{"id":"https://openalex.org/W4406238158","doi":"https://doi.org/10.1109/bibm62325.2024.10822097","title":"SMMGCL: a novel multi-level graph contrastive learning framework for integrating spatial multi-omics data","display_name":"SMMGCL: a novel multi-level graph contrastive learning framework for integrating spatial multi-omics data","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406238158","doi":"https://doi.org/10.1109/bibm62325.2024.10822097"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822097","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822097","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","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/A5100408160","display_name":"Bo Wang","orcid":"https://orcid.org/0000-0002-9620-3413"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Wang","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100431670","display_name":"Wei Liu","orcid":"https://orcid.org/0000-0001-7624-3402"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Liu","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101750544","display_name":"Jiawei Luo","orcid":"https://orcid.org/0000-0003-4737-9014"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiawei Luo","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020334528","display_name":"Xiangtao Chen","orcid":"https://orcid.org/0000-0002-5102-1472"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangtao Chen","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111430977","display_name":"Chee Keong Kwoh","orcid":null},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Chee Keong Kwoh","raw_affiliation_strings":["Nanyang Technological University,College of Computing &amp; Data Science,Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nanyang Technological University,College of Computing &amp; Data Science,Singapore","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.9124,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.88686929,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"1213","last_page":"1218"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9735000133514404,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9735000133514404,"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":0.9021999835968018,"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":0.7250623106956482},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5195827484130859},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.41350260376930237},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.35339289903640747},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.329693466424942},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.1965552568435669},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.18765941262245178},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13898879289627075}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7250623106956482},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5195827484130859},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.41350260376930237},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35339289903640747},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.329693466424942},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1965552568435669},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.18765941262245178},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13898879289627075}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822097","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822097","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W2990346675","https://openalex.org/W3027051073","https://openalex.org/W3044145717","https://openalex.org/W3050508217","https://openalex.org/W3125488134","https://openalex.org/W3129866267","https://openalex.org/W3164692211","https://openalex.org/W3201518044","https://openalex.org/W4211225597","https://openalex.org/W4220979272","https://openalex.org/W4226192560","https://openalex.org/W4313424250","https://openalex.org/W4313454424","https://openalex.org/W4321611267","https://openalex.org/W4322738920","https://openalex.org/W4324344255","https://openalex.org/W4378212119","https://openalex.org/W4378212624","https://openalex.org/W4384665375","https://openalex.org/W4385459199","https://openalex.org/W4389938094","https://openalex.org/W4390814844","https://openalex.org/W4399892951"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Recent":[0],"advances":[1],"in":[2,204],"spatial":[3,40,88,147,183,205],"omics":[4,9,29,130],"technologies":[5],"have":[6],"allowed":[7],"various":[8],"data":[10,42],"to":[11,34,58,75,94,111,117,145,180],"be":[12],"obtained":[13],"from":[14,193,217],"a":[15,49,83,104,134,140,153],"single":[16],"tissue":[17],"section.":[18],"To":[19],"fully":[20],"explore":[21,118],"the":[22,119,150,218],"relationships":[23],"among":[24],"these":[25],"different":[26,129],"types":[27],"of":[28],"data,":[30],"it":[31],"is":[32,213],"urgent":[33],"develop":[35],"more":[36,181],"effective":[37],"methods":[38,203],"for":[39,69,211,215],"multi-omics":[41,78,184,206],"integration.":[43,185],"In":[44],"this":[45],"work,":[46],"we":[47,80,124],"propose":[48],"novel":[50],"Multi-level":[51],"Graph":[52],"Contrastive":[53],"Learning":[54],"framework,":[55],"named":[56],"SMMGCL,":[57],"simultaneously":[59],"mine":[60],"complementary":[61],"information":[62],"at":[63,221],"both":[64],"spot":[65,91],"and":[66,166,178,190],"graph":[67,141],"levels":[68],"integrating":[70],"Spatial":[71],"Multi-omics":[72],"data.":[73],"Specifically,":[74],"adaptively":[76],"fuse":[77],"modalities,":[79],"first":[81],"design":[82],"multi-modality":[84],"autoencoder":[85],"that":[86,197],"integrates":[87],"locations":[89],"with":[90,169],"omic":[92],"expressions":[93],"extract":[95,146],"modality-specific":[96],"embeddings.":[97],"These":[98],"embeddings":[99],"are":[100],"then":[101,138],"fused":[102],"into":[103,133],"consensus":[105],"representation":[106],"using":[107],"an":[108],"attention":[109],"mechanism":[110],"capture":[112],"spot-level":[113,165],"cross-omics":[114,155],"representations.":[115],"Next,":[116],"complex":[120],"inter-omic":[121],"structural":[122],"information,":[123],"connect":[125],"corresponding":[126],"spots":[127],"across":[128,149,194],"adjacency":[131],"graphs":[132],"heterogeneous":[135],"graph.":[136],"We":[137],"employ":[139],"convolutional":[142],"network":[143],"(GCN)":[144],"correlations":[148],"omics,":[151],"learning":[152],"graph-level":[154,167],"global":[156],"representation.":[157],"Finally,":[158],"SMMGCL":[159,198,212],"aligns":[160],"feature":[161],"similarity":[162,172],"matrixes":[163],"between":[164],"representations":[168],"their":[170],"pseudo-label":[171],"matrix,":[173],"ensuring":[174],"multi-level":[175],"clustering":[176],"consistency":[177],"leading":[179],"accurate":[182],"Experimental":[186],"results":[187],"on":[188],"simulated":[189],"real":[191],"datasets":[192],"tissues":[195],"show":[196],"consistently":[199],"outperforms":[200],"other":[201],"state-of-the-art":[202],"integration":[207],"performance.":[208],"The":[209],"code":[210],"available":[214],"download":[216],"GitHub":[219],"repository":[220],"https://github.com/cs-wangbo/SMMGCL.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
