{"id":"https://openalex.org/W7166522751","doi":"https://doi.org/10.1093/bioinformatics/btag465","title":"ARISE: RNA-anchored shared-edge topology and hierarchical fusion for spatial multi-omics integration","display_name":"ARISE: RNA-anchored shared-edge topology and hierarchical fusion for spatial multi-omics integration","publication_year":2026,"publication_date":"2026-06-25","ids":{"openalex":"https://openalex.org/W7166522751","doi":"https://doi.org/10.1093/bioinformatics/btag465","pmid":"https://pubmed.ncbi.nlm.nih.gov/42366683"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag465","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag465","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag465","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008261150","display_name":"X Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I49232843","display_name":"Changchun University","ror":"https://ror.org/02an57k10","country_code":"CN","type":"education","lineage":["https://openalex.org/I49232843"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangxiang Wang","raw_affiliation_strings":["School of Artificial Intelligence, Jilin University , Changchun 130012,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence, Jilin University , Changchun 130012,","institution_ids":["https://openalex.org/I194450716","https://openalex.org/I49232843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057904586","display_name":"Yanchi Su","orcid":"https://orcid.org/0000-0001-5011-694X"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanchi Su","raw_affiliation_strings":["School of Information Science and Technology, Northeast Normal University , Changchun 130117,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Northeast Normal University , Changchun 130117,","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123272821","display_name":"Gaoyang Hao","orcid":null},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I49232843","display_name":"Changchun University","ror":"https://ror.org/02an57k10","country_code":"CN","type":"education","lineage":["https://openalex.org/I49232843"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gaoyang Hao","raw_affiliation_strings":["School of Artificial Intelligence, Jilin University , Changchun 130012,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence, Jilin University , Changchun 130012,","institution_ids":["https://openalex.org/I194450716","https://openalex.org/I49232843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101940083","display_name":"Meng Wang","orcid":"https://orcid.org/0000-0001-9590-4202"},"institutions":[{"id":"https://openalex.org/I184843921","display_name":"Hebei University of Technology","ror":"https://ror.org/018hded08","country_code":"CN","type":"education","lineage":["https://openalex.org/I184843921"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Meng Wang","raw_affiliation_strings":["School of Artificial Intelligence, Hebei University of Technology , Tianjin 300401,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence, Hebei University of Technology , Tianjin 300401,","institution_ids":["https://openalex.org/I184843921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100633632","display_name":"Yue Wang","orcid":"https://orcid.org/0000-0003-0098-5359"},"institutions":[{"id":"https://openalex.org/I184843921","display_name":"Hebei University of Technology","ror":"https://ror.org/018hded08","country_code":"CN","type":"education","lineage":["https://openalex.org/I184843921"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yunhe Wang","raw_affiliation_strings":["School of Artificial Intelligence, Hebei University of Technology , Tianjin 300401,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence, Hebei University of Technology , Tianjin 300401,","institution_ids":["https://openalex.org/I184843921"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102888868","display_name":"Xin Li","orcid":"https://orcid.org/0000-0002-7513-9475"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I49232843","display_name":"Changchun University","ror":"https://ror.org/02an57k10","country_code":"CN","type":"education","lineage":["https://openalex.org/I49232843"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangtao Li","raw_affiliation_strings":["School of Artificial Intelligence, Jilin University , Changchun 130012,"],"raw_orcid":"https://orcid.org/0000-0002-8716-9823","affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence, Jilin University , Changchun 130012,","institution_ids":["https://openalex.org/I194450716","https://openalex.org/I49232843"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.72246835,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5285999774932861,"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":0.5285999774932861,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.2240000069141388,"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":0.13819999992847443,"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/spurious-relationship","display_name":"Spurious relationship","score":0.548799991607666},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5270000100135803},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.486299991607666},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.454800009727478},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.424699991941452},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.421099990606308},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.38769999146461487},{"id":"https://openalex.org/keywords/intersection","display_name":"Intersection (aeronautics)","score":0.37869998812675476}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7142000198364258},{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.548799991607666},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5270000100135803},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.486299991607666},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.47279998660087585},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.454800009727478},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.424699991941452},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.421099990606308},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.38769999146461487},{"id":"https://openalex.org/C64543145","wikidata":"https://www.wikidata.org/wiki/Q162942","display_name":"Intersection (aeronautics)","level":2,"score":0.37869998812675476},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.3677999973297119},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3253999948501587},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.3176000118255615},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.30869999527931213},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.304500013589859},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.3037000000476837},{"id":"https://openalex.org/C12426560","wikidata":"https://www.wikidata.org/wiki/Q189569","display_name":"Basis (linear algebra)","level":2,"score":0.30149999260902405},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.29100000858306885},{"id":"https://openalex.org/C13670688","wikidata":"https://www.wikidata.org/wiki/Q3500548","display_name":"Space partitioning","level":2,"score":0.2838999927043915},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.2603999972343445},{"id":"https://openalex.org/C158525013","wikidata":"https://www.wikidata.org/wiki/Q2593739","display_name":"Fusion","level":2,"score":0.259799987077713}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"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},{"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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag465","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag465","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42366683","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42366683","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13360277","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13360277/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag465","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag465","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3605434345","display_name":null,"funder_award_id":"62076109","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5746813410","display_name":null,"funder_award_id":"62472195","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8297086914","display_name":null,"funder_award_id":"20260102302JC","funder_id":"https://openalex.org/F4320310121","funder_display_name":"Natural Science Foundation of Jilin Province"}],"funders":[{"id":"https://openalex.org/F4320310121","display_name":"Natural Science Foundation of Jilin Province","ror":null},{"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":12,"referenced_works":["https://openalex.org/W3108118546","https://openalex.org/W3129866267","https://openalex.org/W3210002151","https://openalex.org/W4226192560","https://openalex.org/W4322738920","https://openalex.org/W4324344255","https://openalex.org/W4388017732","https://openalex.org/W4399892951","https://openalex.org/W4400678867","https://openalex.org/W4406401130","https://openalex.org/W4407605708","https://openalex.org/W7124552529"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Spatial":[1,66],"multi-omics":[2,76,133,190],"technologies":[3],"jointly":[4],"profile":[5],"transcriptomes,":[6],"proteins":[7],"and":[8,54,87,97,137,142,152,176,185],"chromatin":[9],"accessibility":[10],"in":[11,140,206],"situ,":[12],"enabling":[13],"integrative":[14],"analysis":[15],"of":[16,118,154],"tissue":[17,155],"organization":[18],"across":[19],"molecular":[20],"layers.":[21],"However,":[22],"most":[23],"existing":[24,159],"graph-based":[25],"integration":[26],"methods":[27],"rely":[28],"on":[29,93],"independently":[30],"constructed":[31],"modality-specific":[32],"k-nearest-neighbor":[33],"graphs.":[34],"When":[35],"auxiliary":[36,91],"modalities":[37,92],"are":[38],"sparse":[39],"or":[40],"noisy,":[41],"these":[42],"graphs":[43],"can":[44],"become":[45],"topologically":[46],"discordant,":[47],"propagate":[48],"spurious":[49],"edges,":[50],"weaken":[51],"cross-modal":[52,150],"alignment,":[53],"reduce":[55],"spatial":[56,75,132,147,189],"domain":[57,148,172],"resolution.":[58],"RESULTS:":[59],"We":[60,104],"present":[61],"Anchored":[62],"RNA":[63,70,85],"for":[64,74,127,188],"Integrated":[65],"Embedding":[67],"(ARISE),":[68],"an":[69],"expression":[71],"anchored":[72],"framework":[73,187],"integration.":[77,191],"ARISE":[78,145,181],"defines":[79],"a":[80,115,124,183],"shared-edge":[81],"topology":[82,128],"by":[83],"intersecting":[84],"feature-similarity":[86],"spatial-proximity":[88],"graphs,":[89],"encodes":[90],"this":[94,207],"common":[95],"scaffold,":[96],"integrates":[98],"them":[99],"through":[100],"inside-out":[101],"hierarchical":[102],"fusion.":[103],"further":[105],"show":[106],"theoretically":[107],"that":[108,180],"graph":[109,120],"intersection":[110],"minimizes":[111],"false-positive":[112],"edges":[113],"within":[114],"broad":[116],"class":[117],"k-of-r":[119],"fusion":[121],"rules,":[122],"providing":[123],"principled":[125],"basis":[126],"anchoring.":[129],"Across":[130],"various":[131],"benchmarks":[134],"spanning":[135],"simulated":[136],"real":[138],"datasets":[139],"bi-modal":[141],"tri-modal":[143],"settings,":[144],"improves":[146],"identification,":[149],"consistency,":[151],"preservation":[153],"structure":[156],"relative":[157],"to":[158],"methods.":[160],"Furthermore,":[161],"the":[162],"learned":[163],"representation":[164],"supports":[165],"biologically":[166],"meaningful":[167],"downstream":[168],"analyses,":[169],"including":[170],"marker-based":[171],"annotation,":[173],"pathway":[174],"enrichment,":[175],"cis-regulatory":[177],"inference,":[178],"indicating":[179],"yields":[182],"robust":[184],"interpretable":[186],"AVAILABILITY":[192],"AND":[193],"IMPLEMENTATION:":[194],"The":[195,202],"source":[196],"code":[197],"is":[198,209],"available":[199,210],"at":[200,211],"https://github.com/XiangxiangWang-code/ARISE.":[201],"archived":[203],"version":[204],"used":[205],"study":[208],"https://doi.org/10.6084/m9.figshare.32686137.v2.":[212]},"counts_by_year":[],"updated_date":"2026-07-27T08:26:11.824852","created_date":"2026-06-30T00:00:00"}