalex.org/W2790455901","https://openalex.org/W2800392236","https://openalex.org/W2803300773","https://openalex.org/W2889453805","https://openalex.org/W2897044695","https://openalex.org/W2899224111","https://openalex.org/W2949693884","https://openalex.org/W2952615074","https://openalex.org/W2992151131","https://openalex.org/W2999977864","https://openalex.org/W3003257820","https://openalex.org/W3007935255","https://openalex.org/W3011286936","https://openalex.org/W3023748646","https://openalex.org/W3036371598","https://openalex.org/W3044737312","https://openalex.org/W3044842300","https://openalex.org/W3068772833","https://openalex.org/W3099810371","https://openalex.org/W3105973851","https://openalex.org/W3112563877","https://openalex.org/W3129476455","https://openalex.org/W3130232612","https://openalex.org/W3132661792","https://openalex.org/W3134482219","https://openalex.org/W3184931457","https://openalex.org/W3198281602","https://openalex.org/W3202164241","https://openalex.org/W3203689742","https://openalex.org/W3211696641","https://openalex.org/W3212135550","https://openalex.org/W3214755680","https://openalex.org/W4200615353","https://openalex.org/W4220799063","https://openalex.org/W4220921784","https://openalex.org/W4223939691","https://openalex.org/W4226156408","https://openalex.org/W4283585907","https://openalex.org/W4288758477","https://openalex.org/W4290188763","https://openalex.org/W4293150341","https://openalex.org/W4294216483","https://openalex.org/W4294664317","https://openalex.org/W4295101996","https://openalex.org/W4300862018","https://openalex.org/W4304690654","https://openalex.org/W4309944312","https://openalex.org/W4312094540","https://openalex.org/W4317757307","https://openalex.org/W4383342368","https://openalex.org/W4384071384","https://openalex.org/W4385987383","https://openalex.org/W4387583204","https://openalex.org/W4388997570","https://openalex.org/W4389339556","https://openalex.org/W4389478442","https://openalex.org/W4389488172","https://openalex.org/W4390972792","https://openalex.org/W4390974497","https://openalex.org/W4399211696","https://openalex.org/W4399630649","https://openalex.org/W4402604581","https://openalex.org/W4403918319","https://openalex.org/W6750043948","https://openalex.org/W6755684251","https://openalex.org/W6801979098","https://openalex.org/W6845919458","https://openalex.org/W6939525617"],"related_works":["https://openalex.org/W2095253586","https://openalex.org/W2393629471","https://openalex.org/W3213901947","https://openalex.org/W1995707336","https://openalex.org/W2799510265","https://openalex.org/W4312191234","https://openalex.org/W4235133350","https://openalex.org/W3032525852","https://openalex.org/W3206205086","https://openalex.org/W4234853763"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":2}],"updated_date":"2026-06-13T06:13:01.061226","created_date":"2025-10-10T00:00:00"}
