{"id":"https://openalex.org/W7143405001","doi":"https://doi.org/10.48550/arxiv.2603.25980","title":"A Priori Sampling of Transition States with Guided Diffusion","display_name":"A Priori Sampling of Transition States with Guided Diffusion","publication_year":2026,"publication_date":"2026-03-26","ids":{"openalex":"https://openalex.org/W7143405001","doi":"https://doi.org/10.48550/arxiv.2603.25980"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2603.25980","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.25980","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":false,"raw_source_name":null,"raw_type":"article"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2603.25980","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5130920371","display_name":"Hyukjun Lim","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Lim, Hyukjun","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5130923533","display_name":"Soojung Yang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yang, Soojung","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121477539","display_name":"Lucas Pin\u00e8de","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pin\u00e8de, Lucas","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071155016","display_name":"Miguel Steiner","orcid":"https://orcid.org/0000-0002-7634-7268"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Steiner, Miguel","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5130974106","display_name":"Yuanqi Du","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Du, Yuanqi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5130993442","display_name":"Rafael G\u00f3mez-Bombarelli","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"G\u00f3mez-Bombarelli, Rafael","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5130920371"],"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/T10044","display_name":"Protein Structure and Dynamics","score":0.659600019454956,"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":0.659600019454956,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.04619999974966049,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.03310000151395798,"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/a-priori-and-a-posteriori","display_name":"A priori and a posteriori","score":0.6086999773979187},{"id":"https://openalex.org/keywords/reaction-coordinate","display_name":"Reaction coordinate","score":0.5909000039100647},{"id":"https://openalex.org/keywords/metastability","display_name":"Metastability","score":0.5648000240325928},{"id":"https://openalex.org/keywords/transition-state","display_name":"Transition state","score":0.5331000089645386},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.5232999920845032},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.47929999232292175},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.446399986743927},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.4320000112056732},{"id":"https://openalex.org/keywords/transition-state-theory","display_name":"Transition state theory","score":0.42480000853538513},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.39959999918937683}],"concepts":[{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.6226999759674072},{"id":"https://openalex.org/C75553542","wikidata":"https://www.wikidata.org/wiki/Q178161","display_name":"A priori and a posteriori","level":2,"score":0.6086999773979187},{"id":"https://openalex.org/C18553476","wikidata":"https://www.wikidata.org/wiki/Q1076414","display_name":"Reaction coordinate","level":2,"score":0.5909000039100647},{"id":"https://openalex.org/C89464430","wikidata":"https://www.wikidata.org/wiki/Q849516","display_name":"Metastability","level":2,"score":0.5648000240325928},{"id":"https://openalex.org/C89031862","wikidata":"https://www.wikidata.org/wiki/Q906964","display_name":"Transition state","level":3,"score":0.5331000089645386},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.5232999920845032},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.47929999232292175},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4713999927043915},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.446399986743927},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.4320000112056732},{"id":"https://openalex.org/C57476982","wikidata":"https://www.wikidata.org/wiki/Q582857","display_name":"Transition state theory","level":4,"score":0.42480000853538513},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.42179998755455017},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.39959999918937683},{"id":"https://openalex.org/C55128770","wikidata":"https://www.wikidata.org/wiki/Q5275440","display_name":"Diffusion map","level":4,"score":0.3930000066757202},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.3840000033378601},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.37290000915527344},{"id":"https://openalex.org/C194232998","wikidata":"https://www.wikidata.org/wiki/Q1606712","display_name":"Transition (genetics)","level":3,"score":0.3720000088214874},{"id":"https://openalex.org/C2777303404","wikidata":"https://www.wikidata.org/wiki/Q759757","display_name":"Convergence (economics)","level":2,"score":0.3695000112056732},{"id":"https://openalex.org/C62752575","wikidata":"https://www.wikidata.org/wiki/Q6822487","display_name":"Metadynamics","level":3,"score":0.36010000109672546},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.35589998960494995},{"id":"https://openalex.org/C2776902872","wikidata":"https://www.wikidata.org/wiki/Q352410","display_name":"ASTRA","level":2,"score":0.3409999907016754},{"id":"https://openalex.org/C2775936607","wikidata":"https://www.wikidata.org/wiki/Q466845","display_name":"Tracking (education)","level":2,"score":0.3262999951839447},{"id":"https://openalex.org/C159886148","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov process","level":2,"score":0.320499986410141},{"id":"https://openalex.org/C27753989","wikidata":"https://www.wikidata.org/wiki/Q284885","display_name":"Superposition principle","level":2,"score":0.3068000078201294},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3052000105381012},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.29919999837875366},{"id":"https://openalex.org/C70557757","wikidata":"https://www.wikidata.org/wiki/Q7834432","display_name":"Transition rate matrix","level":2,"score":0.2962999939918518},{"id":"https://openalex.org/C62354387","wikidata":"https://www.wikidata.org/wiki/Q875399","display_name":"Boundary (topology)","level":2,"score":0.28029999136924744},{"id":"https://openalex.org/C2681867","wikidata":"https://www.wikidata.org/wiki/Q690935","display_name":"Saddle point","level":2,"score":0.2761000096797943},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.2727000117301941},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2646999955177307},{"id":"https://openalex.org/C52740198","wikidata":"https://www.wikidata.org/wiki/Q1539564","display_name":"Importance sampling","level":3,"score":0.2635999917984009},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.2624000012874603},{"id":"https://openalex.org/C68710425","wikidata":"https://www.wikidata.org/wiki/Q5275442","display_name":"Diffusion process","level":3,"score":0.2565999925136566},{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.2563000023365021},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.25529998540878296},{"id":"https://openalex.org/C47822265","wikidata":"https://www.wikidata.org/wiki/Q854457","display_name":"Complex system","level":2,"score":0.25450000166893005},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2533000111579895}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2603.25980","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.25980","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"article"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2603.25980","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.25980","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[{"score":0.9040764570236206,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Transition":[0],"states,":[1],"the":[2,7,12,51,69,97,126,130,153],"first-order":[3,168],"saddle":[4],"points":[5],"on":[6,115,172],"potential":[8],"energy":[9],"surfaces,":[10],"govern":[11],"kinetics":[13],"and":[14,19,32,158,182,193],"mechanisms":[15],"of":[16,38,89,132,139,201],"chemical":[17,184],"reactions":[18],"conformational":[20,180],"changes.":[21],"Locating":[22],"them":[23],"is":[24,65],"challenging":[25],"because":[26],"transition":[27,98,169,188],"pathways":[28],"are":[29],"topologically":[30],"complex":[31,202],"can":[33],"proceed":[34],"via":[35,135],"an":[36,102],"ensemble":[37],"diverse":[39],"routes.":[40],"Existing":[41],"methods":[42],"address":[43],"these":[44],"challenges":[45],"by":[46,83],"introducing":[47,84],"heuristic":[48,81],"assumptions":[49],"about":[50],"pathway":[52],"or":[53,67],"reaction":[54,150,196],"coordinates,":[55],"which":[56,95],"limits":[57],"their":[58],"applicability":[59],"when":[60,68],"a":[61,111,136,149,183],"good":[62],"initial":[63],"guess":[64,70],"unavailable":[66],"precludes":[71],"alternative,":[72],"potentially":[73],"relevant":[74],"pathways.":[75],"We":[76],"propose":[77],"to":[78,164,178],"bypass":[79],"such":[80],"limitations":[82],"ASTRA,":[85],"A":[86,142],"Priori":[87],"Sampling":[88],"TRAnsition":[90],"States":[91],"with":[92,161,190],"Guided":[93],"Diffusion,":[94],"reframes":[96],"state":[99],"search":[100],"as":[101],"inference-time":[103],"scaling":[104],"problem":[105],"for":[106],"generative":[107],"models.":[108],"ASTRA":[109,122,186],"trains":[110],"score-based":[112],"diffusion":[113],"model":[114],"configurations":[116],"from":[117,152,175],"known":[118],"metastable":[119,133],"states.":[120,170],"Then,":[121],"guides":[123],"inference":[124],"toward":[125],"isodensity":[127],"surface":[128],"separating":[129],"basins":[131],"states":[134,189],"principled":[137],"composition":[138],"conditional":[140],"scores.":[141],"Score-Aligned":[143],"Ascent":[144],"(SAA)":[145],"process":[146],"then":[147],"approximates":[148],"coordinate":[151],"difference":[154],"between":[155],"conditioned":[156],"scores":[157],"combines":[159],"it":[160],"physical":[162],"forces":[163],"drive":[165],"convergence":[166],"onto":[167],"Validated":[171],"benchmarks":[173],"ranging":[174],"2D":[176],"potentials":[177],"biomolecular":[179],"changes":[181],"reaction,":[185],"locates":[187],"high":[191],"precision":[192],"discovers":[194],"multiple":[195],"pathways,":[197],"enabling":[198],"mechanistic":[199],"studies":[200],"molecular":[203],"systems.":[204]},"counts_by_year":[],"updated_date":"2026-05-01T06:04:38.248271","created_date":"2026-03-31T00:00:00"}