{"id":"https://openalex.org/W4416361412","doi":"https://doi.org/10.48550/arxiv.2511.13124","title":"Departures: Distributional Transport for Single-Cell Perturbation Prediction with Neural Schr\u00f6dinger Bridges","display_name":"Departures: Distributional Transport for Single-Cell Perturbation Prediction with Neural Schr\u00f6dinger Bridges","publication_year":2025,"publication_date":"2025-11-17","ids":{"openalex":"https://openalex.org/W4416361412","doi":"https://doi.org/10.48550/arxiv.2511.13124"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2511.13124","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2511.13124","pdf_url":"https://arxiv.org/pdf/2511.13124","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2511.13124","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007336805","display_name":"Changxi Chi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chi, Changxi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068887242","display_name":"Yufei Huang","orcid":"https://orcid.org/0000-0001-6268-5357"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Huang, Yufei","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000395252","display_name":"Junshi Xia","orcid":"https://orcid.org/0000-0002-5586-6536"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xia, Jun","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100680275","display_name":"Jiangbin Zheng","orcid":"https://orcid.org/0000-0001-5249-2148"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zheng, Jiangbin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102750871","display_name":"Yunfan Liu","orcid":"https://orcid.org/0000-0002-5316-8961"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liu, Yunfan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007012841","display_name":"Zelin Zang","orcid":"https://orcid.org/0000-0003-2831-5437"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zang, Zelin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5082786719","display_name":"Stan Z. Li","orcid":"https://orcid.org/0000-0002-2961-8096"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Stan Z.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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":0.9778000116348267,"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":0.9778000116348267,"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":0.006099999882280827,"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":0.003800000064074993,"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/perturbation","display_name":"Perturbation (astronomy)","score":0.6848000288009644},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.567300021648407},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.5634999871253967},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.5422999858856201},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.41510000824928284},{"id":"https://openalex.org/keywords/pairing","display_name":"Pairing","score":0.3813999891281128},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.35429999232292175},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.35339999198913574}],"concepts":[{"id":"https://openalex.org/C177918212","wikidata":"https://www.wikidata.org/wiki/Q803623","display_name":"Perturbation (astronomy)","level":2,"score":0.6848000288009644},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.567300021648407},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.5634999871253967},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.5422999858856201},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5349000096321106},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.41510000824928284},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.39410001039505005},{"id":"https://openalex.org/C14103023","wikidata":"https://www.wikidata.org/wiki/Q11681459","display_name":"Pairing","level":3,"score":0.3813999891281128},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3698999881744385},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.35429999232292175},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.35339999198913574},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.3456000089645386},{"id":"https://openalex.org/C165160513","wikidata":"https://www.wikidata.org/wiki/Q7524249","display_name":"Singular perturbation","level":2,"score":0.32989999651908875},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.32899999618530273},{"id":"https://openalex.org/C159886148","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov process","level":2,"score":0.3228999972343445},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3059999942779541},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.30480000376701355},{"id":"https://openalex.org/C47446073","wikidata":"https://www.wikidata.org/wiki/Q5165890","display_name":"Control theory (sociology)","level":3,"score":0.29649999737739563},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.289900004863739},{"id":"https://openalex.org/C149441793","wikidata":"https://www.wikidata.org/wiki/Q200726","display_name":"Probability distribution","level":2,"score":0.27889999747276306},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.26759999990463257},{"id":"https://openalex.org/C34862557","wikidata":"https://www.wikidata.org/wiki/Q178985","display_name":"Ode","level":2,"score":0.2606000006198883},{"id":"https://openalex.org/C197055811","wikidata":"https://www.wikidata.org/wiki/Q207522","display_name":"Probability density function","level":2,"score":0.2587999999523163},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.25459998846054077}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:arXiv.org:2511.13124","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2511.13124","pdf_url":"https://arxiv.org/pdf/2511.13124","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},{"id":"pmh:oai:ojs.aaai.org:article/39190","is_oa":false,"landing_page_url":"https://ojs.aaai.org/index.php/AAAI/article/view/39190","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2159-5399","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.48550/arxiv.2511.13124","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2511.13124","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2511.13124","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2511.13124","pdf_url":"https://arxiv.org/pdf/2511.13124","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Predicting":[0],"single-cell":[1,38,69,118,196,213],"perturbation":[2,51,70,88,122,192,204],"outcomes":[3],"directly":[4,110,160],"advances":[5],"gene":[6,179],"function":[7],"analysis":[8],"and":[9,22,49,116,149,182,194,202,215],"facilitates":[10],"drug":[11,203],"candidate":[12],"selection,":[13],"making":[14],"it":[15],"a":[16,27,165],"key":[17],"driver":[18],"of":[19,37,57,114,153],"both":[20,47],"basic":[21],"translational":[23],"biomedical":[24],"research.":[25],"However,":[26],"major":[28],"bottleneck":[29],"in":[30],"this":[31,91],"task":[32],"is":[33],"the":[34,41,54,104,112,150,155,169,183],"unpaired":[35,68],"nature":[36,56],"data,":[39,71],"as":[40],"same":[42],"cell":[43],"cannot":[44],"be":[45],"observed":[46],"before":[48],"after":[50],"due":[52],"to":[53,66,109,133,144,168],"destructive":[55],"sequencing.":[58],"Although":[59],"some":[60],"neural":[61],"generative":[62],"transport":[63,107],"models":[64],"attempt":[65],"tackle":[67],"they":[72],"either":[73],"lack":[74],"explicit":[75],"conditioning":[76],"or":[77],"depend":[78],"on":[79,130,199],"prior":[80,125],"spaces":[81],"for":[82],"indirect":[83],"distribution":[84],"alignment,":[85],"limiting":[86],"precise":[87],"modeling.":[89],"In":[90],"work,":[92],"we":[93,139],"approximate":[94,172],"Schr\u00f6dinger":[95],"Bridge":[96],"(SB),":[97],"which":[98],"defines":[99],"stochastic":[100],"dynamic":[101],"mappings":[102],"recovering":[103],"entropy-regularized":[105],"optimal":[106,135],"(OT),":[108],"align":[111],"distributions":[113],"control":[115],"perturbed":[117],"populations":[119],"across":[120],"different":[121],"conditions.":[123],"Unlike":[124],"SB":[126,174],"approximations":[127],"that":[128,207],"rely":[129],"bidirectional":[131,147],"modeling":[132,177,193],"infer":[134],"source-target":[136],"sample":[137],"coupling,":[138],"leverage":[140],"Minibatch-OT":[141],"based":[142],"pairing":[143,159],"avoid":[145],"such":[146],"inference":[148],"associated":[151],"ill-posedness":[152],"defining":[154],"reverse":[156],"process.":[157],"This":[158],"guides":[161],"bridge":[162],"learning,":[163],"yielding":[164],"scalable":[166],"approximation":[167],"SB.":[170],"We":[171],"two":[173],"models,":[175],"one":[176],"discrete":[178],"activation":[180],"states":[181],"other":[184],"continuous":[185],"expression":[186],"distributions.":[187],"Joint":[188],"training":[189],"enables":[190],"accurate":[191],"captures":[195,211],"heterogeneity.":[197],"Experiments":[198],"public":[200],"genetic":[201],"datasets":[205],"show":[206],"our":[208],"model":[209],"effectively":[210],"heterogeneous":[212],"responses":[214],"achieves":[216],"state-of-the-art":[217],"performance.":[218]},"counts_by_year":[],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2025-11-19T00:00:00"}