{"id":"https://openalex.org/W4412493751","doi":"https://doi.org/10.1109/tmi.2025.3590484","title":"Self-Supervised Neuron Morphology Representation With Graph Transformer","display_name":"Self-Supervised Neuron Morphology Representation With Graph Transformer","publication_year":2025,"publication_date":"2025-07-18","ids":{"openalex":"https://openalex.org/W4412493751","doi":"https://doi.org/10.1109/tmi.2025.3590484","pmid":"https://pubmed.ncbi.nlm.nih.gov/40679878"},"language":"en","primary_location":{"id":"doi:10.1109/tmi.2025.3590484","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tmi.2025.3590484","pdf_url":null,"source":{"id":"https://openalex.org/S58069681","display_name":"IEEE Transactions on Medical Imaging","issn_l":"0278-0062","issn":["0278-0062","1558-254X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"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 Medical Imaging","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5089083697","display_name":"Pengpeng Sheng","orcid":"https://orcid.org/0000-0001-5528-9970"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengpeng Sheng","raw_affiliation_strings":["National Key Laboratory of Opto-Electronic Information Acquisition and Protection Technology, Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing, Anhui University, Hefei, China"],"raw_orcid":"https://orcid.org/0000-0001-5528-9970","affiliations":[{"raw_affiliation_string":"National Key Laboratory of Opto-Electronic Information Acquisition and Protection Technology, Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing, Anhui University, Hefei, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073574475","display_name":"Gangming Zhao","orcid":"https://orcid.org/0000-0001-8441-5462"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gangming Zhao","raw_affiliation_strings":["National Key Laboratory of Opto-Electronic Information Acquisition and Protection Technology, Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing, Anhui University, Hefei, China"],"raw_orcid":"https://orcid.org/0000-0001-8441-5462","affiliations":[{"raw_affiliation_string":"National Key Laboratory of Opto-Electronic Information Acquisition and Protection Technology, Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing, Anhui University, Hefei, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114860447","display_name":"Tingting Han","orcid":"https://orcid.org/0009-0006-8419-1247"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tingting Han","raw_affiliation_strings":["National Key Laboratory of Opto-Electronic Information Acquisition and Protection Technology, Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing, Anhui University, Hefei, China"],"raw_orcid":"https://orcid.org/0009-0006-8419-1247","affiliations":[{"raw_affiliation_string":"National Key Laboratory of Opto-Electronic Information Acquisition and Protection Technology, Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing, Anhui University, Hefei, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067303374","display_name":"Lei Qu","orcid":"https://orcid.org/0000-0002-2129-5253"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Qu","raw_affiliation_strings":["National Key Laboratory of Opto-Electronic Information Acquisition and Protection Technology, Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing, Anhui University, Hefei, China"],"raw_orcid":"https://orcid.org/0000-0002-2129-5253","affiliations":[{"raw_affiliation_string":"National Key Laboratory of Opto-Electronic Information Acquisition and Protection Technology, Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing, Anhui University, Hefei, China","institution_ids":["https://openalex.org/I143868143"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I143868143"],"apc_list":null,"apc_paid":null,"fwci":1.5555,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.84071153,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"44","issue":"12","first_page":"5332","last_page":"5344"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.965399980545044,"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.965399980545044,"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"}},{"id":"https://openalex.org/T10320","display_name":"Neural Networks and Applications","score":0.9455999732017517,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9380999803543091,"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":0.5366705060005188},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5193380117416382},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.48627912998199463},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4290786683559418},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.403359591960907},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.38713356852531433},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.23823732137680054},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12383246421813965},{"id":"https://openalex.org/keywords/voltage","display_name":"Voltage","score":0.11060839891433716}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5366705060005188},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5193380117416382},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.48627912998199463},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4290786683559418},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.403359591960907},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.38713356852531433},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.23823732137680054},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12383246421813965},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.11060839891433716},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","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":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":true},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":true},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tmi.2025.3590484","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tmi.2025.3590484","pdf_url":null,"source":{"id":"https://openalex.org/S58069681","display_name":"IEEE Transactions on Medical Imaging","issn_l":"0278-0062","issn":["0278-0062","1558-254X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"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 Medical Imaging","raw_type":"journal-article"},{"id":"pmid:40679878","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40679878","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":"IEEE transactions on medical imaging","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2906025512","display_name":null,"funder_award_id":"2022ZD0205204","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G478943886","display_name":null,"funder_award_id":"62271003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G75087359","display_name":null,"funder_award_id":"62401009","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7563287808","display_name":null,"funder_award_id":"62201008","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8056404967","display_name":null,"funder_award_id":"2022ZD0205200","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1903709925","https://openalex.org/W1975032719","https://openalex.org/W1981934656","https://openalex.org/W1988535312","https://openalex.org/W2005165207","https://openalex.org/W2040879146","https://openalex.org/W2061186544","https://openalex.org/W2067337882","https://openalex.org/W2074151160","https://openalex.org/W2074633779","https://openalex.org/W2092463343","https://openalex.org/W2121289914","https://openalex.org/W2157700389","https://openalex.org/W2158536428","https://openalex.org/W2171114940","https://openalex.org/W2178605380","https://openalex.org/W2242861054","https://openalex.org/W2309258625","https://openalex.org/W2326092449","https://openalex.org/W2425174756","https://openalex.org/W2467946152","https://openalex.org/W2604655459","https://openalex.org/W2785523628","https://openalex.org/W2791989763","https://openalex.org/W2949311293","https://openalex.org/W2971899185","https://openalex.org/W2979750740","https://openalex.org/W2987372156","https://openalex.org/W3005098536","https://openalex.org/W3010129624","https://openalex.org/W3035524453","https://openalex.org/W3134409008","https://openalex.org/W3150791846","https://openalex.org/W3202358235","https://openalex.org/W4200271479","https://openalex.org/W4221083769","https://openalex.org/W4281901526","https://openalex.org/W4287027946","https://openalex.org/W4296437652","https://openalex.org/W4324332956","https://openalex.org/W4376225645","https://openalex.org/W4377225333","https://openalex.org/W4391428168","https://openalex.org/W4393158689","https://openalex.org/W4401692204","https://openalex.org/W4407392318"],"related_works":["https://openalex.org/W2772917594","https://openalex.org/W2036807459","https://openalex.org/W2058170566","https://openalex.org/W2755342338","https://openalex.org/W2166024367","https://openalex.org/W3116076068","https://openalex.org/W2229312674","https://openalex.org/W2951359407","https://openalex.org/W2079911747","https://openalex.org/W1969923398"],"abstract_inverted_index":{"Effective":[0],"representation":[1,129],"of":[2,17,74,84,130,185,192],"neuronal":[3,18,54,89,106,131,176],"morphology":[4,19,132,166],"is":[5,179,200],"essential":[6],"for":[7,43],"cell":[8],"typing":[9],"and":[10,35,49,78,108,127,151,168,194],"understanding":[11],"brain":[12],"function.":[13],"However,":[14],"the":[15,69,79,182,189],"complexity":[16],"manifests":[20],"not":[21],"only":[22],"in":[23,29,46,149,164,175],"inter-class":[24],"structural":[25,90],"differences":[26],"but":[27],"also":[28],"intra-class":[30],"variations":[31],"across":[32,105],"developmental":[33],"stages":[34],"environmental":[36],"conditions.":[37],"Such":[38],"diversity":[39],"poses":[40],"significant":[41],"challenges":[42],"existing":[44],"methods":[45],"balancing":[47],"robustness":[48],"discriminative":[50],"power":[51],"when":[52],"representing":[53],"morphology.":[55,120],"To":[56,137],"address":[57],"this,":[58],"we":[59,142],"propose":[60],"SGTMorph,":[61],"a":[62,94,110,125,144],"hybrid":[63],"Graph":[64],"Transformer":[65],"framework":[66],"that":[67],"leverages":[68],"local":[70],"topological":[71,152],"modeling":[72],"capabilities":[73],"graph":[75],"neural":[76],"networks":[77],"global":[80],"relational":[81],"reasoning":[82],"strengths":[83],"Transformers":[85],"to":[86,100,115],"explicitly":[87],"encode":[88],"information.":[91],"SGTMorph":[92],"incorporates":[93],"random":[95],"walk-based":[96],"positional":[97],"encoding":[98,113],"scheme":[99],"facilitate":[101],"effective":[102],"information":[103],"propagation":[104],"graphs":[107],"introduces":[109],"spatially":[111],"invariant":[112],"mechanism":[114],"improve":[116],"adaptability":[117],"with":[118],"diverse":[119],"This":[121],"integrated":[122],"approach":[123],"enables":[124],"robust":[126],"comprehensive":[128],"while":[133],"maintaining":[134],"biological":[135],"fidelity.":[136],"enable":[138],"label-free":[139],"feature":[140],"learning,":[141],"devise":[143],"self-supervised":[145],"learning":[146],"strategy":[147],"grounded":[148],"geometric":[150],"similarity":[153],"metrics.":[154],"Extensive":[155],"experiments":[156],"on":[157],"five":[158],"datasets":[159],"demonstrate":[160],"SGTMorph's":[161],"superior":[162],"performance":[163],"neuron":[165],"classification":[167],"retrieval":[169],"tasks.":[170],"Furthermore,":[171],"Its":[172],"practical":[173],"utility":[174],"function":[177],"research":[178],"validated":[180],"through":[181],"accurate":[183],"predictions":[184],"two":[186],"functional":[187],"features:":[188],"laminar":[190],"distribution":[191],"somas":[193],"axonal":[195],"projection":[196],"patterns.":[197],"The":[198],"code":[199],"available":[201],"at":[202],"https://github.com/big-rain/SGTMorph.":[203]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}