{"id":"https://openalex.org/W7125789387","doi":"https://doi.org/10.1109/tcbbio.2026.3658320","title":"HFFST: A Hierarchical Feature Fusion Algorithm for Spatial Gene Expression Prediction Using Histopathology Images","display_name":"HFFST: A Hierarchical Feature Fusion Algorithm for Spatial Gene Expression Prediction Using Histopathology Images","publication_year":2026,"publication_date":"2026-01-27","ids":{"openalex":"https://openalex.org/W7125789387","doi":"https://doi.org/10.1109/tcbbio.2026.3658320","pmid":"https://pubmed.ncbi.nlm.nih.gov/41591852"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2026.3658320","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3658320","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/A5124051343","display_name":"Yue Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yue Wang","raw_affiliation_strings":["Faculty of Research Center for Frontier Fundamental Studies, Zhejiang Lab, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Research Center for Frontier Fundamental Studies, Zhejiang Lab, Hangzhou, China","institution_ids":["https://openalex.org/I4210123185"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123945027","display_name":"Yanan Li","orcid":null},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanan Li","raw_affiliation_strings":["Faculty of Research Center for Frontier Fundamental Studies, Zhejiang Lab, Hangzhou, China"],"raw_orcid":"https://orcid.org/0000-0001-8482-7221","affiliations":[{"raw_affiliation_string":"Faculty of Research Center for Frontier Fundamental Studies, Zhejiang Lab, Hangzhou, China","institution_ids":["https://openalex.org/I4210123185"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123940927","display_name":"Changjiang Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Changjiang Zhou","raw_affiliation_strings":["Faculty of Research Center for Frontier Fundamental Studies, Zhejiang Lab, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Research Center for Frontier Fundamental Studies, Zhejiang Lab, Hangzhou, China","institution_ids":["https://openalex.org/I4210123185"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124034920","display_name":"Xiao Ma","orcid":null},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao Ma","raw_affiliation_strings":["Faculty of Research Center for Frontier Fundamental Studies, Zhejiang Lab, Hangzhou, China"],"raw_orcid":"https://orcid.org/0009-0002-7260-9504","affiliations":[{"raw_affiliation_string":"Faculty of Research Center for Frontier Fundamental Studies, Zhejiang Lab, Hangzhou, China","institution_ids":["https://openalex.org/I4210123185"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5123926337","display_name":"Ji Qi","orcid":null},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ji Qi","raw_affiliation_strings":["Faculty of Research Center for Frontier Fundamental Studies, Zhejiang Lab, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Research Center for Frontier Fundamental Studies, Zhejiang Lab, Hangzhou, China","institution_ids":["https://openalex.org/I4210123185"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210123185"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08118777,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"23","issue":"2","first_page":"795","last_page":"804"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.6499999761581421,"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":0.6499999761581421,"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/T10862","display_name":"AI in cancer detection","score":0.11249999701976776,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.06419999897480011,"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/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.6158000230789185},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5475000143051147},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.5127000212669373},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.45719999074935913},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4059999883174896},{"id":"https://openalex.org/keywords/feature-extraction","display_name":"Feature extraction","score":0.4034999907016754},{"id":"https://openalex.org/keywords/sensor-fusion","display_name":"Sensor fusion","score":0.3582000136375427},{"id":"https://openalex.org/keywords/fusion","display_name":"Fusion","score":0.3467999994754791}],"concepts":[{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.6158000230789185},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6047999858856201},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5927000045776367},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5475000143051147},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.5127000212669373},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4832000136375427},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.45719999074935913},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4059999883174896},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.4034999907016754},{"id":"https://openalex.org/C33954974","wikidata":"https://www.wikidata.org/wiki/Q486494","display_name":"Sensor fusion","level":2,"score":0.3582000136375427},{"id":"https://openalex.org/C158525013","wikidata":"https://www.wikidata.org/wiki/Q2593739","display_name":"Fusion","level":2,"score":0.3467999994754791},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.31929999589920044},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2913999855518341},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.2833000123500824},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2784000039100647},{"id":"https://openalex.org/C69744172","wikidata":"https://www.wikidata.org/wiki/Q860822","display_name":"Image fusion","level":3,"score":0.27720001339912415},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.2759999930858612},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.26030001044273376},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.258899986743927},{"id":"https://openalex.org/C2986522900","wikidata":"https://www.wikidata.org/wiki/Q2178623","display_name":"Spatial relationship","level":2,"score":0.25859999656677246},{"id":"https://openalex.org/C151201525","wikidata":"https://www.wikidata.org/wiki/Q177239","display_name":"Limit (mathematics)","level":2,"score":0.25679999589920044},{"id":"https://openalex.org/C28719098","wikidata":"https://www.wikidata.org/wiki/Q44946","display_name":"Point (geometry)","level":2,"score":0.2531000077724457},{"id":"https://openalex.org/C2982962833","wikidata":"https://www.wikidata.org/wiki/Q17092450","display_name":"Information fusion","level":2,"score":0.2529999911785126}],"mesh":[{"descriptor_ui":"D000098437","descriptor_name":"Prediction Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098437","descriptor_name":"Prediction Algorithms","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":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":"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":"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":"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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","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":"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":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2026.3658320","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3658320","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:41591852","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41591852","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/G1273514138","display_name":null,"funder_award_id":"T2293752","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G564781264","display_name":null,"funder_award_id":"T2293750","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"The":[0],"emergence":[1],"of":[2,10],"spatial":[3,41,71,96,128,133],"transcriptomics":[4],"has":[5,123],"greatly":[6],"advanced":[7],"our":[8,87],"understanding":[9],"disease":[11],"mechanisms,":[12],"identified":[13],"novel":[14],"therapeutic":[15],"targets,":[16],"and":[17,28,82,111,131],"contributed":[18],"to":[19,39,94],"progress":[20],"in":[21,126],"personalized":[22],"medicine.":[23],"However,":[24],"its":[25,32],"high":[26],"costs":[27],"technical":[29],"complexity":[30],"limit":[31],"widespread":[33],"application.":[34],"A":[35],"promising":[36],"alternative":[37],"is":[38],"predict":[40,95],"gene":[42,72,129],"expression":[43,73,130],"from":[44,58,74,84,119],"H&E-stained":[45,75],"pathology":[46,76],"images,":[47,86],"yet":[48],"existing":[49],"methods":[50],"have":[51],"not":[52],"fully":[53],"exploited":[54],"the":[55,101],"hierarchical":[56,65],"information":[57],"pathological":[59],"images.":[60,77],"We":[61],"propose":[62],"HFFST,":[63],"a":[64,90],"feature":[66,80],"fusion":[67,83],"algorithm":[68],"for":[69],"predicting":[70,127],"Leveraging":[78],"multi-level":[79],"extraction":[81],"whole-slide":[85],"method":[88],"employs":[89],"coarse-to-fine":[91],"regression":[92],"framework":[93],"transcriptomic":[97],"profiles.":[98],"To":[99],"validate":[100],"algorithm's":[102],"performance,":[103],"we":[104],"conducted":[105],"cross-validation":[106],"on":[107],"five":[108],"public":[109],"datasets":[110],"performed":[112],"external":[113],"validation":[114],"using":[115],"high-resolution":[116],"Visium":[117],"data":[118],"10X":[120],"Genomics.":[121],"HFFST":[122],"shown":[124],"promise":[125],"identifying":[132],"regions,":[134],"demonstrating":[135],"certain":[136],"advantages":[137],"over":[138],"state-of-the-art":[139],"methods.":[140]},"counts_by_year":[],"updated_date":"2026-07-18T07:39:51.176621","created_date":"2026-01-28T00:00:00"}