{"id":"https://openalex.org/W4406260499","doi":"https://doi.org/10.1109/bibm62325.2024.10822744","title":"Sparse Attention-based Hierarchical Node Representation for Spatial Domain Identification","display_name":"Sparse Attention-based Hierarchical Node Representation for Spatial Domain Identification","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406260499","doi":"https://doi.org/10.1109/bibm62325.2024.10822744"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822744","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822744","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","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/A5101990146","display_name":"Wei Peng","orcid":"https://orcid.org/0000-0002-4994-8965"},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Peng","raw_affiliation_strings":["Kunming University of Science and Technology Computer Technology Application Key Lab of Yunnan Province, Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Kunming University of Science and Technology Computer Technology Application Key Lab of Yunnan Province, Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China","institution_ids":["https://openalex.org/I10660446"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhihao Ping","orcid":null},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhihao Ping","raw_affiliation_strings":["Kunming University of Science and Technology Computer Technology Application Key Lab of Yunnan Province, Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Kunming University of Science and Technology Computer Technology Application Key Lab of Yunnan Province, Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China","institution_ids":["https://openalex.org/I10660446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100752235","display_name":"Wei Dai","orcid":"https://orcid.org/0000-0002-3093-6454"},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Dai","raw_affiliation_strings":["Kunming University of Science and Technology Computer Technology Application Key Lab of Yunnan Province, Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Kunming University of Science and Technology Computer Technology Application Key Lab of Yunnan Province, Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China","institution_ids":["https://openalex.org/I10660446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102760647","display_name":"Xiaodong Fu","orcid":"https://orcid.org/0000-0002-1354-2293"},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaodong Fu","raw_affiliation_strings":["Kunming University of Science and Technology Computer Technology Application Key Lab of Yunnan Province, Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Kunming University of Science and Technology Computer Technology Application Key Lab of Yunnan Province, Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China","institution_ids":["https://openalex.org/I10660446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100418765","display_name":"Li Liu","orcid":"https://orcid.org/0000-0001-9685-6599"},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Liu","raw_affiliation_strings":["Kunming University of Science and Technology Computer Technology Application Key Lab of Yunnan Province, Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China","Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Kunming University of Science and Technology Computer Technology Application Key Lab of Yunnan Province, Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China","institution_ids":["https://openalex.org/I10660446"]},{"raw_affiliation_string":"Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China","institution_ids":["https://openalex.org/I10660446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100350053","display_name":"Lijun Liu","orcid":"https://orcid.org/0000-0003-4543-0111"},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lijun Liu","raw_affiliation_strings":["Kunming University of Science and Technology Computer Technology Application Key Lab of Yunnan Province, Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China","Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Kunming University of Science and Technology Computer Technology Application Key Lab of Yunnan Province, Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China","institution_ids":["https://openalex.org/I10660446"]},{"raw_affiliation_string":"Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China","institution_ids":["https://openalex.org/I10660446"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101597063","display_name":"Ning Yu","orcid":"https://orcid.org/0009-0000-2198-5409"},"institutions":[{"id":"https://openalex.org/I4864440","display_name":"SUNY Brockport","ror":"https://ror.org/0306aeb62","country_code":"US","type":"education","lineage":["https://openalex.org/I4864440"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ning Yu","raw_affiliation_strings":["State University of New York,The College at Brockport,Department of Computing Sciences,Brockport,NY,14422"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State University of New York,The College at Brockport,Department of Computing Sciences,Brockport,NY,14422","institution_ids":["https://openalex.org/I4864440"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"573","last_page":"578"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.7541000247001648,"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"}},"topics":[{"id":"https://openalex.org/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.7541000247001648,"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/T13717","display_name":"Advanced Algorithms and Applications","score":0.6915000081062317,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12676","display_name":"Machine Learning and ELM","score":0.6414999961853027,"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/computer-science","display_name":"Computer science","score":0.7328224778175354},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6097184419631958},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5564137101173401},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5337632298469543},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5204282402992249},{"id":"https://openalex.org/keywords/sparse-approximation","display_name":"Sparse approximation","score":0.48780396580696106},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.463672399520874},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.418165922164917},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3470619320869446},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.128536194562912},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07253354787826538}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7328224778175354},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6097184419631958},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5564137101173401},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5337632298469543},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5204282402992249},{"id":"https://openalex.org/C124066611","wikidata":"https://www.wikidata.org/wiki/Q28684319","display_name":"Sparse approximation","level":2,"score":0.48780396580696106},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.463672399520874},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.418165922164917},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3470619320869446},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.128536194562912},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07253354787826538},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822744","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822744","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"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":20,"referenced_works":["https://openalex.org/W2037144271","https://openalex.org/W2471536144","https://openalex.org/W2586560471","https://openalex.org/W2763148304","https://openalex.org/W2800392236","https://openalex.org/W2897249806","https://openalex.org/W2950479715","https://openalex.org/W3028794237","https://openalex.org/W3036371598","https://openalex.org/W3108118546","https://openalex.org/W3112563877","https://openalex.org/W3126958162","https://openalex.org/W3194628804","https://openalex.org/W4226192560","https://openalex.org/W4235169531","https://openalex.org/W4322738920","https://openalex.org/W4390970632","https://openalex.org/W4400519508","https://openalex.org/W6735913928","https://openalex.org/W6766978945"],"related_works":["https://openalex.org/W2062195135","https://openalex.org/W2898732673","https://openalex.org/W2410053581","https://openalex.org/W2383658677","https://openalex.org/W3123203398","https://openalex.org/W2795079307","https://openalex.org/W1972473893","https://openalex.org/W2793058541","https://openalex.org/W2387058352","https://openalex.org/W1588041347"],"abstract_inverted_index":{"Using":[0],"deep":[1],"learning":[2,82],"models":[3],"on":[4,45,110,171,197],"spatial":[5,11,18,40,84,88,118],"transcriptomics":[6,89],"data":[7,106,217],"to":[8,132,153,187],"identify":[9],"the":[10,17,54,154,172,177,181,191,198],"domain":[12,41,85],"is":[13],"crucial":[14],"for":[15,29,39,83],"uncovering":[16],"distribution":[19],"of":[20,60,120],"cells":[21],"and":[22,34,57,79,100,117,148,168,218],"gene":[23,114,164],"expression":[24,115,165],"patterns":[25],"within":[26],"tissues,":[27],"essential":[28],"understanding":[30],"complex":[31],"biological":[32,61],"processes":[33],"disease":[35],"mechanisms.":[36],"Existing":[37],"methods":[38,212],"partitioning":[42],"often":[43],"rely":[44],"predefined":[46],"adjacency":[47],"relationships":[48],"at":[49],"a":[50,69,98,125],"single":[51],"scale,":[52],"overlooking":[53],"hierarchical":[55,76,128,139],"structure":[56,140],"functional":[58],"characteristics":[59],"tissues.":[62],"In":[63],"this":[64],"paper,":[65],"we":[66],"propose":[67],"SpaNFM,":[68],"novel":[70],"method":[71],"that":[72,207],"leverages":[73],"sparse":[74,126],"attention-based":[75,127],"node":[77,99,129,135,146,156,174,183],"representation":[78],"multi-view":[80],"contrastive":[81,169],"identification":[86],"in":[87,213],"data.":[90],"The":[91,158,204,216],"SpaNFM":[92,123,196,208],"first":[93],"treats":[94],"each":[95],"spot":[96],"as":[97],"constructs":[101],"two":[102,178],"views":[103],"using":[104,163,190],"different":[105],"augmentation":[107],"techniques":[108],"based":[109],"tissue":[111],"image":[112],"information,":[113],"profiles,":[116],"coordinates":[119],"cells.":[121],"Subsequently,":[122],"utilizes":[124],"fusion":[130],"module":[131],"generate":[133],"coarse-grained":[134,173],"representations.":[136],"This":[137],"fine-to-coarse":[138],"integrates":[141],"complementary":[142],"information":[143],"from":[144,176],"multi-granularity":[145],"features":[147,184],"reduces":[149],"model":[150,159],"complexity":[151],"due":[152],"decreased":[155],"size.":[157],"parameters":[160],"are":[161,185,220],"updated":[162],"reconstruction":[166],"loss":[167,170],"representations":[175],"views.":[179],"Finally,":[180],"learned":[182],"subjected":[186],"downstream":[188],"clustering":[189],"Leiden":[192],"algorithm.":[193],"We":[194],"tested":[195],"human":[199],"dorsolateral":[200],"prefrontal":[201],"cortex":[202],"dataset.":[203],"results":[205],"demonstrate":[206],"outperforms":[209],"other":[210],"state-of-the-art":[211],"most":[214],"cases.":[215],"code":[219],"available":[221],"at:":[222],"https://github.com/weiba/SpaNFM":[223]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
