{"id":"https://openalex.org/W4410737814","doi":"https://doi.org/10.1109/tsipn.2025.3573591","title":"scGraPhT: Merging Transformers and Graph Neural Networks for Single-Cell Annotation","display_name":"scGraPhT: Merging Transformers and Graph Neural Networks for Single-Cell Annotation","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4410737814","doi":"https://doi.org/10.1109/tsipn.2025.3573591"},"language":"en","primary_location":{"id":"doi:10.1109/tsipn.2025.3573591","doi":"https://doi.org/10.1109/tsipn.2025.3573591","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tsipn.2025.3573591","pdf_url":null,"source":{"id":"https://openalex.org/S4306422866","display_name":"IEEE Transactions on Signal and Information Processing over Networks","issn_l":"2373-776X","issn":["2373-776X","2373-7778"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-b","jufo-1","ki-jl-1","norway-2","poland-20","russia-white-list-1"],"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Signal and Information Processing over Networks","raw_type":"journal-article"},"volume":null,"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/A5026057567","display_name":"Emirhan Ko\u00e7","orcid":"https://orcid.org/0000-0002-7275-1570","observed_orcids":["https://orcid.org/0000-0002-7275-1570"]},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Emirhan Ko\u00e7","raw_affiliation_strings":["Department of Electrical and Electronics Engineering, Bilkent University, Ankara, Türkiye","Dept. of Electrical and Electronics Engineering, Bilkent University, Ankara, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-7275-1570","affiliations":[{"raw_affiliation_string":"Department of Electrical and Electronics Engineering, Bilkent University, Ankara, Türkiye","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Dept. of Electrical and Electronics Engineering, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117700043","display_name":"Emre Kulkul","orcid":"https://orcid.org/0009-0008-0210-4942","observed_orcids":["https://orcid.org/0009-0008-0210-4942"]},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Emre Kulkul","raw_affiliation_strings":["Department of Electrical and Electronics Engineering, Bilkent University, Ankara, Türkiye","Dept. of Electrical and Electronics Engineering, Bilkent University, Ankara, Turkey"],"raw_orcid":"https://orcid.org/0009-0008-0210-4942","affiliations":[{"raw_affiliation_string":"Department of Electrical and Electronics Engineering, Bilkent University, Ankara, Türkiye","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Dept. of Electrical and Electronics Engineering, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117700044","display_name":"G\u00fclara Kaynar","orcid":"https://orcid.org/0009-0003-5163-9963","observed_orcids":["https://orcid.org/0009-0003-5163-9963"]},"institutions":[{"id":"https://openalex.org/I1351752","display_name":"Ko\u00e7 University","ror":"https://ror.org/00jzwgz36","country_code":"TR","type":"education","lineage":["https://openalex.org/I1351752"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"G\u00fclara Kaynar","raw_affiliation_strings":["Department of Computer Engineering, Koç University, Istanbul, Türkiye","Dept. of Computer Engineering, Koç University, Istanbul, Turkey"],"raw_orcid":"https://orcid.org/0009-0003-5163-9963","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Koç University, Istanbul, Türkiye","institution_ids":["https://openalex.org/I1351752"]},{"raw_affiliation_string":"Dept. of Computer Engineering, Koç University, Istanbul, Turkey","institution_ids":["https://openalex.org/I1351752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032375235","display_name":"Tolga \u00c7ukur","orcid":"https://orcid.org/0000-0002-2296-851X","observed_orcids":["https://orcid.org/0000-0002-2296-851X"]},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Tolga \u00c7ukur","raw_affiliation_strings":["Department of Electrical and Electronics Engineering, Bilkent University, Ankara, Türkiye","Dept. of Electrical and Electronics Engineering, Bilkent University, Ankara, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-2296-851X","affiliations":[{"raw_affiliation_string":"Department of Electrical and Electronics Engineering, Bilkent University, Ankara, Türkiye","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Dept. of Electrical and Electronics Engineering, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003715208","display_name":"Murat A\u00e7ar","orcid":"https://orcid.org/0000-0003-3289-8751","observed_orcids":["https://orcid.org/0000-0003-3289-8751"]},"institutions":[{"id":"https://openalex.org/I1351752","display_name":"Ko\u00e7 University","ror":"https://ror.org/00jzwgz36","country_code":"TR","type":"education","lineage":["https://openalex.org/I1351752"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Murat Acar","raw_affiliation_strings":["Department of Basic Medical Sciences, School of Medicine, Koç University, Istanbul, Türkiye","Dept. of Basic Medical Sciences, School of Medicine, Koç University, Istanbul, Turkey"],"raw_orcid":"https://orcid.org/0000-0003-3289-8751","affiliations":[{"raw_affiliation_string":"Department of Basic Medical Sciences, School of Medicine, Koç University, Istanbul, Türkiye","institution_ids":["https://openalex.org/I1351752"]},{"raw_affiliation_string":"Dept. of Basic Medical Sciences, School of Medicine, Koç University, Istanbul, Turkey","institution_ids":["https://openalex.org/I1351752"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062231547","display_name":"Aykut Ko\u00e7","orcid":"https://orcid.org/0000-0002-6348-2663","observed_orcids":["https://orcid.org/0000-0002-6348-2663"]},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Aykut Ko\u00e7","raw_affiliation_strings":["Department of Electrical and Electronics Engineering, Bilkent University, Ankara, Türkiye","Dept. of Electrical and Electronics Engineering, Bilkent University, Ankara, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-6348-2663","affiliations":[{"raw_affiliation_string":"Department of Electrical and Electronics Engineering, Bilkent University, Ankara, Türkiye","institution_ids":["https://openalex.org/I168864056"]},{"raw_affiliation_string":"Dept. of Electrical and Electronics Engineering, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":1.2741,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.77844689,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"11","issue":null,"first_page":"505","last_page":"519"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994999766349792,"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":0.9994999766349792,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0,"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":0.0,"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/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.8870000243186951},{"id":"https://openalex.org/keywords/cell-type-identification","display_name":"cell type annotation","score":0.9829999804496765},{"id":"https://openalex.org/keywords/graph-neural-networks","display_name":"graph neural networks","score":0.7400000095367432},{"id":"https://openalex.org/keywords/pre-trained-transformers","display_name":"pre-trained transformer models","score":0.6549999713897705}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5533179044723511},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.49667292833328247},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.47829943895339966},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.46498650312423706},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4393949508666992},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4008629620075226},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.24445125460624695},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.15665385127067566},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.13466504216194153},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tsipn.2025.3573591","doi":"https://doi.org/10.1109/tsipn.2025.3573591","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tsipn.2025.3573591","pdf_url":null,"source":{"id":"https://openalex.org/S4306422866","display_name":"IEEE Transactions on Signal and Information Processing over Networks","issn_l":"2373-776X","issn":["2373-776X","2373-7778"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-b","jufo-1","ki-jl-1","norway-2","poland-20","russia-white-list-1"],"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Signal and Information Processing over Networks","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":96,"referenced_works":["https://openalex.org/W2010653277","https://openalex.org/W2151506973","https://openalex.org/W2166676212","https://openalex.org/W2231058499","https://openalex.org/W2523369352","https://openalex.org/W2523419694","https://openalex.org/W2523620612","https://openalex.org/W2526262591","https://openalex.org/W2551194178","https://openalex.org/W2612519453","https://openalex.org/W2616247523","https://openalex.org/W2766959028","https://openalex.org/W2783252067","https://openalex.org/W2792693509","https://openalex.org/W2796170779","https://openalex.org/W2800392236","https://openalex.org/W2802502226","https://openalex.org/W2888562574","https://openalex.org/W2896457183","https://openalex.org/W2901677030","https://openalex.org/W2907514116","https://openalex.org/W2950684648","https://openalex.org/W2951560273","https://openalex.org/W2951737297","https://openalex.org/W2951914955","https://openalex.org/W2962946486","https://openalex.org/W2964643116","https://openalex.org/W2966569571","https://openalex.org/W2990211277","https://openalex.org/W2996147503","https://openalex.org/W3000350302","https://openalex.org/W3004512212","https://openalex.org/W3013731060","https://openalex.org/W3022825011","https://openalex.org/W3047307039","https://openalex.org/W3087547719","https://openalex.org/W3093900604","https://openalex.org/W3109418966","https://openalex.org/W3113251307","https://openalex.org/W3117136530","https://openalex.org/W3125524953","https://openalex.org/W3126902084","https://openalex.org/W3163842339","https://openalex.org/W3173753074","https://openalex.org/W3176693948","https://openalex.org/W3177020879","https://openalex.org/W3180540559","https://openalex.org/W3196689760","https://openalex.org/W3198628780","https://openalex.org/W3200735485","https://openalex.org/W3202393418","https://openalex.org/W3202569993","https://openalex.org/W4205827254","https://openalex.org/W4225568512","https://openalex.org/W4280596398","https://openalex.org/W4280630188","https://openalex.org/W4285198706","https://openalex.org/W4292738906","https://openalex.org/W4293519310","https://openalex.org/W4297243391","https://openalex.org/W4304172601","https://openalex.org/W4310640856","https://openalex.org/W4316096017","https://openalex.org/W4317568173","https://openalex.org/W4321234725","https://openalex.org/W4366526178","https://openalex.org/W4382239952","https://openalex.org/W4384522208","https://openalex.org/W4385295765","https://openalex.org/W4385405421","https://openalex.org/W4385759167","https://openalex.org/W4387047963","https://openalex.org/W4389506111","https://openalex.org/W4389949222","https://openalex.org/W4392168151","https://openalex.org/W4392356342","https://openalex.org/W4393032946","https://openalex.org/W4393153069","https://openalex.org/W4393315949","https://openalex.org/W4393336899","https://openalex.org/W4394881579","https://openalex.org/W4396896612","https://openalex.org/W4396966060","https://openalex.org/W4399971825","https://openalex.org/W4400975060","https://openalex.org/W4402684071","https://openalex.org/W6639506587","https://openalex.org/W6764733053","https://openalex.org/W6838322825","https://openalex.org/W6846558242","https://openalex.org/W6850806529","https://openalex.org/W6855995905","https://openalex.org/W6856795681","https://openalex.org/W6858707758","https://openalex.org/W6859826115","https://openalex.org/W6860511354"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W4405124681","https://openalex.org/W1533177136","https://openalex.org/W4380994516"],"abstract_inverted_index":{"The":[0],"invention":[1],"of":[2,11,151,156,178,295,301],"single-cell":[3,244],"RNA":[4],"sequencing":[5],"(scRNA-seq)":[6],"has":[7,31],"enabled":[8],"transcriptomic":[9],"examination":[10],"cells":[12,48,104],"on":[13,50,78,116,137,219,262],"an":[14],"individual":[15],"basis,":[16],"uncovering":[17],"cell-to-cell":[18],"phenotypic":[19],"heterogeneity":[20],"within":[21],"isogenic":[22],"cell":[23,28],"populations":[24],"and":[25,46,189,200,298],"tissues.":[26],"Inevitably,":[27],"type":[29],"annotation":[30,245,272],"emerged":[32],"as":[33,89,103,248,257],"a":[34,148,163,171,182,208,222,286],"fundamental,":[35],"albeit":[36],"challenging":[37],"task":[38],"in":[39,67,95,216],"scRNA-seq":[40,179,265],"data":[41,85,180],"analysis,":[42],"which":[43],"involves":[44],"identifying":[45],"characterizing":[47,96],"based":[49],"their":[51,60,93,144],"unique":[52],"molecular":[53],"profiles.":[54],"Recently,":[55],"deep":[56],"learning":[57],"techniques":[58],"with":[59,181],"data-driven":[61],"priors":[62],"have":[63],"shown":[64],"significant":[65],"promise":[66],"this":[68,159],"task.":[69],"On":[70],"the":[71,152,213,292,296],"one":[72],"hand,":[73],"task-agnostic":[74],"transformer":[75,173,224],"networks":[76,111],"pre-trained":[77,172,223],"large-scale":[79],"biological":[80,100],"databases":[81],"can":[82,113,126,236],"capture":[83,186],"generalizable":[84],"representations":[86,177,220,256],"to":[87,119,146,174,185,206,240,303],"serve":[88],"foundation":[90],"models":[91],"despite":[92],"ineffectiveness":[94],"intricate":[97],"relationships":[98,202],"between":[99],"entities":[101],"such":[102,247],"or":[105,140,250],"genes.":[106],"Contrarily,":[107],"task-specific":[108],"graph":[109,214],"neural":[110],"(GNNs)":[112],"be":[114,238],"trained":[115],"target":[117],"datasets":[118,266],"sensitively":[120],"characterize":[121],"entity":[122],"relationships,":[123,142],"but":[124],"they":[125],"suffer":[127],"from":[128,193,221],"relatively":[129],"poor":[130],"generalizability.":[131],"Furthermore,":[132],"existing":[133],"GNNs":[134],"focus":[135],"exclusively":[136],"either":[138],"homogeneous":[139,199],"heterogeneous":[141,201],"limiting":[143],"ability":[145],"offer":[147,207,278],"complete":[149],"picture":[150],"diverse":[153],"inner":[154],"structure":[155],"cells.":[157],"In":[158],"study,":[160],"we":[161],"propose":[162],"novel":[164],"merged":[165],"transformer-graph":[166],"model,":[167,225],"scGraPhT,":[168],"that":[169,252,268,290],"integrates":[170],"extract":[175],"rich":[176],"multi-layered":[183],"GNN":[184],"cell-cell,":[187],"cell-gene,":[188],"gene-gene":[190],"relationships.":[191],"Different":[192],"previous":[194],"GNNs,":[195],"scGraPhT":[196,217,235,269,302],"examines":[197],"both":[198],"through":[203],"subgraph":[204],"layers":[205],"more":[209],"comprehensive":[210],"assessment.":[211],"Since":[212],"construction":[215],"relies":[218],"our":[226],"approach":[227],"does":[228],"not":[229],"require":[230],"costly":[231],"training":[232],"procedures.":[233],"Moreover,":[234],"also":[237],"adapted":[239],"leverage":[241],"any":[242],"transformer-based":[243,299],"method,":[246],"scGPT":[249],"scBERT,":[251],"produces":[253],"suitable":[254],"embedding":[255],"input":[258],"for":[259],"GNNs.":[260],"Demonstrations":[261],"three":[263],"benchmark":[264],"indicate":[267],"outperforms":[270],"state-of-the-art":[271],"methods":[273],"without":[274],"compromising":[275],"efficiency.":[276],"We":[277],"insights":[279],"into":[280],"performance":[281],"improvements":[282],"by":[283],"employing":[284],"Grad-CAM,":[285],"visual":[287],"explainability":[288],"method":[289],"elucidates":[291],"complementary":[293],"nature":[294],"GNN-":[297],"components":[300],"improve":[304],"its":[305],"predictive":[306],"performance.":[307]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":1}],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2025-10-10T00:00:00"}