{"id":"https://openalex.org/W7138009533","doi":"https://doi.org/10.48550/arxiv.2603.14717","title":"Training-Free Generation of Protein Sequences from Small Family Alignments via Stochastic Attention","display_name":"Training-Free Generation of Protein Sequences from Small Family Alignments via Stochastic Attention","publication_year":2026,"publication_date":"2026-03-16","ids":{"openalex":"https://openalex.org/W7138009533","doi":"https://doi.org/10.48550/arxiv.2603.14717"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2603.14717","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.14717","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.2603.14717","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003161155","display_name":"Jeffrey D. Varner","orcid":"https://orcid.org/0000-0002-2558-7026"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Varner, Jeffrey D.","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5003161155"],"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":0.6298999786376953,"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":0.6298999786376953,"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":0.08940000087022781,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.030700000002980232,"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/overfitting","display_name":"Overfitting","score":0.7304999828338623},{"id":"https://openalex.org/keywords/softmax-function","display_name":"Softmax function","score":0.5760999917984009},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.508899986743927},{"id":"https://openalex.org/keywords/amino-acid-substitution","display_name":"Amino acid substitution","score":0.4902999997138977},{"id":"https://openalex.org/keywords/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.4214000105857849},{"id":"https://openalex.org/keywords/boltzmann-machine","display_name":"Boltzmann machine","score":0.38999998569488525},{"id":"https://openalex.org/keywords/protein-family","display_name":"Protein family","score":0.3855000138282776},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.38100001215934753},{"id":"https://openalex.org/keywords/mixture-model","display_name":"Mixture model","score":0.3666999936103821}],"concepts":[{"id":"https://openalex.org/C22019652","wikidata":"https://www.wikidata.org/wiki/Q331309","display_name":"Overfitting","level":3,"score":0.7304999828338623},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5874000191688538},{"id":"https://openalex.org/C188441871","wikidata":"https://www.wikidata.org/wiki/Q7554146","display_name":"Softmax function","level":3,"score":0.5760999917984009},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.508899986743927},{"id":"https://openalex.org/C2993683473","wikidata":"https://www.wikidata.org/wiki/Q30693176","display_name":"Amino acid substitution","level":4,"score":0.4902999997138977},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4821000099182129},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.438400000333786},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.4214000105857849},{"id":"https://openalex.org/C192576344","wikidata":"https://www.wikidata.org/wiki/Q194706","display_name":"Boltzmann machine","level":3,"score":0.38999998569488525},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.3855000138282776},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.38100001215934753},{"id":"https://openalex.org/C61224824","wikidata":"https://www.wikidata.org/wiki/Q2260434","display_name":"Mixture model","level":2,"score":0.3666999936103821},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.36399999260902405},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3456999957561493},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34040001034736633},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.33880001306533813},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.3240000009536743},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.32120001316070557},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.3181000053882599},{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.3181000053882599},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30399999022483826},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.30169999599456787},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2953000068664551},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.2906999886035919},{"id":"https://openalex.org/C177769412","wikidata":"https://www.wikidata.org/wiki/Q278090","display_name":"Prior probability","level":3,"score":0.28450000286102295},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2799000144004822},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.27480000257492065},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.27309998869895935},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2703999876976013},{"id":"https://openalex.org/C2778355321","wikidata":"https://www.wikidata.org/wiki/Q17079427","display_name":"Identity (music)","level":2,"score":0.26930001378059387},{"id":"https://openalex.org/C149441793","wikidata":"https://www.wikidata.org/wiki/Q200726","display_name":"Probability distribution","level":2,"score":0.26919999718666077},{"id":"https://openalex.org/C2992240565","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Protein evolution","level":3,"score":0.26759999990463257},{"id":"https://openalex.org/C14301744","wikidata":"https://www.wikidata.org/wiki/Q579211","display_name":"Ramachandran plot","level":3,"score":0.26080000400543213},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.2565999925136566}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2603.14717","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.14717","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.2603.14717","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.14717","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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Most":[0],"protein":[1,34],"families":[2],"have":[3],"fewer":[4],"than":[5,102],"100":[6],"known":[7],"members,":[8],"a":[9,23,33,37,50,140],"regime":[10],"where":[11],"deep":[12],"generative":[13],"models":[14],"overfit":[15],"or":[16],"collapse.":[17],"We":[18],"propose":[19],"stochastic":[20],"attention":[21,53],"(SA),":[22],"training-free":[24],"sampler":[25],"that":[26,121],"treats":[27],"the":[28,115,125],"modern":[29],"Hopfield":[30],"energy":[31],"over":[32],"alignment":[35,68],"as":[36],"Boltzmann":[38],"distribution":[39],"and":[40,61,85,91,114],"draws":[41],"samples":[42],"via":[43],"Langevin":[44],"dynamics.":[45],"The":[46,142],"score":[47],"function":[48],"is":[49,147],"closed-form":[51],"softmax":[52],"operation":[54],"requiring":[55],"no":[56,58,62],"training,":[57],"pretraining":[59],"data,":[60],"GPU,":[63],"with":[64,77],"cost":[65],"linear":[66],"in":[67,105,137],"size.":[69],"Across":[70],"eight":[71,108],"Pfam":[72],"families,":[73],"SA":[74,127,159],"generates":[75],"sequences":[76,94,120],"low":[78],"amino":[79,167],"acid":[80,168],"compositional":[81],"divergence,":[82],"substantial":[83],"novelty,":[84],"structural":[86],"plausibility":[87],"confirmed":[88],"by":[89],"ESMFold":[90],"AlphaFold2.":[92],"Generated":[93],"fold":[95],"more":[96],"faithfully":[97],"to":[98,130],"canonical":[99],"family":[100],"structures":[101],"natural":[103],"members":[104],"six":[106],"of":[107],"families.":[109],"Against":[110],"profile":[111],"HMMs,":[112],"EvoDiff,":[113],"MSA":[116],"Transformer,":[117],"which":[118],"produce":[119],"drift":[122],"far":[123],"outside":[124],"family,":[126],"maintains":[128],"51":[129],"66":[131],"percent":[132],"identity":[133],"while":[134],"remaining":[135],"novel,":[136],"seconds":[138],"on":[139],"laptop.":[141],"critical":[143],"temperature":[144],"governing":[145],"generation":[146],"predicted":[148],"from":[149],"PCA":[150],"dimensionality":[151],"alone,":[152],"enabling":[153],"fully":[154],"automatic":[155],"operation.":[156],"Controls":[157],"confirm":[158],"encodes":[160],"correlated":[161],"substitution":[162],"patterns,":[163],"not":[164],"just":[165],"per-position":[166],"frequencies.":[169]},"counts_by_year":[],"updated_date":"2026-03-18T06:31:55.123368","created_date":"2026-03-18T00:00:00"}