{"id":"https://openalex.org/W4416513251","doi":"https://doi.org/10.1109/tvcg.2025.3634875","title":"TrajLens: Visual Analysis for Constructing Cell Developmental Trajectories in Cross-Sample Exploration","display_name":"TrajLens: Visual Analysis for Constructing Cell Developmental Trajectories in Cross-Sample Exploration","publication_year":2025,"publication_date":"2025-11-21","ids":{"openalex":"https://openalex.org/W4416513251","doi":"https://doi.org/10.1109/tvcg.2025.3634875","pmid":"https://pubmed.ncbi.nlm.nih.gov/41269813"},"language":"en","primary_location":{"id":"doi:10.1109/tvcg.2025.3634875","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tvcg.2025.3634875","pdf_url":null,"source":{"id":"https://openalex.org/S84775595","display_name":"IEEE Transactions on Visualization and Computer Graphics","issn_l":"1077-2626","issn":["1077-2626","1941-0506","2160-9306"],"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 Visualization and Computer Graphics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://ink.library.smu.edu.sg/sis_research/11053","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Qipeng Wang","orcid":"https://orcid.org/0009-0001-0350-4701"},"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":"Qipeng Wang","raw_affiliation_strings":["Sichuan University, China"],"affiliations":[{"raw_affiliation_string":"Sichuan University, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030982591","display_name":"Shaolun Ruan","orcid":null},"institutions":[{"id":"https://openalex.org/I79891267","display_name":"Singapore Management University","ror":"https://ror.org/050qmg959","country_code":"SG","type":"education","lineage":["https://openalex.org/I79891267"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Shaolun Ruan","raw_affiliation_strings":["Singapore Management University, Singapore"],"affiliations":[{"raw_affiliation_string":"Singapore Management University, Singapore","institution_ids":["https://openalex.org/I79891267"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Rui Sheng","orcid":"https://orcid.org/0000-0001-9321-6756"},"institutions":[{"id":"https://openalex.org/I200769079","display_name":"Hong Kong University of Science and Technology","ror":"https://ror.org/00q4vv597","country_code":"HK","type":"education","lineage":["https://openalex.org/I200769079"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Rui Sheng","raw_affiliation_strings":["Hong Kong University of Science and Technology, Hong Kong, Hong Kong","Hong Kong University of Science and Technology, Hong Kong"],"affiliations":[{"raw_affiliation_string":"Hong Kong University of Science and Technology, Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I200769079"]},{"raw_affiliation_string":"Hong Kong University of Science and Technology, Hong Kong","institution_ids":["https://openalex.org/I200769079"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100424394","display_name":"Yong Wang","orcid":"https://orcid.org/0000-0002-0092-0793"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Yong Wang","raw_affiliation_strings":["Nanyang Technological University, Singapore"],"affiliations":[{"raw_affiliation_string":"Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Min Zhu","orcid":"https://orcid.org/0000-0002-5664-1558"},"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":"Min Zhu","raw_affiliation_strings":["Sichuan University, China"],"affiliations":[{"raw_affiliation_string":"Sichuan University, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091466289","display_name":"Huamin Qu","orcid":"https://orcid.org/0000-0002-3344-9694"},"institutions":[{"id":"https://openalex.org/I200769079","display_name":"Hong Kong University of Science and Technology","ror":"https://ror.org/00q4vv597","country_code":"HK","type":"education","lineage":["https://openalex.org/I200769079"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Huamin Qu","raw_affiliation_strings":["Hong Kong University of Science and Technology, Hong Kong, Hong Kong","Hong Kong University of Science and Technology, Hong Kong"],"affiliations":[{"raw_affiliation_string":"Hong Kong University of Science and Technology, Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I200769079"]},{"raw_affiliation_string":"Hong Kong University of Science and Technology, Hong Kong","institution_ids":["https://openalex.org/I200769079"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I24185976"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.31227422,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"32","issue":"1","first_page":"1219","last_page":"1229"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9660000205039978,"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":0.9660000205039978,"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":0.02419999986886978,"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/T10775","display_name":"Generative Adversarial Networks and Image Synthesis","score":0.0008999999845400453,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/visualization","display_name":"Visualization","score":0.6625000238418579},{"id":"https://openalex.org/keywords/visual-analytics","display_name":"Visual analytics","score":0.661899983882904},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.5795000195503235},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5252000093460083},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5076000094413757},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.4767000079154968},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4372999966144562}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7742000222206116},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6625000238418579},{"id":"https://openalex.org/C59732488","wikidata":"https://www.wikidata.org/wiki/Q2528440","display_name":"Visual analytics","level":3,"score":0.661899983882904},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.5795000195503235},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5252000093460083},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5231000185012817},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5076000094413757},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.4767000079154968},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4372999966144562},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3732999861240387},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.31790000200271606},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.30070000886917114},{"id":"https://openalex.org/C79158427","wikidata":"https://www.wikidata.org/wiki/Q485396","display_name":"Analytics","level":2,"score":0.2847999930381775},{"id":"https://openalex.org/C178253425","wikidata":"https://www.wikidata.org/wiki/Q162668","display_name":"Visual perception","level":3,"score":0.27880001068115234},{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.2750000059604645},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26510000228881836},{"id":"https://openalex.org/C14669888","wikidata":"https://www.wikidata.org/wiki/Q4014850","display_name":"Creative visualization","level":3,"score":0.2621000111103058},{"id":"https://openalex.org/C2777055276","wikidata":"https://www.wikidata.org/wiki/Q7936580","display_name":"Visual approach","level":2,"score":0.25270000100135803},{"id":"https://openalex.org/C175154964","wikidata":"https://www.wikidata.org/wiki/Q380077","display_name":"Task analysis","level":3,"score":0.25220000743865967}],"mesh":[{"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":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1109/tvcg.2025.3634875","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tvcg.2025.3634875","pdf_url":null,"source":{"id":"https://openalex.org/S84775595","display_name":"IEEE Transactions on Visualization and Computer Graphics","issn_l":"1077-2626","issn":["1077-2626","1941-0506","2160-9306"],"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 Visualization and Computer Graphics","raw_type":"journal-article"},{"id":"pmid:41269813","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41269813","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 visualization and computer graphics","raw_type":null},{"id":"pmh:oai:ink.library.smu.edu.sg:sis_research-12054","is_oa":true,"landing_page_url":"https://ink.library.smu.edu.sg/sis_research/11053","pdf_url":null,"source":{"id":"https://openalex.org/S4306401925","display_name":"Singapore Management University Institutional Knowledge (InK) (Singapore Management University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79891267","host_organization_name":"Singapore Management University","host_organization_lineage":["https://openalex.org/I79891267"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://doi.org/10.1109/TVCG.2025.3634875","raw_type":"Journal Article"},{"id":"pmh:oai:repository.hkust.edu.hk:1783.1-167072","is_oa":false,"landing_page_url":"http://repository.hkust.edu.hk/ir/Record/1783.1-167072","pdf_url":null,"source":{"id":"https://openalex.org/S4306401796","display_name":"Rare & Special e-Zone (The Hong Kong University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I200769079","host_organization_name":"Hong Kong University of Science and Technology","host_organization_lineage":["https://openalex.org/I200769079"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"pmh:oai:ink.library.smu.edu.sg:sis_research-12054","is_oa":true,"landing_page_url":"https://ink.library.smu.edu.sg/sis_research/11053","pdf_url":null,"source":{"id":"https://openalex.org/S4306401925","display_name":"Singapore Management University Institutional Knowledge (InK) (Singapore Management University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79891267","host_organization_name":"Singapore Management University","host_organization_lineage":["https://openalex.org/I79891267"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://doi.org/10.1109/TVCG.2025.3634875","raw_type":"Journal Article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6043036435","display_name":null,"funder_award_id":"62172289","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":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Constructing":[0],"cell":[1,30,85,104,120,137,150],"developmental":[2,31,86,105,123],"trajectories":[3,32,49,106],"is":[4],"a":[5,79,92],"critical":[6],"task":[7],"in":[8,99],"single-cell":[9],"RNA":[10],"sequencing":[11],"(scRNA-seq)":[12],"analysis,":[13],"enabling":[14,153],"the":[15,63,103,114,132,148],"inference":[16],"of":[17,70,131,136,168],"potential":[18],"cellular":[19,52],"progression":[20],"paths.":[21],"However,":[22],"current":[23],"automated":[24],"methods":[25],"are":[26],"limited":[27],"to":[28,38,44,62,82,155,178],"establishing":[29],"within":[33],"individual":[34],"samples,":[35,127],"necessitating":[36],"biologists":[37,98,154],"manually":[39],"link":[40],"cells":[41],"across":[42,125],"samples":[43],"construct":[45],"complete":[46],"cross-sample":[47,84],"evolutionary":[48,134],"that":[50,96,116],"consider":[51],"spatial":[53,65,133],"dynamics.":[54],"This":[55],"process":[56],"demands":[57],"substantial":[58],"human":[59],"effort":[60],"due":[61],"complex":[64],"correspondence":[66],"between":[67],"each":[68],"pair":[69],"samples.":[71],"To":[72,159],"address":[73],"this":[74],"challenge,":[75],"we":[76,112,142,164],"first":[77],"proposed":[78],"GNN-based":[80],"model":[81,170],"predict":[83],"trajectories.":[87,140],"We":[88],"then":[89],"developed":[90],"TrajLens,":[91],"visual":[93],"analytics":[94],"system":[95],"supports":[97],"exploring":[100],"and":[101,122,175,182],"refining":[102],"based":[107],"on":[108,119,147],"predicted":[109],"links.":[110],"Specifically,":[111],"designed":[113],"visualization":[115],"integrates":[117],"features":[118],"distribution":[121,151],"direction":[124],"multiple":[126],"providing":[128],"an":[129],"overview":[130],"patterns":[135],"populations":[138],"along":[139],"Additionally,":[141],"included":[143],"contour":[144],"maps":[145],"superimposed":[146],"original":[149],"data,":[152],"explore":[156],"them":[157],"intuitively.":[158],"demonstrate":[160],"our":[161,169],"system's":[162],"performance,":[163],"conducted":[165],"quantitative":[166],"evaluations":[167],"with":[171],"two":[172],"case":[173],"studies":[174],"expert":[176],"interviews":[177],"validate":[179],"its":[180],"usefulness":[181],"effectiveness.":[183]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-11-23T00:00:00"}
