{"id":"https://openalex.org/W7224744859","doi":"https://doi.org/10.54097/6pg9t237","title":"HiFi-ST: Histology-Conditioned Local Coordinate Modeling for Spatial Gene Expression Prediction","display_name":"HiFi-ST: Histology-Conditioned Local Coordinate Modeling for Spatial Gene Expression Prediction","publication_year":2026,"publication_date":"2026-10-29","ids":{"openalex":"https://openalex.org/W7224744859","doi":"https://doi.org/10.54097/6pg9t237"},"language":"en","primary_location":{"id":"doi:10.54097/6pg9t237","doi":"https://doi.org/10.54097/6pg9t237","is_oa":true,"landing_page_url":"https://doi.org/10.54097/6pg9t237","pdf_url":"https://drpress.org/ojs/index.php/fcis/article/download/36263/35358","source":{"id":"https://openalex.org/S4387283309","display_name":"Frontiers in Computing and Intelligent Systems","issn_l":"2832-6024","issn":["2832-6024"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Computing and Intelligent Systems","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://drpress.org/ojs/index.php/fcis/article/download/36263/35358","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5160161266","display_name":"Lei Tang","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Lei Tang","raw_affiliation_strings":["School of Mathematics and Computer Science, Yunnan Minzu University, Kunming, Yunnan, 650500, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics and Computer Science, Yunnan Minzu University, Kunming, Yunnan, 650500, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5160161266"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.77040502,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"18","issue":"2","first_page":"29","last_page":"35"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9911999702453613,"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":0.9911999702453613,"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":0.005400000140070915,"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":0.000699999975040555,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/spatial-gene-expression-prediction","display_name":"spatial gene expression prediction","score":0.8740000128746033},{"id":"https://openalex.org/keywords/spatial-transcriptomics","display_name":"spatial transcriptomics","score":0.8379999995231628},{"id":"https://openalex.org/keywords/h-e-images","display_name":"H&E images","score":0.7139999866485596},{"id":"https://openalex.org/keywords/stochastic-aggregation","display_name":"stochastic aggregation","score":0.7889999747276306},{"id":"https://openalex.org/keywords/her2-positive-breast-cancer","display_name":"HER2-positive breast cancer","score":0.9089999794960022},{"id":"https://openalex.org/keywords/cutaneous-squamous-cell-carcinoma","display_name":"cutaneous squamous cell carcinoma","score":0.9570000171661377},{"id":"https://openalex.org/keywords/tissue-morphology","display_name":"tissue morphology","score":0.5180000066757202},{"id":"https://openalex.org/keywords/spatial-clustering","display_name":"spatial clustering","score":0.6460000276565552}],"concepts":[{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.661899983882904},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.6570000052452087},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5241000056266785},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.49079999327659607},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4765999913215637},{"id":"https://openalex.org/C150060386","wikidata":"https://www.wikidata.org/wiki/Q7574054","display_name":"Spatial correlation","level":2,"score":0.45910000801086426},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.45739999413490295},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4433000087738037},{"id":"https://openalex.org/C158709400","wikidata":"https://www.wikidata.org/wiki/Q3578586","display_name":"Spatial ecology","level":2,"score":0.43869999051094055},{"id":"https://openalex.org/C152139883","wikidata":"https://www.wikidata.org/wiki/Q252973","display_name":"Mutual information","level":2,"score":0.41839998960494995},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.415800005197525},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4000999927520752},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.38429999351501465},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3781000077724457},{"id":"https://openalex.org/C151201525","wikidata":"https://www.wikidata.org/wiki/Q177239","display_name":"Limit (mathematics)","level":2,"score":0.37299999594688416},{"id":"https://openalex.org/C94747663","wikidata":"https://www.wikidata.org/wiki/Q7574086","display_name":"Spatial variability","level":2,"score":0.31630000472068787},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.30300000309944153},{"id":"https://openalex.org/C80551277","wikidata":"https://www.wikidata.org/wiki/Q11210","display_name":"Coordinate system","level":2,"score":0.2946999967098236},{"id":"https://openalex.org/C2780092901","wikidata":"https://www.wikidata.org/wiki/Q3433612","display_name":"Correlation coefficient","level":2,"score":0.2937999963760376},{"id":"https://openalex.org/C173727882","wikidata":"https://www.wikidata.org/wiki/Q5153620","display_name":"Common spatial pattern","level":2,"score":0.29339998960494995},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.27129998803138733},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2702000141143799}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.54097/6pg9t237","doi":"https://doi.org/10.54097/6pg9t237","is_oa":true,"landing_page_url":"https://doi.org/10.54097/6pg9t237","pdf_url":"https://drpress.org/ojs/index.php/fcis/article/download/36263/35358","source":{"id":"https://openalex.org/S4387283309","display_name":"Frontiers in Computing and Intelligent Systems","issn_l":"2832-6024","issn":["2832-6024"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Computing and Intelligent Systems","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.54097/6pg9t237","doi":"https://doi.org/10.54097/6pg9t237","is_oa":true,"landing_page_url":"https://doi.org/10.54097/6pg9t237","pdf_url":"https://drpress.org/ojs/index.php/fcis/article/download/36263/35358","source":{"id":"https://openalex.org/S4387283309","display_name":"Frontiers in Computing and Intelligent Systems","issn_l":"2832-6024","issn":["2832-6024"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Computing and Intelligent Systems","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7224744859.pdf","grobid_xml":"https://content.openalex.org/works/W7224744859.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W2471536144","https://openalex.org/W2760103357","https://openalex.org/W2937443931","https://openalex.org/W3036371598","https://openalex.org/W3092450854","https://openalex.org/W3198511950","https://openalex.org/W3216067893","https://openalex.org/W4285803722","https://openalex.org/W4390242455","https://openalex.org/W4403853489","https://openalex.org/W7133227398"],"related_works":["https://openalex.org/W4414081644","https://openalex.org/W7169615526","https://openalex.org/W7213751111","https://openalex.org/W3216067893","https://openalex.org/W7167729897","https://openalex.org/W4415084568","https://openalex.org/W4285803722","https://openalex.org/W4413341259","https://openalex.org/W4416528032","https://openalex.org/W4399836976"],"abstract_inverted_index":{"Spatial":[0],"transcriptomics":[1],"(ST)":[2],"enables":[3],"the":[4,19,145,181],"characterization":[5],"of":[6,21,103,170,178,183],"spatial":[7,37,56,139,150,184,198],"gene":[8,38,199],"expression":[9,39,71,84,140,147,200],"patterns":[10,151],"in":[11],"tissues,":[12],"but":[13],"its":[14],"discrete":[15],"measurement":[16],"locations":[17],"limit":[18],"availability":[20],"spatially":[22],"resolved":[23],"molecular":[24],"information.":[25,58],"To":[26],"address":[27],"this":[28],"challenge,":[29],"we":[30],"propose":[31],"HiFi-ST,":[32],"a":[33,127,165,173],"histology-conditioned":[34],"framework":[35],"for":[36],"prediction":[40,134,201],"based":[41],"on":[42,87,121,136],"local":[43,60,207],"coordinate":[44,57,61,208],"modeling.":[45],"HiFi-ST":[46,116,191],"integrates":[47],"multiscale":[48,204],"hematoxylin":[49],"and":[50,69,93,106,123,132,172,210],"eosin":[51],"(H&E)":[52],"image":[53],"representations":[54],"with":[55,110,153],"Multiple":[59],"queries":[62],"are":[63,73],"performed":[64],"within":[65],"each":[66],"spot":[67],"neighborhood,":[68],"their":[70],"predictions":[72],"combined":[74],"through":[75],"stochastic":[76],"aggregation":[77],"to":[78,187,196],"generate":[79],"spot-level":[80,211],"estimates":[81],"under":[82],"observed":[83],"supervision.":[85],"Experiments":[86],"three":[88],"public":[89],"datasets,":[90],"HER2+,":[91],"cSCC,":[92],"Alex_NatGen,":[94,124],"achieved":[95,117,164],"mean":[96,166,174],"gene-wise":[97],"Pearson":[98],"correlation":[99,120],"coefficients":[100],"(PCC":[101],"(ACG))":[102],"0.3547,":[104],"0.3314,":[105],"0.3385,":[107],"respectively.":[108],"Compared":[109],"previously":[111],"published":[112],"benchmark":[113],"reference":[114],"results,":[115],"higher":[118,129],"overall":[119],"HER2+":[122,162],"while":[125],"obtaining":[126],"slightly":[128],"PCC":[130],"(ACG)":[131],"lower":[133],"errors":[135],"cSCC.":[137],"Gene-level":[138],"analyses":[141],"further":[142],"demonstrated":[143],"that":[144],"predicted":[146],"preserved":[148],"selected":[149],"associated":[152],"tissue":[154],"morphology.":[155],"In":[156],"addition,":[157],"spatial-domain":[158],"clustering":[159],"across":[160],"six":[161],"sections":[163],"adjusted":[167],"Rand":[168],"index":[169],"0.3610":[171],"normalized":[175],"mutual":[176],"information":[177,185],"0.3847,":[179],"indicating":[180],"preservation":[182],"relevant":[186],"tissue-region":[188],"organization.":[189],"Overall,":[190],"provides":[192],"an":[193],"effective":[194],"approach":[195],"histology-driven":[197],"by":[202],"integrating":[203],"morphological":[205],"features,":[206],"modeling,":[209],"aggregation.":[212]},"counts_by_year":[],"updated_date":"2026-11-01T11:40:01.658920","created_date":"2026-10-31T00:00:00"}