{"id":"https://openalex.org/W7225413645","doi":"https://doi.org/10.64898/2026.11.05.764599","title":"scCont: Interpretable Contrastive Learning for Functional Characterization of Cellular State Transitions","display_name":"scCont: Interpretable Contrastive Learning for Functional Characterization of Cellular State Transitions","publication_year":2026,"publication_date":"2026-11-06","ids":{"openalex":"https://openalex.org/W7225413645","doi":"https://doi.org/10.64898/2026.11.05.764599"},"language":"en","primary_location":{"id":"doi:10.64898/2026.11.05.764599","doi":"https://doi.org/10.64898/2026.11.05.764599","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.05.764599","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.05.764599.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.05.764599.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017367809","display_name":"Neal Kewalramani","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Neal Kewalramani","raw_affiliation_strings":["Boston University;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boston University;","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076755077","display_name":"Stefan Wuchty","orcid":"https://orcid.org/0000-0001-8916-6522","observed_orcids":["https://orcid.org/0000-0001-8916-6522"]},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stefan Wuchty","raw_affiliation_strings":["Univ. of Miami;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Univ. of Miami;","institution_ids":["https://openalex.org/I145608581"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064525211","display_name":"Mark E. Crovella","orcid":"https://orcid.org/0000-0002-5005-7019","observed_orcids":["https://orcid.org/0000-0002-5005-7019"]},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Crovella","raw_affiliation_strings":["Boston University;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boston University;","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025381118","display_name":"Indranil Paul","orcid":"https://orcid.org/0000-0003-0327-5002","observed_orcids":["https://orcid.org/0000-0003-0327-5002"]},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Indranil Paul","raw_affiliation_strings":["Oregon Health & Science University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Oregon Health & Science University","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076978787","display_name":"Andrew Emili","orcid":"https://orcid.org/0000-0001-8995-246X","observed_orcids":["https://orcid.org/0000-0001-8995-246X"]},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew Emili","raw_affiliation_strings":["Oregon Health & Science University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Oregon Health & Science University","institution_ids":["https://openalex.org/I165690674"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5017367809"],"corresponding_institution_ids":["https://openalex.org/I111088046"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T10621","display_name":"Gene Regulatory Network Analysis","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/contrastive-learning","display_name":"contrastive learning","score":0.8510000109672546},{"id":"https://openalex.org/keywords/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.7179999947547913},{"id":"https://openalex.org/keywords/cell-state-transitions","display_name":"cell state transitions","score":0.6830000281333923},{"id":"https://openalex.org/keywords/epithelial-mesenchymal-transition","display_name":"epithelial-mesenchymal transition","score":0.9580000042915344},{"id":"https://openalex.org/keywords/interpretability","display_name":"interpretability","score":0.6790000200271606},{"id":"https://openalex.org/keywords/shapley-value","display_name":"Shapley value","score":0.781000018119812},{"id":"https://openalex.org/keywords/k-nearest-neighbors","display_name":"k-nearest neighbors","score":0.6589999794960022},{"id":"https://openalex.org/keywords/unsupervised-learning","display_name":"unsupervised learning","score":0.7089999914169312},{"id":"https://openalex.org/keywords/time-course-transcriptomics","display_name":"time-course transcriptomics","score":0.5180000066757202}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8596000075340271},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7480999827384949},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7160999774932861},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6345999836921692},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5285999774932861},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.49639999866485596},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.46970000863075256},{"id":"https://openalex.org/C8038995","wikidata":"https://www.wikidata.org/wiki/Q1152135","display_name":"Unsupervised learning","level":2,"score":0.4228000044822693},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4072999954223633},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3395000100135803},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.335999995470047},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.3246000111103058},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.31150001287460327},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.30230000615119934},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.296099990606308},{"id":"https://openalex.org/C151319957","wikidata":"https://www.wikidata.org/wiki/Q752739","display_name":"Asynchronous communication","level":2,"score":0.29100000858306885},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.2890999913215637},{"id":"https://openalex.org/C100776233","wikidata":"https://www.wikidata.org/wiki/Q2532492","display_name":"Bridge (graph theory)","level":2,"score":0.2858999967575073},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.28349998593330383},{"id":"https://openalex.org/C94966114","wikidata":"https://www.wikidata.org/wiki/Q29256","display_name":"Black box","level":2,"score":0.2784999907016754},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.27379998564720154},{"id":"https://openalex.org/C2779478453","wikidata":"https://www.wikidata.org/wiki/Q6889748","display_name":"Modularity (biology)","level":2,"score":0.2734000086784363},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2711000144481659},{"id":"https://openalex.org/C175154964","wikidata":"https://www.wikidata.org/wiki/Q380077","display_name":"Task analysis","level":3,"score":0.2637999951839447},{"id":"https://openalex.org/C194232998","wikidata":"https://www.wikidata.org/wiki/Q1606712","display_name":"Transition (genetics)","level":3,"score":0.25839999318122864},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.25780001282691956}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.11.05.764599","doi":"https://doi.org/10.64898/2026.11.05.764599","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.05.764599","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.05.764599.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.11.05.764599","doi":"https://doi.org/10.64898/2026.11.05.764599","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.05.764599","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.05.764599.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G9000919882","display_name":"Predoctoral Training in Bioinformatics and Computational Biology","funder_award_id":"T32GM150533","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225413645.pdf","grobid_xml":"https://content.openalex.org/works/W7225413645.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2123937928","https://openalex.org/W2170331002","https://openalex.org/W3012280517","https://openalex.org/W4321748573"],"related_works":["https://openalex.org/W3196971188","https://openalex.org/W4389847959","https://openalex.org/W7155551727","https://openalex.org/W4297457819","https://openalex.org/W7169866816","https://openalex.org/W4406497717","https://openalex.org/W4399986066","https://openalex.org/W4405108207","https://openalex.org/W7134964213","https://openalex.org/W7112922691"],"abstract_inverted_index":{"Timecourse":[0],"single-cell":[1],"RNA":[2],"(scRNA)":[3],"datasets":[4,156],"have":[5],"become":[6],"indispensable":[7],"biological":[8,51,183],"tools":[9],"for":[10,72],"studying":[11],"and":[12,129,157,166,181],"uncovering":[13],"the":[14,24,55,175],"underlying":[15],"regulatory":[16],"processes":[17],"driving":[18],"continuous":[19],"cell-state":[20],"transitions":[21],"such":[22,147],"as":[23,148],"epithelial-to-mesenchymal":[25],"transition.":[26],"However,":[27],"these":[28],"highly":[29],"fluid,":[30],"non-linear":[31],"gene":[32,125],"program":[33],"dynamics":[34,141,165],"remain":[35],"difficult":[36],"to":[37,98,115,173],"disentangle.":[38],"While":[39],"deep":[40,178],"neural":[41],"network":[42,113],"models":[43],"can":[44],"effectively":[45,143,167],"map":[46],"complex":[47],"topologies,":[48],"they":[49],"are":[50],"black":[52],"boxes,":[53],"lacking":[54],"gene-level":[56],"interpretability":[57],"required":[58],"by":[59,134],"experimental":[60],"practitioners.":[61],"Here,":[62],"we":[63],"introduce":[64],"scCont,":[65],"a":[66,104],"fully":[67],"unsupervised":[68,94],"contrastive":[69],"learning":[70,179],"framework":[71],"extracting":[73],"interpretable":[74,140,163],"functional":[75,124,164,170],"transition":[76],"units":[77],"from":[78],"scRNA-seq":[79],"data.":[80],"Rather":[81],"than":[82,144],"relying":[83],"on":[84,192],"explicit":[85],"temporal":[86],"labels":[87],"or":[88],"clustering":[89],"priors,":[90],"scCont":[91,110,137,161,185],"uses":[92],"an":[93,187],"k-nearest":[95],"neighbors":[96],"approach":[97],"project":[99],"local":[100],"transcriptomic":[101],"neighborhoods":[102],"into":[103,123],"low-dimensional":[105],"embedding.":[106],"During":[107],"post-training":[108],"analysis,":[109],"employs":[111],"Shapley":[112],"attribution":[114],"determine":[116],"gene-latent":[117],"relationships,":[118],"mapping":[119],"latent":[120],"dimensions":[121],"directly":[122],"programs.":[126],"We":[127],"quantitatively":[128],"qualitatively":[130],"validate":[131],"this":[132],"representation":[133,180],"demonstrating":[135],"that":[136],"captures":[138],"biologically":[139],"more":[142],"baseline":[145],"methods":[146],"LDVAE.":[149],"Evaluated":[150],"across":[151],"13":[152],"diverse":[153],"EMT":[154],"timecourse":[155],"four":[158],"simulated":[159],"datasets,":[160],"exposes":[162],"maps":[168],"context-dependent":[169],"groups,":[171],"helping":[172],"bridge":[174],"gap":[176],"between":[177],"translational":[182],"utility.":[184],"is":[186],"open":[188],"source":[189],"software":[190],"available":[191],"GitHub":[193],"(https://github.com/nramani611/scCont).":[194]},"counts_by_year":[],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2026-11-07T00:00:00"}
