{"id":"https://openalex.org/W7161725658","doi":"https://doi.org/10.48550/arxiv.2605.16581","title":"Structure-Aware Masking for Protein Representation Learning","display_name":"Structure-Aware Masking for Protein Representation Learning","publication_year":2026,"publication_date":"2026-05-15","ids":{"openalex":"https://openalex.org/W7161725658","doi":"https://doi.org/10.48550/arxiv.2605.16581"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2605.16581","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.16581","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.2605.16581","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5136471940","display_name":"Thomas Walton","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Walton, Thomas","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136476816","display_name":"Ayan Goel","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Goel, Ayan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5136474887","display_name":"Amirali Aghazadeh","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Aghazadeh, Amirali","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":3,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.27410000562667847,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.27410000562667847,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.18490000069141388,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.11299999803304672,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/masking","display_name":"Masking (illustration)","score":0.8123999834060669},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5648000240325928},{"id":"https://openalex.org/keywords/backward-masking","display_name":"Backward masking","score":0.43050000071525574},{"id":"https://openalex.org/keywords/sequence-labeling","display_name":"Sequence labeling","score":0.4027000069618225},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.36880001425743103},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3483999967575073}],"concepts":[{"id":"https://openalex.org/C2777402240","wikidata":"https://www.wikidata.org/wiki/Q6783436","display_name":"Masking (illustration)","level":2,"score":0.8123999834060669},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6062999963760376},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5648000240325928},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4876999855041504},{"id":"https://openalex.org/C2776817677","wikidata":"https://www.wikidata.org/wiki/Q4839818","display_name":"Backward masking","level":3,"score":0.43050000071525574},{"id":"https://openalex.org/C35639132","wikidata":"https://www.wikidata.org/wiki/Q7452468","display_name":"Sequence labeling","level":3,"score":0.4027000069618225},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.36880001425743103},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3483999967575073},{"id":"https://openalex.org/C77801330","wikidata":"https://www.wikidata.org/wiki/Q1363413","display_name":"Auditory masking","level":3,"score":0.34130001068115234},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.3228999972343445},{"id":"https://openalex.org/C40506919","wikidata":"https://www.wikidata.org/wiki/Q7452469","display_name":"Sequence learning","level":2,"score":0.30239999294281006},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.29829999804496765},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.27649998664855957},{"id":"https://openalex.org/C28490314","wikidata":"https://www.wikidata.org/wiki/Q189436","display_name":"Speech recognition","level":1,"score":0.2687000036239624},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2667999863624573}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2605.16581","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.16581","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.2605.16581","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.16581","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":[{"id":"https://metadata.un.org/sdg/4","score":0.6273122429847717,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Masked":[0],"language":[1,11],"modeling":[2,106],"(MLM)":[3],"is":[4],"the":[5,93,102],"standard":[6,131],"objective":[7,104],"for":[8,112],"training":[9],"protein":[10,45,113,118],"models,":[12],"typically":[13],"implemented":[14],"by":[15,49],"randomly":[16],"masking":[17,70,85,94,157],"individual":[18],"residues":[19,76],"at":[20,135],"a":[21,68,127,159],"fixed":[22],"rate":[23],"(e.g.,":[24],"15%).":[25],"This":[26],"practice":[27],"implicitly":[28],"assumes":[29],"that":[30,57,72,109,145],"all":[31],"sequence":[32],"positions":[33],"contribute":[34],"equally":[35],"to":[36,126],"representation":[37],"learning.":[38],"In":[39],"downstream":[40,117],"fitness":[41,119],"prediction":[42,120],"tasks,":[43,121],"however,":[44],"sequences":[46],"are":[47,110],"governed":[48],"three-dimensional":[50,82],"structural":[51],"dependencies":[52],"and":[53],"long-range":[54,107],"residue":[55,97],"contacts":[56],"induce":[58],"strong":[59],"nonlocal":[60],"couplings":[61],"between":[62],"residues.":[63],"We":[64],"introduce":[65],"Bucket":[66,99,122],"Masking,":[67],"structure-aware":[69],"strategy":[71],"selects":[73],"groups":[74],"of":[75],"based":[77],"on":[78,96],"their":[79],"proximity":[80],"in":[81],"space,":[83],"preferentially":[84],"structurally":[86],"coupled":[87],"regions":[88],"during":[89],"training.":[90],"By":[91],"conditioning":[92],"distribution":[95],"contacts,":[98],"Masking":[100,123],"shifts":[101],"learning":[103],"toward":[105],"interactions":[108],"critical":[111],"function.":[114],"Across":[115],"four":[116],"enables":[124],"up":[125],"14%":[128],"improvement":[129],"over":[130],"random":[132],"masking,":[133],"excelling":[134],"predicting":[136],"higher-order":[137],"mutational":[138],"interactions.":[139],"Through":[140],"controlled":[141],"ablations,":[142],"we":[143],"show":[144],"these":[146],"improvements":[147],"arise":[148],"from":[149],"mask":[150],"placement":[151],"rather":[152],"than":[153],"span":[154],"size,":[155],"establishing":[156],"as":[158],"positional":[160],"inductive":[161],"bias.":[162]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2026-05-20T00:00:00"}