{"id":"https://openalex.org/W4290154117","doi":"https://doi.org/10.1038/s43588-022-00266-5","title":"Cell clustering for spatial transcriptomics data with graph neural networks","display_name":"Cell clustering for spatial transcriptomics data with graph neural networks","publication_year":2022,"publication_date":"2022-06-27","ids":{"openalex":"https://openalex.org/W4290154117","doi":"https://doi.org/10.1038/s43588-022-00266-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/38177586"},"language":"en","primary_location":{"id":"doi:10.1038/s43588-022-00266-5","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-022-00266-5","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/A5100357066","display_name":"Jiachen Li","orcid":"https://orcid.org/0000-0001-9137-6262"},"institutions":[{"id":"https://openalex.org/I1327237609","display_name":"Ministry of Education of the People's Republic of China","ror":"https://ror.org/01mv9t934","country_code":"CN","type":"government","lineage":["https://openalex.org/I1327237609","https://openalex.org/I4210127390"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jiachen Li","raw_affiliation_strings":["Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China","Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China","institution_ids":["https://openalex.org/I1327237609"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066373402","display_name":"Siheng Chen","orcid":"https://orcid.org/0000-0002-9144-0583"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210099312","display_name":"Shandong Jiaotong University","ror":"https://ror.org/01848hk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210099312"]},{"id":"https://openalex.org/I4210100255","display_name":"Beijing Academy of Artificial Intelligence","ror":"https://ror.org/016a74861","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210100255"]},{"id":"https://openalex.org/I4391012619","display_name":"Shanghai Artificial Intelligence Laboratory","ror":"https://ror.org/03wkvpx79","country_code":null,"type":"facility","lineage":["https://openalex.org/I4391012619"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Siheng Chen","raw_affiliation_strings":["Cooperative Medianet Innovation Center (CMIC), Shanghai Jiao Tong University, Shanghai, China","Shanghai Artificial Intelligence Laboratory, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Cooperative Medianet Innovation Center (CMIC), Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I4210099312","https://openalex.org/I183067930"]},{"raw_affiliation_string":"Shanghai Artificial Intelligence Laboratory, Shanghai, China","institution_ids":["https://openalex.org/I4210100255","https://openalex.org/I4391012619"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091365447","display_name":"Xiaoyong Pan","orcid":"https://orcid.org/0000-0001-5010-464X"},"institutions":[{"id":"https://openalex.org/I1327237609","display_name":"Ministry of Education of the People's Republic of China","ror":"https://ror.org/01mv9t934","country_code":"CN","type":"government","lineage":["https://openalex.org/I1327237609","https://openalex.org/I4210127390"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyong Pan","raw_affiliation_strings":["Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China","Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China","institution_ids":["https://openalex.org/I1327237609"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082583182","display_name":"Ye Yuan","orcid":"https://orcid.org/0000-0002-4270-8002"},"institutions":[{"id":"https://openalex.org/I1327237609","display_name":"Ministry of Education of the People's Republic of China","ror":"https://ror.org/01mv9t934","country_code":"CN","type":"government","lineage":["https://openalex.org/I1327237609","https://openalex.org/I4210127390"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ye Yuan","raw_affiliation_strings":["Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China. yuanye_auto@sjtu.edu.cn","Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China. yuanye_auto@sjtu.edu.cn","Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China. yuanye_auto@sjtu.edu.cn","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China. yuanye_auto@sjtu.edu.cn","institution_ids":["https://openalex.org/I1327237609"]},{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076024045","display_name":"Hong\u2010Bin Shen","orcid":"https://orcid.org/0000-0002-4029-3325"},"institutions":[{"id":"https://openalex.org/I1327237609","display_name":"Ministry of Education of the People's Republic of China","ror":"https://ror.org/01mv9t934","country_code":"CN","type":"government","lineage":["https://openalex.org/I1327237609","https://openalex.org/I4210127390"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hong-Bin Shen","raw_affiliation_strings":["Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China. hbshen@sjtu.edu.cn","Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China. hbshen@sjtu.edu.cn","Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China. hbshen@sjtu.edu.cn","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China. hbshen@sjtu.edu.cn","institution_ids":["https://openalex.org/I1327237609"]},{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100357066"],"corresponding_institution_ids":["https://openalex.org/I1327237609","https://openalex.org/I183067930"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":null,"fwci":16.9257,"has_fulltext":false,"cited_by_count":213,"citation_normalized_percentile":{"value":0.99627397,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"2","issue":"6","first_page":"399","last_page":"408"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9883000254631042,"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":0.9387000203132629,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.7326717972755432},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.5655600428581238},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5050106644630432},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4939132332801819},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4531916677951813},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.42050665616989136},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.386919766664505},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3511843979358673},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32685720920562744},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.21065068244934082},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14770984649658203},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1017906665802002},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08259910345077515}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7326717972755432},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.5655600428581238},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5050106644630432},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4939132332801819},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4531916677951813},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42050665616989136},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.386919766664505},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3511843979358673},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32685720920562744},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.21065068244934082},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14770984649658203},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1017906665802002},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08259910345077515},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1038/s43588-022-00266-5","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-022-00266-5","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:38177586","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38177586","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W143170392","https://openalex.org/W1921320152","https://openalex.org/W1995547461","https://openalex.org/W1996435746","https://openalex.org/W2042789810","https://openalex.org/W2087528029","https://openalex.org/W2126537932","https://openalex.org/W2131681506","https://openalex.org/W2132069716","https://openalex.org/W2467355029","https://openalex.org/W2471536144","https://openalex.org/W2485836676","https://openalex.org/W2510746232","https://openalex.org/W2520858613","https://openalex.org/W2765719287","https://openalex.org/W2769248706","https://openalex.org/W2769379242","https://openalex.org/W2792626041","https://openalex.org/W2800392236","https://openalex.org/W2809368942","https://openalex.org/W2897249806","https://openalex.org/W2898824002","https://openalex.org/W2899235059","https://openalex.org/W2915848182","https://openalex.org/W2923300855","https://openalex.org/W2942880491","https://openalex.org/W2946365419","https://openalex.org/W2949177718","https://openalex.org/W2952383043","https://openalex.org/W2971653850","https://openalex.org/W2972445800","https://openalex.org/W2973055525","https://openalex.org/W2978551960","https://openalex.org/W2984472267","https://openalex.org/W3008188998","https://openalex.org/W3017023874","https://openalex.org/W3032266082","https://openalex.org/W3042986566","https://openalex.org/W3092450854","https://openalex.org/W3099768174","https://openalex.org/W3100390963","https://openalex.org/W3105973851","https://openalex.org/W3106188259","https://openalex.org/W3108118546","https://openalex.org/W3112563877","https://openalex.org/W3113349968","https://openalex.org/W3126958162","https://openalex.org/W3132829024","https://openalex.org/W3134482219","https://openalex.org/W3164692211","https://openalex.org/W3165120573","https://openalex.org/W3204015056","https://openalex.org/W4206189113","https://openalex.org/W4233721145","https://openalex.org/W6755861362","https://openalex.org/W6784195601","https://openalex.org/W6968585384"],"related_works":["https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2028462563","https://openalex.org/W2942994004","https://openalex.org/W2982720988","https://openalex.org/W3150324899","https://openalex.org/W2523545060","https://openalex.org/W4229998356","https://openalex.org/W4379374180","https://openalex.org/W3025157844"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":24},{"year":2025,"cited_by_count":64},{"year":2024,"cited_by_count":87},{"year":2023,"cited_by_count":27},{"year":2022,"cited_by_count":11}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
