{"id":"https://openalex.org/W7163676259","doi":"https://doi.org/10.1109/tcbbio.2026.3683521","title":"Robust Algorithm With Contrastive Learning for Identifying Spatial Domains From Noised Spatial Transcriptomics Data","display_name":"Robust Algorithm With Contrastive Learning for Identifying Spatial Domains From Noised Spatial Transcriptomics Data","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7163676259","doi":"https://doi.org/10.1109/tcbbio.2026.3683521","pmid":"https://pubmed.ncbi.nlm.nih.gov/42247557"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2026.3683521","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3683521","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","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/A5065059553","display_name":"Yaxiong Ma","orcid":"https://orcid.org/0000-0002-6086-0454"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaxiong Ma","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University, Xian, China"],"raw_orcid":"https://orcid.org/0000-0002-6086-0454","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xian, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101600879","display_name":"Kai Kang","orcid":"https://orcid.org/0000-0003-1648-7370"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kai Kang","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University, Xian, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xian, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003485495","display_name":"MF Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Min Zhang","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University, Xian, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xian, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137995271","display_name":"Peifeng Liang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210127460","display_name":"Ningxia Medical University","ror":"https://ror.org/02h8a1848","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210127460"]},{"id":"https://openalex.org/I4210139449","display_name":"Ningxia Medical University General Hospital","ror":"https://ror.org/049dkqr57","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210139449"]},{"id":"https://openalex.org/I4210164393","display_name":"The Fourth People's Hospital of Ningxia Hui Autonomous Region","ror":"https://ror.org/05kjn8d41","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210164393"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peifeng Liang","raw_affiliation_strings":["Department of Medical Affair, People&#x0027;s Hospital of Ningxia Hui Autonomous Region, Ningxia Medical University, Yinchuan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Affair, People&#x0027;s Hospital of Ningxia Hui Autonomous Region, Ningxia Medical University, Yinchuan, China","institution_ids":["https://openalex.org/I4210139449","https://openalex.org/I4210127460","https://openalex.org/I4210164393"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5137946188","display_name":"Xiaoke Ma","orcid":"https://orcid.org/0000-0002-5604-7137"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoke Ma","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University, Xian, China"],"raw_orcid":"https://orcid.org/0000-0002-5604-7137","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xian, China","institution_ids":["https://openalex.org/I149594827"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.83899617,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"23","issue":"3","first_page":"1451","last_page":"1462"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.8689000010490417,"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":0.8689000010490417,"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":0.06769999861717224,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.007199999876320362,"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/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5264000296592712},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.44369998574256897},{"id":"https://openalex.org/keywords/noisy-data","display_name":"Noisy data","score":0.3977000117301941},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.2919999957084656},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.29170000553131104},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.2838999927043915}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6014999747276306},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5985999703407288},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5264000296592712},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5126000046730042},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.44369998574256897},{"id":"https://openalex.org/C2781170535","wikidata":"https://www.wikidata.org/wiki/Q30587856","display_name":"Noisy data","level":2,"score":0.3977000117301941},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.2919999957084656},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.29170000553131104},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.2838999927043915},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.27300000190734863},{"id":"https://openalex.org/C2982736386","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Statistical learning","level":2,"score":0.27079999446868896},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.260699987411499},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.25450000166893005}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2026.3683521","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3683521","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42247557","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42247557","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4252882605","display_name":null,"funder_award_id":"62272361","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5490784155","display_name":null,"funder_award_id":"U22A20345","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8378338857","display_name":"\u591a\u6a21\u5f0f\u5e72\u9884\u63aa\u65bd\u4e0bICU\u5355\u5143\u8010\u7532\u6c27\u897f\u6797\u91d1\u9ec4\u8272\u8461\u8404\u7403\u83cc\u4f20\u64ad\u52a8\u6001\u53ca\u5176\u6a21\u578b\u4eff\u771f\u7814\u7a76","funder_award_id":"81760608","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Spatial":[0],"transcriptomics":[1,5,102],"(ST)":[2],"technologies":[3],"capture":[4],"of":[6,14,16,27,77,83,106,111,118,133,149,151,182],"genens":[7],"with":[8,22,101,141,189],"spatial":[9,23,39,75,88,99,104,159,183],"context,":[10],"enabling":[11],"systematic":[12],"exploration":[13],"micro-environment":[15],"tissues":[17],"that":[18,199],"is":[19,136,155,174,201],"highly":[20],"associated":[21],"domains.":[24,184],"And,":[25,114],"noise":[26,45,117,132,191],"ST":[28,79,84,112,119,134,215],"data":[29,85,120,135],"poses":[30],"a":[31,61],"great":[32],"challenge":[33],"on":[34,186],"designing":[35],"algorithms":[36],"for":[37,73,212],"identifying":[38,74,87],"domains,":[40],"whereas":[41],"available":[42],"methods":[43],"remove":[44],"by":[46,121,161],"employing":[47],"pre-processing":[48],"procedure,":[49],"resulting":[50],"in":[51],"the":[52,128,178],"undesirable":[53],"performance.":[54],"To":[55,145],"overcome":[56],"this":[57],"limitation,":[58],"we":[59],"propose":[60],"robust":[62,206],"and":[63,86,98,103,166,180,196,205],"joint":[64],"framework,":[65],"called":[66],"jNFACL":[67,94,115,200],"(joint":[68],"Network-based":[69],"Feature-Affinity":[70],"Contrastive":[71],"Learning),":[72],"domains":[76,89],"noised":[78,214],"data,":[80],"where":[81,131,171],"deniosing":[82],"are":[90],"simultaneously":[91],"integrated.":[92],"Specifically,":[93],"first":[95],"constructs":[96],"expression":[97],"graphs":[100,126],"coordinates":[105],"spots,":[107,152],"which":[108],"removes":[109],"heterogeneity":[110],"data.":[113,216],"separates":[116],"jointly":[122],"projecting":[123],"these":[124],"constructed":[125],"into":[127],"shared":[129],"subspace,":[130],"separated":[137],"from":[138,193],"feature":[139],"level":[140],"nonnegative":[142],"matrix":[143],"factorization.":[144],"further":[146],"enhance":[147],"quality":[148],"features":[150],"contrastive":[153],"learning":[154],"adopted":[156],"to":[157],"leverages":[158],"neighborhoods":[160],"pulling":[162],"similar":[163],"spots":[164,169],"together":[165],"pushing":[167],"dissimilar":[168],"apart,":[170],"self-supervision":[172],"information":[173],"incorporated,":[175],"thereby":[176],"improving":[177],"characterization":[179],"identification":[181],"Experiments":[185],"various":[187],"datasets":[188],"different":[190],"levels":[192],"multiple":[194],"platforms":[195],"species":[197],"demonstrate":[198],"much":[202],"more":[203],"accurate":[204],"than":[207],"state-of-the-art":[208],"methods,":[209],"providing":[210],"alternatives":[211],"analyzing":[213]},"counts_by_year":[],"updated_date":"2026-06-17T08:01:34.144755","created_date":"2026-06-06T00:00:00"}
