{"id":"https://openalex.org/W7147540191","doi":"https://doi.org/10.48550/arxiv.2603.26705","title":"PI-Mamba: Linear-Time Protein Backbone Generation via Spectrally Initialized Flow Matching","display_name":"PI-Mamba: Linear-Time Protein Backbone Generation via Spectrally Initialized Flow Matching","publication_year":2026,"publication_date":"2026-03-17","ids":{"openalex":"https://openalex.org/W7147540191","doi":"https://doi.org/10.48550/arxiv.2603.26705"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2603.26705","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.26705","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":false,"raw_source_name":null,"raw_type":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2603.26705","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5132567799","display_name":"Tianyu Wu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wu, Tianyu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5132714670","display_name":"Lin Zhu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhu, Lin","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/T10044","display_name":"Protein Structure and Dynamics","score":0.7346000075340271,"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":0.7346000075340271,"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":0.039500001817941666,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.017400000244379044,"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/initialization","display_name":"Initialization","score":0.7572000026702881},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.5127000212669373},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.5008999705314636},{"id":"https://openalex.org/keywords/differentiable-function","display_name":"Differentiable function","score":0.4921000003814697},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4876999855041504},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.4717999994754791},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.4453999996185303},{"id":"https://openalex.org/keywords/quadratic-equation","display_name":"Quadratic equation","score":0.4113999903202057},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.37209999561309814}],"concepts":[{"id":"https://openalex.org/C114466953","wikidata":"https://www.wikidata.org/wiki/Q6034165","display_name":"Initialization","level":2,"score":0.7572000026702881},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6104000210762024},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5623999834060669},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.5127000212669373},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.5008999705314636},{"id":"https://openalex.org/C202615002","wikidata":"https://www.wikidata.org/wiki/Q783507","display_name":"Differentiable function","level":2,"score":0.4921000003814697},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4876999855041504},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4717999994754791},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.4453999996185303},{"id":"https://openalex.org/C129844170","wikidata":"https://www.wikidata.org/wiki/Q41299","display_name":"Quadratic equation","level":2,"score":0.4113999903202057},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.37209999561309814},{"id":"https://openalex.org/C38349280","wikidata":"https://www.wikidata.org/wiki/Q1434290","display_name":"Flow (mathematics)","level":2,"score":0.36660000681877136},{"id":"https://openalex.org/C17020691","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operator (biology)","level":5,"score":0.36550000309944153},{"id":"https://openalex.org/C159694833","wikidata":"https://www.wikidata.org/wiki/Q2321565","display_name":"Iterative method","level":2,"score":0.35109999775886536},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3476000130176544},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.32820001244544983},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.32089999318122864},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.3086000084877014},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.30160000920295715},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.29580000042915344},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.28790000081062317},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.28600001335144043},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.2851000130176544},{"id":"https://openalex.org/C147764199","wikidata":"https://www.wikidata.org/wiki/Q6865248","display_name":"Minification","level":2,"score":0.28130000829696655},{"id":"https://openalex.org/C198927703","wikidata":"https://www.wikidata.org/wiki/Q4373881","display_name":"Sequential quadratic programming","level":3,"score":0.28049999475479126},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.26980000734329224},{"id":"https://openalex.org/C23379248","wikidata":"https://www.wikidata.org/wiki/Q200904","display_name":"Epipolar geometry","level":3,"score":0.26510000228881836},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26330000162124634},{"id":"https://openalex.org/C198352243","wikidata":"https://www.wikidata.org/wiki/Q37105","display_name":"Line (geometry)","level":2,"score":0.2630999982357025},{"id":"https://openalex.org/C18762648","wikidata":"https://www.wikidata.org/wiki/Q42213","display_name":"Work (physics)","level":2,"score":0.25929999351501465},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.25839999318122864}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2603.26705","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.26705","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":"doi:10.48550/arxiv.2603.26705","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.26705","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":false,"raw_source_name":null,"raw_type":"Preprint"},"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":{"Motivation:":[0],"Generative":[1],"models":[2],"for":[3],"protein":[4],"backbone":[5,90],"design":[6],"have":[7],"to":[8,17,36,130],"simultaneously":[9],"ensure":[10],"geometric":[11],"validity,":[12],"sampling":[13],"efficiency,":[14],"and":[15,43,77,89,103,118],"scalability":[16],"long":[18],"sequences.":[19],"However,":[20],"most":[21],"existing":[22],"approaches":[23],"rely":[24],"on":[25,135],"iterative":[26],"refinement,":[27],"quadratic":[28],"attention":[29],"mechanisms,":[30],"or":[31],"post-hoc":[32],"geometry":[33,60,116],"correction,":[34],"leading":[35],"a":[37,52,69,74,81,94,136],"persistent":[38],"trade-off":[39],"between":[40],"computational":[41],"efficiency":[42],"structural":[44],"fidelity.":[45],"Results:":[46],"We":[47],"present":[48],"Physics-Informed":[49],"Mamba":[50],"(PI-Mamba),":[51],"generative":[53],"model":[54,102],"that":[55],"enforces":[56],"exact":[57],"local":[58,115],"covalent":[59],"by":[61],"construction":[62],"while":[63,128],"enabling":[64],"linear-time":[65],"inference.":[66],"PI-Mamba":[67,112],"integrates":[68],"differentiable":[70],"constraint-enforcement":[71],"operator":[72],"into":[73],"flow-matching":[75],"framework":[76],"couples":[78],"it":[79],"with":[80],"Mamba-based":[82],"state-space":[83],"architecture.":[84],"To":[85],"improve":[86],"optimisation":[87],"stability":[88],"realism,":[91],"we":[92],"introduce":[93],"spectral":[95],"initialization":[96],"derived":[97],"from":[98],"the":[99],"Rouse":[100],"polymer":[101],"an":[104],"auxiliary":[105],"cis-proline":[106],"awareness":[107],"head.":[108],"Across":[109],"benchmark":[110],"tasks,":[111],"achieves":[113],"0.0\\%":[114],"violations":[117],"high":[119],"designability":[120],"(scTM":[121],"=":[122,126],"$0.91\\pm":[123],"0.03$,":[124],"n":[125],"100),":[127],"scaling":[129],"proteins":[131],"exceeding":[132],"2,000":[133],"residues":[134],"single":[137],"A5000":[138],"GPU":[139],"(24":[140],"GB).":[141]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2026-04-02T00:00:00"}
