{"id":"https://openalex.org/W7161758386","doi":"https://doi.org/10.1109/isbi61048.2026.11515324","title":"hSNMF: Hybrid Spatially Regularized NMF for Image-Derived Spatial Transcriptomics","display_name":"hSNMF: Hybrid Spatially Regularized NMF for Image-Derived Spatial Transcriptomics","publication_year":2026,"publication_date":"2026-04-08","ids":{"openalex":"https://openalex.org/W7161758386","doi":"https://doi.org/10.1109/isbi61048.2026.11515324"},"language":null,"primary_location":{"id":"doi:10.1109/isbi61048.2026.11515324","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isbi61048.2026.11515324","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2026 IEEE 23rd International Symposium on Biomedical Imaging (ISBI)","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/A5050375180","display_name":"Md Ishtyaq Mahmud","orcid":"https://orcid.org/0000-0001-6280-7035"},"institutions":[{"id":"https://openalex.org/I44461941","display_name":"University of Houston","ror":"https://ror.org/048sx0r50","country_code":"US","type":"education","lineage":["https://openalex.org/I44461941"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Md Ishtyaq Mahmud","raw_affiliation_strings":["University of Houston,Department of Electrical and Computer Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Houston,Department of Electrical and Computer Engineering","institution_ids":["https://openalex.org/I44461941"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136540954","display_name":"Veena Kochat","orcid":null},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]},{"id":"https://openalex.org/I87890613","display_name":"Epigenomics (Germany)","ror":"https://ror.org/0490dah44","country_code":"DE","type":"company","lineage":["https://openalex.org/I87890613"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Veena Kochat","raw_affiliation_strings":["MD Anderson Cancer Center,Department of Genomic Medicine and MDACC Epigenomics Therapy Initiative (METI),Houston,TX,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MD Anderson Cancer Center,Department of Genomic Medicine and MDACC Epigenomics Therapy Initiative (METI),Houston,TX,USA","institution_ids":["https://openalex.org/I87890613","https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046347930","display_name":"Suresh Satpati","orcid":null},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]},{"id":"https://openalex.org/I87890613","display_name":"Epigenomics (Germany)","ror":"https://ror.org/0490dah44","country_code":"DE","type":"company","lineage":["https://openalex.org/I87890613"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Suresh Satpati","raw_affiliation_strings":["MD Anderson Cancer Center,Department of Genomic Medicine and MDACC Epigenomics Therapy Initiative (METI),Houston,TX,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MD Anderson Cancer Center,Department of Genomic Medicine and MDACC Epigenomics Therapy Initiative (METI),Houston,TX,USA","institution_ids":["https://openalex.org/I87890613","https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136603184","display_name":"Jagan Mohan Reddy Dwarampudi","orcid":null},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]},{"id":"https://openalex.org/I87890613","display_name":"Epigenomics (Germany)","ror":"https://ror.org/0490dah44","country_code":"DE","type":"company","lineage":["https://openalex.org/I87890613"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Jagan Mohan Reddy Dwarampudi","raw_affiliation_strings":["MD Anderson Cancer Center,Department of Genomic Medicine and MDACC Epigenomics Therapy Initiative (METI),Houston,TX,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MD Anderson Cancer Center,Department of Genomic Medicine and MDACC Epigenomics Therapy Initiative (METI),Houston,TX,USA","institution_ids":["https://openalex.org/I87890613","https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5125030100","display_name":"Humaira Anzum","orcid":null},"institutions":[{"id":"https://openalex.org/I44461941","display_name":"University of Houston","ror":"https://ror.org/048sx0r50","country_code":"US","type":"education","lineage":["https://openalex.org/I44461941"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Humaira Anzum","raw_affiliation_strings":["University of Houston,Department of Electrical and Computer Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Houston,Department of Electrical and Computer Engineering","institution_ids":["https://openalex.org/I44461941"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136608831","display_name":"Kunal Rai","orcid":null},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]},{"id":"https://openalex.org/I87890613","display_name":"Epigenomics (Germany)","ror":"https://ror.org/0490dah44","country_code":"DE","type":"company","lineage":["https://openalex.org/I87890613"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Kunal Rai","raw_affiliation_strings":["MD Anderson Cancer Center,Department of Genomic Medicine and MDACC Epigenomics Therapy Initiative (METI),Houston,TX,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MD Anderson Cancer Center,Department of Genomic Medicine and MDACC Epigenomics Therapy Initiative (METI),Houston,TX,USA","institution_ids":["https://openalex.org/I87890613","https://openalex.org/I1343551460"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073938611","display_name":"Tania Banerjee","orcid":"https://orcid.org/0000-0003-4737-0001"},"institutions":[{"id":"https://openalex.org/I44461941","display_name":"University of Houston","ror":"https://ror.org/048sx0r50","country_code":"US","type":"education","lineage":["https://openalex.org/I44461941"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tania Banerjee","raw_affiliation_strings":["University of Houston,Department of Electrical and Computer Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Houston,Department of Electrical and Computer Engineering","institution_ids":["https://openalex.org/I44461941"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5050375180"],"corresponding_institution_ids":["https://openalex.org/I44461941"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.89089581,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9789999723434448,"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":0.9789999723434448,"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":0.003100000089034438,"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":0.003000000026077032,"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":0.557699978351593},{"id":"https://openalex.org/keywords/non-negative-matrix-factorization","display_name":"Non-negative matrix factorization","score":0.48339998722076416},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.31690001487731934},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.3037000000476837},{"id":"https://openalex.org/keywords/image-processing","display_name":"Image processing","score":0.2906000018119812},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.27799999713897705}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.611299991607666},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.557699978351593},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5296000242233276},{"id":"https://openalex.org/C152671427","wikidata":"https://www.wikidata.org/wiki/Q10843505","display_name":"Non-negative matrix factorization","level":4,"score":0.48339998722076416},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.31690001487731934},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.3037000000476837},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.2906000018119812},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.27799999713897705},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2741999924182892},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.2709999978542328},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.26829999685287476},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.2628999948501587},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.26269999146461487},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.25769999623298645},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2547999918460846},{"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/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.2524000108242035}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/isbi61048.2026.11515324","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isbi61048.2026.11515324","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2026 IEEE 23rd International Symposium on Biomedical Imaging (ISBI)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320333269","display_name":"Southeastern Transportation Research, Innovation, Development and Education Center","ror":"https://ror.org/02kn1zm32"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1902027874","https://openalex.org/W2817838603","https://openalex.org/W3171692328","https://openalex.org/W4294052977","https://openalex.org/W4306194402","https://openalex.org/W4309918428","https://openalex.org/W4377093458","https://openalex.org/W4389938094","https://openalex.org/W4393089338","https://openalex.org/W4399512711","https://openalex.org/W4403433028","https://openalex.org/W4404140967","https://openalex.org/W4417201432","https://openalex.org/W7113901142"],"related_works":[],"abstract_inverted_index":{"High-resolution":[0],"spatial":[1,15,68,88,99,123,151,182],"transcriptomics":[2,69],"platforms,":[3],"such":[4],"as":[5],"Xenium,":[6],"generate":[7],"single-cell":[8],"images":[9,43],"that":[10,85,121],"capture":[11],"both":[12],"molecular":[13],"and":[14,28,49,61,129,146,172,177,185],"context,":[16],"but":[17],"their":[18],"extremely":[19],"high":[20],"dimensionality":[21],"poses":[22],"major":[23],"challenges":[24],"for":[25,56,67],"representation":[26],"learning":[27],"clustering.":[29],"In":[30],"this":[31],"study,":[32],"we":[33,77,102],"analyze":[34],"data":[35],"from":[36],"the":[37],"Xenium":[38],"platform,":[39],"which":[40,108],"captures":[41],"high-resolution":[42],"of":[44],"tumor":[45],"microarray":[46],"(TMA)":[47],"tissues":[48],"converts":[50],"them":[51],"into":[52],"cell-by-gene":[53],"matrices":[54],"suitable":[55],"computational":[57],"analysis.":[58],"We":[59],"benchmark":[60],"extend":[62],"nonnegative":[63],"matrix":[64],"factorization":[65],"(NMF)":[66],"by":[70,90,114],"introducing":[71],"two":[72],"spatially":[73,110],"regularized":[74,111],"variants.":[75],"First,":[76],"propose":[78],"Spatial":[79,105],"NMF":[80,94,106,112],"(SNMF),":[81],"a":[82,118,126,133,142],"lightweight":[83],"baseline":[84],"enforces":[86],"local":[87],"smoothness":[89],"diffusing":[91],"each":[92],"cell's":[93],"factor":[95],"vector":[96],"over":[97],"its":[98],"neighborhood.":[100],"Second,":[101],"introduce":[103],"Hybrid":[104],"(hSNMF),":[107],"performs":[109],"followed":[113],"Leiden":[115],"clustering":[116],"on":[117,141],"hybrid":[119],"adjacency":[120],"integrates":[122],"proximity":[124],"(via":[125],"contact\u2014radius":[127],"graph)":[128],"transcriptomic":[130],"similarity":[131],"through":[132],"tunable":[134],"mixing":[135],"parameter":[136],"<tex":[137,154,158,165,169],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[138,155,159,166,170],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$\\alpha$</tex>.":[139],"Evaluated":[140],"cholangiocarcinoma":[143],"dataset,":[144],"SNMF":[145],"hSNMF":[147],"achieve":[148],"markedly":[149],"improved":[150],"compactness":[152],"(CHAOS":[153],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$&lt;0.004$</tex>,":[156],"Moran's":[157],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$I&gt;0.96$</tex>),":[160],"greater":[161],"cluster":[162],"separability":[163],"(Silhouette":[164],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$&gt;0.12$</tex>,":[167],"DBI":[168],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$&lt;1.8$</tex>),":[171],"higher":[173],"biological":[174],"coherence":[175],"(CMC":[176],"enrichment)":[178],"compared":[179],"to":[180],"other":[181],"baselines.":[183],"Availability":[184],"implementation:":[186],"https://github.com/ishtyaqmahmud/hSNMF":[187]},"counts_by_year":[],"updated_date":"2026-05-22T06:13:13.366637","created_date":"2026-05-21T00:00:00"}
