{"id":"https://openalex.org/W7161540699","doi":"https://doi.org/10.1186/s12859-026-06447-7","title":"From histology to spatial transcriptomics: establishing a lightweight single-patch baseline","display_name":"From histology to spatial transcriptomics: establishing a lightweight single-patch baseline","publication_year":2026,"publication_date":"2026-05-18","ids":{"openalex":"https://openalex.org/W7161540699","doi":"https://doi.org/10.1186/s12859-026-06447-7","pmid":"https://pubmed.ncbi.nlm.nih.gov/42151778"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-026-06447-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06447-7","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s12859-026-06447-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5136380871","display_name":"Hyungyum Jang","orcid":null},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]},{"id":"https://openalex.org/I24214720","display_name":"Hansung University","ror":"https://ror.org/048m9x696","country_code":"KR","type":"education","lineage":["https://openalex.org/I24214720"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Hyungyum Jang","raw_affiliation_strings":["Department of Applied Artificial Intelligence, Hansung University, Samseongyo-ro 16-gil 116, Seongbuk-gu, Seoul, 02876, South Korea","Department of Electrical and Electronic Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, Seoul, 03722, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Artificial Intelligence, Hansung University, Samseongyo-ro 16-gil 116, Seongbuk-gu, Seoul, 02876, South Korea","institution_ids":["https://openalex.org/I24214720"]},{"raw_affiliation_string":"Department of Electrical and Electronic Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, Seoul, 03722, South Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136355663","display_name":"Hyunsoo Shin","orcid":null},"institutions":[{"id":"https://openalex.org/I24214720","display_name":"Hansung University","ror":"https://ror.org/048m9x696","country_code":"KR","type":"education","lineage":["https://openalex.org/I24214720"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Hyunsoo Shin","raw_affiliation_strings":["Department of Applied Artificial Intelligence, Hansung University, Samseongyo-ro 16-gil 116, Seongbuk-gu, Seoul, 02876, South Korea","Department of Applied IT Engineering, Hansung University College of IT Engineering, Samseongyo-ro 16-gil 116, Seongbuk-gu, Seoul, 02876, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Artificial Intelligence, Hansung University, Samseongyo-ro 16-gil 116, Seongbuk-gu, Seoul, 02876, South Korea","institution_ids":["https://openalex.org/I24214720"]},{"raw_affiliation_string":"Department of Applied IT Engineering, Hansung University College of IT Engineering, Samseongyo-ro 16-gil 116, Seongbuk-gu, Seoul, 02876, South Korea","institution_ids":["https://openalex.org/I24214720"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136365051","display_name":"Hawon Lee","orcid":null},"institutions":[{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hawon Lee","raw_affiliation_strings":["Department of Biomedical Sciences, Korea University College of Medicine, Jeongneung-ro 161, Seongbuk-gu, Seoul, 02708, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Sciences, Korea University College of Medicine, Jeongneung-ro 161, Seongbuk-gu, Seoul, 02708, South Korea","institution_ids":["https://openalex.org/I4210161052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136418571","display_name":"Yena Jang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210109935","display_name":"Inje University Busan Paik Hospital","ror":"https://ror.org/01pzf6r50","country_code":"KR","type":"healthcare","lineage":["https://openalex.org/I104338594","https://openalex.org/I4210109935","https://openalex.org/I4405258751"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Yena Jang","raw_affiliation_strings":["Inje University College of Medicine, 75 Bokji-ro, Busanjin-gu, Busan, 47392, South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inje University College of Medicine, 75 Bokji-ro, Busanjin-gu, Busan, 47392, South Korea","institution_ids":["https://openalex.org/I4210109935"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136419445","display_name":"Sunghoon Jung","orcid":null},"institutions":[{"id":"https://openalex.org/I24214720","display_name":"Hansung University","ror":"https://ror.org/048m9x696","country_code":"KR","type":"education","lineage":["https://openalex.org/I24214720"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Sung Hoon Jung","raw_affiliation_strings":["Department of Applied Artificial Intelligence, Hansung University, Samseongyo-ro 16-gil 116, Seongbuk-gu, Seoul, 02876, South Korea. shjung@hansung.ac.kr"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Artificial Intelligence, Hansung University, Samseongyo-ro 16-gil 116, Seongbuk-gu, Seoul, 02876, South Korea. shjung@hansung.ac.kr","institution_ids":["https://openalex.org/I24214720"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003685784","display_name":"Minji Jeon","orcid":"https://orcid.org/0000-0001-5731-6186"},"institutions":[{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Minji Jeon","raw_affiliation_strings":["Department of Biomedical Informatics, Korea University College of Medicine, Jeongneung-ro 161, Seongbuk-gu, Seoul, 02708, South Korea. mjjeon@korea.ac.kr","Department of Biomedical Sciences, Korea University College of Medicine, Jeongneung-ro 161, Seongbuk-gu, Seoul, 02708, South Korea. mjjeon@korea.ac.kr"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Korea University College of Medicine, Jeongneung-ro 161, Seongbuk-gu, Seoul, 02708, South Korea. mjjeon@korea.ac.kr","institution_ids":["https://openalex.org/I4210161052"]},{"raw_affiliation_string":"Department of Biomedical Sciences, Korea University College of Medicine, Jeongneung-ro 161, Seongbuk-gu, Seoul, 02708, South Korea. mjjeon@korea.ac.kr","institution_ids":["https://openalex.org/I4210161052"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5003685784","https://openalex.org/A5136419445"],"corresponding_institution_ids":["https://openalex.org/I24214720","https://openalex.org/I4210161052"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.42855902,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9318000078201294,"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":0.9318000078201294,"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":0.030700000002980232,"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/T10885","display_name":"Gene expression and cancer classification","score":0.004999999888241291,"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/leverage","display_name":"Leverage (statistics)","score":0.7788000106811523},{"id":"https://openalex.org/keywords/baseline","display_name":"Baseline (sea)","score":0.5914000272750854},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.578000009059906},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.4438999891281128},{"id":"https://openalex.org/keywords/spatial-correlation","display_name":"Spatial correlation","score":0.43650001287460327},{"id":"https://openalex.org/keywords/predictive-modelling","display_name":"Predictive modelling","score":0.43220001459121704},{"id":"https://openalex.org/keywords/correlation","display_name":"Correlation","score":0.4226999878883362},{"id":"https://openalex.org/keywords/spatial-contextual-awareness","display_name":"Spatial contextual awareness","score":0.39809998869895935},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.39250001311302185}],"concepts":[{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.7788000106811523},{"id":"https://openalex.org/C12725497","wikidata":"https://www.wikidata.org/wiki/Q810247","display_name":"Baseline (sea)","level":2,"score":0.5914000272750854},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.578000009059906},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5512999892234802},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.4438999891281128},{"id":"https://openalex.org/C150060386","wikidata":"https://www.wikidata.org/wiki/Q7574054","display_name":"Spatial correlation","level":2,"score":0.43650001287460327},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4345000088214874},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.43220001459121704},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.4226999878883362},{"id":"https://openalex.org/C64754055","wikidata":"https://www.wikidata.org/wiki/Q7574053","display_name":"Spatial contextual awareness","level":2,"score":0.39809998869895935},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.39250001311302185},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3887999951839447},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37560001015663147},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.36579999327659607},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.36149999499320984},{"id":"https://openalex.org/C69991583","wikidata":"https://www.wikidata.org/wiki/Q1423575","display_name":"Candidate gene","level":3,"score":0.3515999913215637},{"id":"https://openalex.org/C55078378","wikidata":"https://www.wikidata.org/wiki/Q1136628","display_name":"Pearson product-moment correlation coefficient","level":2,"score":0.3447999954223633},{"id":"https://openalex.org/C2780092901","wikidata":"https://www.wikidata.org/wiki/Q3433612","display_name":"Correlation coefficient","level":2,"score":0.33550000190734863},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3314000070095062},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3287999927997589},{"id":"https://openalex.org/C530470458","wikidata":"https://www.wikidata.org/wiki/Q128581","display_name":"Breast cancer","level":3,"score":0.32850000262260437},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.3255000114440918},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3206000030040741},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.2897999882698059},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.28949999809265137},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.27390000224113464},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.26969999074935913},{"id":"https://openalex.org/C160633673","wikidata":"https://www.wikidata.org/wiki/Q355198","display_name":"Pixel","level":2,"score":0.2678000032901764},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2653000056743622},{"id":"https://openalex.org/C57742111","wikidata":"https://www.wikidata.org/wiki/Q7168","display_name":"Histology","level":2,"score":0.26179999113082886},{"id":"https://openalex.org/C205372480","wikidata":"https://www.wikidata.org/wiki/Q210521","display_name":"Image resolution","level":2,"score":0.2572000026702881},{"id":"https://openalex.org/C27438332","wikidata":"https://www.wikidata.org/wiki/Q2873","display_name":"Principal component analysis","level":2,"score":0.25360000133514404},{"id":"https://openalex.org/C125473707","wikidata":"https://www.wikidata.org/wiki/Q9914","display_name":"H&E stain","level":3,"score":0.25279998779296875},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2524000108242035},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.2502000033855438}],"mesh":[{"descriptor_ui":"D000098415","descriptor_name":"Convolutional Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098415","descriptor_name":"Convolutional Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098415","descriptor_name":"Convolutional Neural Networks","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":true},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","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":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-026-06447-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06447-7","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42151778","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42151778","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:f3f713e4e5a146ab85ff8ebad489c575","is_oa":false,"landing_page_url":"https://doaj.org/article/f3f713e4e5a146ab85ff8ebad489c575","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"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":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 27, Iss 1 (2026)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13466082","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13466082/","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"doi:10.6084/m9.figshare.c.8647828","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.c.8647828","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Collection"},{"id":"doi:10.6084/m9.figshare.c.8647828.v1","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.c.8647828.v1","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Collection"}],"best_oa_location":{"id":"doi:10.1186/s12859-026-06447-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06447-7","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321232","display_name":"Hansung University","ror":"https://ror.org/048m9x696"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W2194775991","https://openalex.org/W2518570910","https://openalex.org/W2585175142","https://openalex.org/W2800392236","https://openalex.org/W2889985731","https://openalex.org/W2984472267","https://openalex.org/W3036882247","https://openalex.org/W3112600195","https://openalex.org/W3212889265","https://openalex.org/W3213918788","https://openalex.org/W4213019189","https://openalex.org/W4385543702","https://openalex.org/W4390661109","https://openalex.org/W4391280845","https://openalex.org/W4392947521","https://openalex.org/W4393515961","https://openalex.org/W4394758412","https://openalex.org/W4398201291","https://openalex.org/W4400889241","https://openalex.org/W4403479110","https://openalex.org/W4404349892","https://openalex.org/W7133227398"],"related_works":[],"abstract_inverted_index":{"Predicting":[0],"spatial":[1,26,61,128,235,244,264,273],"gene":[2,76,206],"expression":[3,77],"from":[4,28,39],"hematoxylin":[5],"and":[6,71,97,104,134,211,268],"eosin":[7],"(H&E)-stained":[8],"histological":[9],"images":[10,31],"is":[11,51,228],"a":[12,68,81,100,107,139,175,183,257],"central":[13],"challenge":[14],"in":[15,237,271],"the":[16,25,35,56,120,159,192,232,261],"field":[17],"of":[18,59,145,234,263],"computational":[19],"pathology.":[20],"Although":[21],"many":[22],"models":[23],"leverage":[24],"context":[27],"entire":[29],"whole-slide":[30],"to":[32,53],"boost":[33],"performance,":[34],"predictive":[36],"capability":[37],"achievable":[38],"single,":[40],"isolated":[41],"tissue":[42,218],"patches":[43],"remains":[44],"unexplored.":[45],"Without":[46],"this":[47,64,188,254],"fundamental":[48],"baseline,":[49],"it":[50],"difficult":[52],"fairly":[54],"measure":[55],"marginal":[57],"benefit":[58],"incorporating":[60],"context.":[62],"In":[63],"study,":[65],"we":[66,117],"established":[67],"lightweight,":[69],"efficient,":[70],"reproducible":[72],"baseline":[73,122,177],"for":[74,84,147,259],"single-patch":[75,156,189],"prediction,":[78],"thereby":[79],"providing":[80],"standardized":[82],"foundation":[83],"future":[85,272],"research.":[86],"We":[87],"trained":[88],"various":[89],"convolution-based":[90],"pretrained":[91],"architectures,":[92],"such":[93],"as":[94],"EfficientNet,":[95],"ResNet,":[96],"DenseNet,":[98],"using":[99,168,179],"fixed":[101],"data":[102],"split":[103],"seed":[105],"on":[106,123,151],"curated":[108],"human":[109],"liver":[110,152],"Visium":[111],"dataset.":[112,130],"To":[113],"assess":[114],"cross-tissue":[115],"generalizability,":[116],"further":[118],"validated":[119],"proposed":[121],"an":[124],"independent":[125,193],"breast":[126,194],"cancer":[127,195],"transcriptomics":[129,274],"Through":[131],"full":[132],"fine-tuning":[133],"morphology-preserving":[135],"augmentation,":[136],"EfficientNet-B0":[137,197],"achieved":[138,199],"maximum":[140],"Pearson":[141],"correlation":[142],"coefficient":[143],"(PCC)":[144],"0.310":[146],"highly":[148],"expressed":[149],"genes":[150,163,173],"tissue,":[153],"surpassing":[154],"previous":[155],"methods.":[157],"Furthermore,":[158],"model":[160,225],"predicted":[161],"50":[162],"with":[164],"PCC":[165],"\u2265":[166],"0.30":[167],"only":[169],"5.3M":[170],"parameters--2.5\u00d7":[171],"more":[172],"than":[174,247],"ResNet-50-based":[176],"despite":[178],"5\u00d7":[180],"fewer":[181],"parameters-suggesting":[182],"favorable":[184],"performance-efficiency":[185],"tradeoff":[186],"within":[187],"setting.":[190],"On":[191],"dataset,":[196],"consistently":[198],"best":[200],"or":[201,250],"near-best":[202],"performance":[203],"across":[204,217],"all":[205],"sets":[207],"under":[208],"both":[209],"single-donor":[210],"multi-donor":[212],"evaluations,":[213],"demonstrating":[214],"stable":[215],"generalization":[216],"types.":[219],"Subsequent":[220],"biological":[221],"analysis":[222],"reveals":[223],"that":[224],"prediction":[226],"accuracy":[227],"primarily":[229],"driven":[230],"by":[231,241],"strength":[233],"organization":[236],"H&E":[238],"histology,":[239],"measured":[240],"Moran's":[242],"I":[243],"autocorrelation,":[245],"rather":[246],"transcript":[248],"abundance":[249],"chemical":[251],"properties.":[252],"Consequently,":[253],"work":[255],"provides":[256],"reference":[258],"quantifying":[260],"contributions":[262],"context,":[265],"multiresolution":[266],"integration,":[267],"architectural":[269],"complexity":[270],"models.":[275]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2026-05-19T00:00:00"}
