{"id":"https://openalex.org/W7216529020","doi":"https://doi.org/10.48550/arxiv.2610.01086","title":"Multi-Scale Temporal Flows for Peptide Trajectory Generation","display_name":"Multi-Scale Temporal Flows for Peptide Trajectory Generation","publication_year":2026,"publication_date":"2026-10-01","ids":{"openalex":"https://openalex.org/W7216529020","doi":"https://doi.org/10.48550/arxiv.2610.01086"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2610.01086","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.01086","pdf_url":"https://arxiv.org/pdf/2610.01086","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,"listed_in":[],"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"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2610.01086","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5154918653","display_name":"Xichen Sun","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sun, Xichen","raw_affiliation_strings":["School of Computer Science and Engineering , Sun Yat-sen University , Guangzhou , Guangdong , China","Shenzhen Loop Area Institute , Shenzhen , Guangdong , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering , Sun Yat-sen University , Guangzhou , Guangdong , China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"Shenzhen Loop Area Institute , Shenzhen , Guangdong , China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5154526257","display_name":"Wentao Wei","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210136793","display_name":"Peng Cheng Laboratory","ror":"https://ror.org/03qdqbt06","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210136793"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei, Wentao","raw_affiliation_strings":["Pengcheng Laboratory , Shenzhen , Guangdong , China","School of Computer Science and Engineering , Sun Yat-sen University , Guangzhou , Guangdong , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pengcheng Laboratory , Shenzhen , Guangdong , China","institution_ids":["https://openalex.org/I4210136793"]},{"raw_affiliation_string":"School of Computer Science and Engineering , Sun Yat-sen University , Guangzhou , Guangdong , China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033349055","display_name":"Xiaoxi Zhang","orcid":"https://orcid.org/0000-0002-0873-8988","observed_orcids":["https://orcid.org/0000-0002-0873-8988"]},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhang, Xiaoxi","raw_affiliation_strings":["School of Computer Science and Engineering , Sun Yat-sen University , Guangzhou , Guangdong , China","Shenzhen Loop Area Institute , Shenzhen , Guangdong , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering , Sun Yat-sen University , Guangzhou , Guangdong , China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"Shenzhen Loop Area Institute , Shenzhen , Guangdong , China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023539493","display_name":"Yuedong Yang","orcid":"https://orcid.org/0000-0002-6782-2813","observed_orcids":["https://orcid.org/0000-0002-6782-2813"]},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4405272214","display_name":"Guangdong Province Key Laboratory of Computational Science","ror":"https://ror.org/03rtxse59","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4405272214"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang, Yuedong","raw_affiliation_strings":["Guangdong Provincial Key Laboratory of Computational Science , Sun Yat-sen University , Guangzhou , Guangdong , China","School of Computer Science and Engineering , Sun Yat-sen University , Guangzhou , Guangdong , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangdong Provincial Key Laboratory of Computational Science , Sun Yat-sen University , Guangzhou , Guangdong , China","institution_ids":["https://openalex.org/I157773358","https://openalex.org/I4405272214"]},{"raw_affiliation_string":"School of Computer Science and Engineering , Sun Yat-sen University , Guangzhou , Guangdong , China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5156011421","display_name":"Jiahua Rao","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rao, Jiahua","raw_affiliation_strings":["School of Computer Science and Engineering , Sun Yat-sen University , Guangzhou , Guangdong , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering , Sun Yat-sen University , Guangzhou , Guangdong , China","institution_ids":["https://openalex.org/I157773358"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"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/T10044","display_name":"Protein Structure and Dynamics","score":0.986299991607666,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.986299991607666,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.00839999970048666,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.0017000000225380063,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/multi-scale-temporal-modeling","display_name":"multi-scale temporal modeling","score":0.6909999847412109},{"id":"https://openalex.org/keywords/cyclic-peptides","display_name":"cyclic peptides","score":0.6499999761581421},{"id":"https://openalex.org/keywords/peptide-conformational-dynamics","display_name":"peptide conformational dynamics","score":0.6060000061988831},{"id":"https://openalex.org/keywords/rare-event-sampling","display_name":"rare event sampling","score":0.5460000038146973},{"id":"https://openalex.org/keywords/flow-based-generative-models","display_name":"flow-based generative models","score":0.6869999766349792},{"id":"https://openalex.org/keywords/peptides","display_name":"peptides","score":0.5759999752044678}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5828999876976013},{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.5716999769210815},{"id":"https://openalex.org/C2778067643","wikidata":"https://www.wikidata.org/wiki/Q166507","display_name":"Interval (graph theory)","level":2,"score":0.5570999979972839},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46299999952316284},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4577000141143799},{"id":"https://openalex.org/C190470478","wikidata":"https://www.wikidata.org/wiki/Q2370229","display_name":"Invariant (physics)","level":2,"score":0.4560000002384186},{"id":"https://openalex.org/C61445026","wikidata":"https://www.wikidata.org/wiki/Q217608","display_name":"Fixed point","level":2,"score":0.42340001463890076},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.4025999903678894},{"id":"https://openalex.org/C162670838","wikidata":"https://www.wikidata.org/wiki/Q6057295","display_name":"Interval temporal logic","level":3,"score":0.35420000553131104},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.33869999647140503},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.31690001487731934},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.31679999828338623},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.3075000047683716},{"id":"https://openalex.org/C47446073","wikidata":"https://www.wikidata.org/wiki/Q5165890","display_name":"Control theory (sociology)","level":3,"score":0.3034999966621399},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3027999997138977},{"id":"https://openalex.org/C28719098","wikidata":"https://www.wikidata.org/wiki/Q44946","display_name":"Point (geometry)","level":2,"score":0.2797999978065491},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.26570001244544983},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.2632000148296356},{"id":"https://openalex.org/C87698059","wikidata":"https://www.wikidata.org/wiki/Q1808960","display_name":"LTI system theory","level":3,"score":0.26260000467300415},{"id":"https://openalex.org/C175291020","wikidata":"https://www.wikidata.org/wiki/Q1156822","display_name":"Offset (computer science)","level":2,"score":0.2623000144958496},{"id":"https://openalex.org/C91188154","wikidata":"https://www.wikidata.org/wiki/Q186247","display_name":"Vector field","level":2,"score":0.25600001215934753}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2610.01086","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.01086","pdf_url":"https://arxiv.org/pdf/2610.01086","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,"listed_in":[],"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":"doi:10.48550/arxiv.2610.01086","doi":"https://doi.org/10.48550/arxiv.2610.01086","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2610.01086","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,"listed_in":[],"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":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2610.01086","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.01086","pdf_url":"https://arxiv.org/pdf/2610.01086","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,"listed_in":[],"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":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7216529020.pdf","grobid_xml":"https://content.openalex.org/works/W7216529020.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W2957988017","https://openalex.org/W4379087891","https://openalex.org/W4403570033","https://openalex.org/W4403795213","https://openalex.org/W7127289411","https://openalex.org/W7128794432","https://openalex.org/W7138912131"],"related_works":["https://openalex.org/W4400090810","https://openalex.org/W7104997350","https://openalex.org/W7126039194","https://openalex.org/W7222986605","https://openalex.org/W4416395593","https://openalex.org/W7215973642","https://openalex.org/W4412827210","https://openalex.org/W7167936631","https://openalex.org/W7138912131","https://openalex.org/W4403795213"],"abstract_inverted_index":{"Peptides":[0],"occupy":[1],"a":[2,12,52,61,78,90,103,120,144,166,188],"particularly":[3],"challenging":[4],"regime":[5],"of":[6,113,143,151,179],"biomolecular":[7],"dynamics.":[8],"Short":[9],"peptides":[10],"lack":[11],"stable":[13],"folded":[14],"core":[15],"and":[16,29,55,134,169,177,182,187,197,211],"populate":[17],"broad":[18],"conformational":[19],"ensembles,":[20],"while":[21],"cyclization":[22],"adds":[23],"ring":[24],"closure,":[25],"non-local":[26],"residue":[27],"coupling,":[28],"stereochemical":[30],"diversity.":[31],"Deep":[32],"generative":[33],"models":[34],"have":[35],"made":[36],"remarkable":[37],"progress":[38],"in":[39,201],"emulating":[40],"molecular-dynamics":[41],"trajectories":[42,205],"directly,":[43],"yet":[44],"each":[45,114,152],"is":[46,81,117,223],"trained":[47],"on":[48,88],"windows":[49],"cut":[50],"at":[51,60,130],"fixed":[53,62],"interval":[54,70,142],"therefore":[56],"observes":[57,126],"the":[58,75,85,127,140,148,155,175],"process":[59],"temporal":[63,105,132,202,221],"resolution.":[64],"More":[65],"fundamentally,":[66],"none":[67],"takes":[68],"that":[69,218],"as":[71],"an":[72,135],"input,":[73],"so":[74,123],"physical":[76],"time":[77,150],"window":[79,116,145],"spans":[80],"never":[82],"represented,":[83],"leaving":[84],"sparse":[86,208],"frames":[87,161,210],"which":[89],"peptide":[91,108],"crosses":[92],"between":[93],"metastable":[94],"states":[95],"difficult":[96],"to":[97],"learn.":[98],"Here,":[99],"we":[100],"introduce":[101],"PepTIDE,":[102],"multi-scale":[104],"framework":[106],"for":[107],"trajectory":[109],"generation.":[110],"The":[111],"stride":[112],"training":[115],"drawn":[118],"from":[119],"continuous":[121],"range,":[122],"one":[124],"model":[125],"same":[128],"dynamics":[129],"many":[131],"resolutions,":[133],"Adaptive":[136],"Physical-Time":[137],"Embedding":[138],"encodes":[139],"relative":[141],"together":[146],"with":[147],"absolute":[149],"frame,":[153],"making":[154],"shared":[156],"velocity":[157],"field":[158],"interval-aware.":[159],"All":[160],"are":[162],"generated":[163],"jointly":[164],"through":[165],"stochastic-interpolant":[167],"flow,":[168],"pair-aware":[170],"invariant":[171],"point":[172],"attention":[173],"captures":[174],"geometry":[176],"topology":[178],"both":[180],"linear":[181],"cyclic":[183],"peptides.":[184],"On":[185],"PepMD":[186],"50-system":[189],"cyclic-peptide":[190],"benchmark,":[191],"PepTIDE":[192],"reaches":[193],"state-of-the-art":[194],"distribution":[195],"agreement":[196],"structural":[198],"validity.":[199],"Read":[200],"order,":[203],"its":[204],"recover":[206],"these":[207,226],"transition":[209],"reproduce":[212],"inter-state":[213],"fluxes":[214],"more":[215],"faithfully,":[216],"confirming":[217],"modeling":[219],"multiple":[220],"scales":[222],"what":[224],"makes":[225],"rare":[227],"events":[228],"accessible.":[229]},"counts_by_year":[],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2026-10-03T00:00:00"}