{"id":"https://openalex.org/W7126029598","doi":"https://doi.org/10.1109/bibm66473.2025.11356766","title":"High-Frequency-Aware Graph Integration for Subcellular Spatial Transcriptomics","display_name":"High-Frequency-Aware Graph Integration for Subcellular Spatial Transcriptomics","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126029598","doi":"https://doi.org/10.1109/bibm66473.2025.11356766"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356766","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356766","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","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/A5114859464","display_name":"Wanwan Shi","orcid":"https://orcid.org/0000-0003-4730-4610"},"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":"Wanwan Shi","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124174594","display_name":"Bo Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210164862","display_name":"Artificial Intelligence in Medicine (Canada)","ror":"https://ror.org/05p590m36","country_code":"CA","type":"company","lineage":["https://openalex.org/I4210164862"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Bo Wang","raw_affiliation_strings":["School of Computers and Artificial Intelligence, Zhengzhou University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computers and Artificial Intelligence, Zhengzhou University,China","institution_ids":["https://openalex.org/I4210164862"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066627747","display_name":"Yahui Long","orcid":"https://orcid.org/0000-0002-2765-3007"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yahui Long","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University,China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124270218","display_name":"Ying Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I173759888","display_name":"Hunan Normal University","ror":"https://ror.org/053w1zy07","country_code":"CN","type":"education","lineage":["https://openalex.org/I173759888"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Liu","raw_affiliation_strings":["College of Information Science and Engineering, Hunan Normal University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Science and Engineering, Hunan Normal University,China","institution_ids":["https://openalex.org/I173759888"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124289709","display_name":"Qiu Xiao","orcid":null},"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":"Qiu Xiao","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031253045","display_name":"Yuting Bai","orcid":"https://orcid.org/0000-0001-8047-1010"},"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":"Yuting Bai","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124247419","display_name":"Xiaoyi Peng","orcid":null},"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":"Xiaoyi Peng","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124207630","display_name":"Xiangtao Chen","orcid":null},"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":["College of Computer Science and Electronic Engineering, Hunan University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5121945908","display_name":"Jiawei Luo","orcid":null},"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":["College of Computer Science and Electronic Engineering, Hunan University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University,China","institution_ids":["https://openalex.org/I16609230"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"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":0.56541408,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"550","last_page":"555"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9943000078201294,"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":0.9943000078201294,"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":0.0008999999845400453,"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":0.0007999999797903001,"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/transcriptome","display_name":"Transcriptome","score":0.5964000225067139},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.552299976348877},{"id":"https://openalex.org/keywords/subcellular-localization","display_name":"Subcellular localization","score":0.5497000217437744},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.5256999731063843},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.46160000562667847},{"id":"https://openalex.org/keywords/protein-subcellular-localization-prediction","display_name":"Protein subcellular localization prediction","score":0.39149999618530273},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.362199991941452},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.3416999876499176}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5964000225067139},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.552299976348877},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5508000254631042},{"id":"https://openalex.org/C2776879804","wikidata":"https://www.wikidata.org/wiki/Q7630919","display_name":"Subcellular localization","level":3,"score":0.5497000217437744},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5256999731063843},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5069000124931335},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.46160000562667847},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4235000014305115},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3978999853134155},{"id":"https://openalex.org/C140051345","wikidata":"https://www.wikidata.org/wiki/Q7251501","display_name":"Protein subcellular localization prediction","level":3,"score":0.39149999618530273},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.362199991941452},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.3416999876499176},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.3402999937534332},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.33500000834465027},{"id":"https://openalex.org/C158709400","wikidata":"https://www.wikidata.org/wiki/Q3578586","display_name":"Spatial ecology","level":2,"score":0.303600013256073},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29789999127388},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.2915000021457672},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.29030001163482666},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.289900004863739},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.28690001368522644},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2865999937057495},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.28610000014305115},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.2694000005722046},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26919999718666077},{"id":"https://openalex.org/C175779824","wikidata":"https://www.wikidata.org/wiki/Q7574078","display_name":"Spatial organization","level":2,"score":0.2563999891281128}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356766","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356766","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4853472965","display_name":null,"funder_award_id":"62372165,62032007,62202152","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":21,"referenced_works":["https://openalex.org/W1965263024","https://openalex.org/W2006255103","https://openalex.org/W2743416243","https://openalex.org/W2800392236","https://openalex.org/W2915001443","https://openalex.org/W2952383043","https://openalex.org/W2990889969","https://openalex.org/W3005119354","https://openalex.org/W3108118546","https://openalex.org/W3164692211","https://openalex.org/W4226192560","https://openalex.org/W4244030505","https://openalex.org/W4286005528","https://openalex.org/W4322738920","https://openalex.org/W4380884725","https://openalex.org/W4382239962","https://openalex.org/W4384665375","https://openalex.org/W4386692444","https://openalex.org/W4402021167","https://openalex.org/W4405461799","https://openalex.org/W4409984740"],"related_works":[],"abstract_inverted_index":{"Recent":[0],"advances":[1],"in":[2,31,143],"spatial":[3,33,74,90,107,125,144],"transcriptomics":[4,34],"have":[5,27],"enabled":[6],"subcellular-resolution":[7],"profiling":[8],"of":[9],"gene":[10,146],"expression,":[11],"offering":[12],"unprecedented":[13],"opportunities":[14],"to":[15,63,97,119],"investigate":[16],"intracellular":[17],"architecture":[18],"and":[19,56,67,149],"local":[20],"microenvironmental":[21],"interactions.":[22],"Graph":[23,85],"neural":[24],"networks":[25],"(GNNs)":[26],"shown":[28],"great":[29],"promise":[30],"modeling":[32],"data.":[35],"However,":[36],"existing":[37],"GNN-based":[38],"methods":[39,142],"primarily":[40],"focus":[41],"on":[42,132],"low-frequency":[43],"signals,":[44],"overlooking":[45],"high-frequency":[46,99],"signals":[47],"critical":[48],"for":[49,88],"resolving":[50],"transcriptional":[51,100,128],"differences":[52],"across":[53],"subcellular":[54,89,133],"compartments":[55],"cell":[57,121],"boundaries.":[58],"This":[59],"limits":[60],"their":[61],"ability":[62],"characterize":[64],"fine-grained":[65],"structural":[66],"functional":[68],"heterogeneity":[69],"within":[70],"tissues,":[71],"hindering":[72],"accurate":[73],"domain":[75],"identification.":[76,151],"In":[77],"this":[78],"study,":[79],"we":[80],"propose":[81],"HiFi-ST,":[82],"a":[83,94,110],"High-Frequency-Aware":[84],"Integration":[86],"framework":[87],"transcriptomics.":[91],"HiFi-ST":[92,137],"employs":[93],"high-pass":[95],"filter":[96],"extract":[98],"differences,":[101],"which":[102],"are":[103],"then":[104],"integrated":[105],"with":[106,127],"contexts":[108],"through":[109],"transformer-based":[111],"architecture.":[112],"A":[113],"contrastive":[114],"learning":[115],"module":[116],"is":[117],"designed":[118],"enhance":[120],"representation":[122],"by":[123],"aligning":[124],"organization":[126],"heterogeneity.":[129],"Comprehensive":[130],"experiments":[131],"datasets":[134],"demonstrated":[135],"that":[136],"consistently":[138],"outperformed":[139],"six":[140],"state-of-the-art":[141],"clustering,":[145],"expression":[147],"enhancement,":[148],"niche":[150]},"counts_by_year":[],"updated_date":"2026-02-01T03:34:12.195049","created_date":"2026-01-30T00:00:00"}