{"id":"https://openalex.org/W4406238151","doi":"https://doi.org/10.1109/bibm62325.2024.10822280","title":"STARGATE: Spatial Transcriptomic Analysis with Recurrent and Graph Attention Techniques using Ensemble Learning","display_name":"STARGATE: Spatial Transcriptomic Analysis with Recurrent and Graph Attention Techniques using Ensemble Learning","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406238151","doi":"https://doi.org/10.1109/bibm62325.2024.10822280"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822280","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822280","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":"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/A5100369052","display_name":"Ning Li","orcid":null},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ning Li","raw_affiliation_strings":["Sichuan University,College of Computer Science,Chengdu,China,610065"],"affiliations":[{"raw_affiliation_string":"Sichuan University,College of Computer Science,Chengdu,China,610065","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005869019","display_name":"Jiayidaer Badai","orcid":"https://orcid.org/0000-0002-1537-2152"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiayidaer Badai","raw_affiliation_strings":["Sichuan University,College of Computer Science,Chengdu,China,610065"],"affiliations":[{"raw_affiliation_string":"Sichuan University,College of Computer Science,Chengdu,China,610065","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028794611","display_name":"Deli Chen","orcid":"https://orcid.org/0000-0001-6767-1376"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dengjie Chen","raw_affiliation_strings":["Fujian A&#x0026;F University,College of Mechanical and Electrical Engineering,Fuzhou,China,350100"],"affiliations":[{"raw_affiliation_string":"Fujian A&#x0026;F University,College of Mechanical and Electrical Engineering,Fuzhou,China,350100","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101717292","display_name":"Ming Xiao","orcid":"https://orcid.org/0000-0001-8608-5903"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ming Xiao","raw_affiliation_strings":["Sichuan University,College of Computer Science,Chengdu,China,610065"],"affiliations":[{"raw_affiliation_string":"Sichuan University,College of Computer Science,Chengdu,China,610065","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100350625","display_name":"Le Zhang","orcid":"https://orcid.org/0000-0002-3708-1727"},"institutions":[{"id":"https://openalex.org/I64852412","display_name":"Sichuan University of Science and Engineering","ror":"https://ror.org/053fzma23","country_code":"CN","type":"education","lineage":["https://openalex.org/I64852412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Le Zhang","raw_affiliation_strings":["Sichuan University,College of Computer Science"],"affiliations":[{"raw_affiliation_string":"Sichuan University,College of Computer Science","institution_ids":["https://openalex.org/I64852412"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100369052"],"corresponding_institution_ids":["https://openalex.org/I24185976"],"apc_list":null,"apc_paid":null,"fwci":0.2473,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.6125844,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"5630","last_page":"5637"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9545999765396118,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9545999765396118,"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/computer-science","display_name":"Computer science","score":0.7446643114089966},{"id":"https://openalex.org/keywords/ensemble-learning","display_name":"Ensemble learning","score":0.49363982677459717},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.45053622126579285},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.448797345161438},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36183279752731323},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.21859002113342285}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7446643114089966},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.49363982677459717},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.45053622126579285},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.448797345161438},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36183279752731323},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.21859002113342285}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822280","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822280","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"},{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"},{"id":"https://openalex.org/F4320329860","display_name":"National Science and Technology Major Project","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W2030644393","https://openalex.org/W2031489346","https://openalex.org/W2064675550","https://openalex.org/W2112796928","https://openalex.org/W2131681506","https://openalex.org/W2150593711","https://openalex.org/W2158698691","https://openalex.org/W2800392236","https://openalex.org/W2899235059","https://openalex.org/W2949177718","https://openalex.org/W2971653850","https://openalex.org/W3092450854","https://openalex.org/W3108118546","https://openalex.org/W3126958162","https://openalex.org/W3134482219","https://openalex.org/W3134766331","https://openalex.org/W3164692211","https://openalex.org/W3165120573","https://openalex.org/W3191824479","https://openalex.org/W3203128182","https://openalex.org/W3203689742","https://openalex.org/W3204015056","https://openalex.org/W4235169531","https://openalex.org/W4250658309","https://openalex.org/W4290154117","https://openalex.org/W4306406844","https://openalex.org/W4312205786","https://openalex.org/W6602002561","https://openalex.org/W6726873649","https://openalex.org/W6779238151"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W3046775127","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474"],"abstract_inverted_index":{"Previous":[0],"research":[1],"has":[2],"identified":[3],"hematoma":[4,26],"as":[5,194,261],"the":[6,45,91,138,165,203,207,230,248],"primary":[7],"cause":[8],"of":[9,41,50,101,142,182,213],"mortality":[10],"and":[11,36,48,69,95,113,126,135,140,177,185,196,223,253,263],"disability":[12],"in":[13],"intraventricular":[14],"hemorrhage":[15],"(IVH),":[16],"yet":[17],"neurologic":[18],"outcomes":[19],"post-IVH":[20],"have":[21],"not":[22],"significantly":[23],"improved":[24],"following":[25],"evacuation.":[27],"Therefore,":[28],"utilizing":[29],"spatial":[30,56,82,93,127,162],"transcriptomics":[31,57,83,163],"sequencing":[32],"technology":[33],"to":[34,65,190,243],"acquire":[35],"analyze":[37],"IVH":[38,161,205],"data":[39,240],"is":[40,235],"significant":[42],"importance":[43],"for":[44,237],"early":[46],"diagnosis":[47],"treatment":[49],"acute":[51],"cerebral":[52],"hemorrhage.":[53],"However,":[54],"existing":[55],"clustering":[58,84,155,200,227,246],"algorithms":[59,192,259],"often":[60],"overlook":[61],"local":[62,96],"information,":[63],"fail":[64],"integrate":[66],"multimodal":[67,81],"data,":[68],"suffer":[70],"from":[71],"performance":[72],"instability.":[73],"To":[74],"address":[75],"these":[76],"issues,":[77],"we":[78],"developed":[79],"a":[80],"algorithm":[85],"named":[86],"STARGATE,":[87],"which":[88,234],"initially":[89],"captures":[90],"global":[92],"topology":[94],"long-sequence":[97],"gene":[98,121],"set":[99],"features":[100,129],"cells":[102],"by":[103],"integrating":[104],"Graph":[105],"Convolutional":[106],"Networks":[107],"(GCNs)":[108],"based":[109],"on":[110,157,202,229],"self-attention":[111],"mechanisms":[112],"Long":[114],"Short-Term":[115],"Memory":[116],"networks":[117],"(LSTMs),":[118],"subsequently":[119],"fuses":[120],"expression,":[122],"tissue":[123],"imagery,":[124],"morphological,":[125],"coordinate":[128],"using":[130],"Gated":[131],"Recurrent":[132],"Units":[133],"(GRUs),":[134],"finally":[136],"enhances":[137],"accuracy":[139,212,222],"robustness":[141],"predictions":[143],"through":[144],"ensemble":[145],"learning":[146],"methods.":[147],"Our":[148],"key":[149],"experimental":[150],"results":[151],"include:":[152],"(1)":[153],"In":[154,199,226],"experiments":[156,201,228],"our":[158],"proprietary":[159],"mouse":[160,204],"dataset,":[164,206],"STARGATE":[166,208,249],"model":[167,209],"achieved":[168],"Adjusted":[169],"Rand":[170],"Index":[171,179],"(ARI),":[172],"Normalized":[173],"Mutual":[174],"Information":[175],"(NMI),":[176],"Fowlkes-Mallows":[178],"(FMI)":[180],"scores":[181],"0.80,":[183],"0.84,":[184],"0.82,":[186],"respectively,":[187],"all":[188],"superior":[189],"classic":[191,258],"such":[193,260],"stLearn":[195],"CCST.":[197],"(2)":[198],"reached":[210],"an":[211,216],"89.63%,":[214],"with":[215],"excellent":[217],"confusion":[218],"matrix,":[219],"demonstrating":[220],"outstanding":[221],"stability.":[224],"(3)":[225],"public":[231],"dataset":[232],"DLFPC,":[233],"known":[236],"its":[238],"high":[239],"complexity":[241],"leading":[242],"generally":[244],"lower":[245],"metrics,":[247],"model's":[250],"ARI,":[251],"NMI,":[252],"FMI":[254],"indicators":[255],"still":[256],"outperformed":[257],"SpaGCN":[262],"Seurat.":[264]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2025-10-10T00:00:00"}
