{"id":"https://openalex.org/W7204614090","doi":null,"title":"Interpretable Deep Learning Models for Trustworthy Prediction of Enzyme Functions","display_name":"Interpretable Deep Learning Models for Trustworthy Prediction of Enzyme Functions","publication_year":2026,"publication_date":"2026-05-15","ids":{"openalex":"https://openalex.org/W7204614090"},"language":"en","primary_location":{"id":"pmh:oai:oasis.library.unlv.edu:thesesdissertations-6539","doi":null,"is_oa":false,"landing_page_url":"https://oasis.library.unlv.edu/thesesdissertations/5534","pdf_url":null,"source":{"id":"https://openalex.org/S4377196371","display_name":"Digital Scholarship - UNLV (University of Nevada Reno)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I134113660","host_organization_name":"University of Nevada, Reno","host_organization_lineage":["https://openalex.org/I134113660"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"UNLV Theses, Dissertations, Professional Papers, and Capstones","raw_type":"text"},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5116100343","display_name":"Louis Dumontet","orcid":"https://orcid.org/0009-0009-8569-768X","observed_orcids":["https://orcid.org/0009-0009-8569-768X"]},"institutions":[{"id":"https://openalex.org/I133999245","display_name":"University of Nevada, Las Vegas","ror":"https://ror.org/0406gha72","country_code":"US","type":"education","lineage":["https://openalex.org/I133999245"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dumontet, Louis","raw_affiliation_strings":["University of Nevada, Las Vegas"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Nevada, Las Vegas","institution_ids":["https://openalex.org/I133999245"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5116100343"],"corresponding_institution_ids":["https://openalex.org/I133999245"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.5004652,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"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":0.9940999746322632,"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":0.9940999746322632,"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":0.0017999999690800905,"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/T10404","display_name":"Enzyme Catalysis and Immobilization","score":0.0008999999845400453,"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/enzyme-function-prediction","display_name":"enzyme function prediction","score":0.996999979019165},{"id":"https://openalex.org/keywords/enzyme-annotation","display_name":"enzyme annotation","score":0.574999988079071},{"id":"https://openalex.org/keywords/explainable-deep-learning","display_name":"explainable deep learning","score":0.9179999828338623},{"id":"https://openalex.org/keywords/kolmogorov-arnold-networks","display_name":"Kolmogorov-Arnold networks","score":0.8519999980926514},{"id":"https://openalex.org/keywords/ec-number-prediction","display_name":"EC number prediction","score":0.6769999861717224},{"id":"https://openalex.org/keywords/plastic-degrading-enzymes","display_name":"plastic-degrading enzymes","score":0.8090000152587891},{"id":"https://openalex.org/keywords/hydrolytic-enzymes","display_name":"hydrolytic enzymes","score":0.7799999713897705},{"id":"https://openalex.org/keywords/convolutional-neural-networks","display_name":"convolutional neural networks","score":0.7149999737739563},{"id":"https://openalex.org/keywords/hierarchical-transformer","display_name":"hierarchical transformer","score":0.6110000014305115},{"id":"https://openalex.org/keywords/incomplete-annotations","display_name":"incomplete annotations","score":0.5120000243186951},{"id":"https://openalex.org/keywords/sequence-motifs","display_name":"sequence motifs","score":0.5849999785423279},{"id":"https://openalex.org/keywords/enzyme-discovery","display_name":"enzyme discovery","score":0.656000018119812}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6872000098228455},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.6425999999046326},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6243000030517578},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6158999800682068},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5788999795913696},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5529000163078308},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.46959999203681946},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.4174000024795532},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.3862999975681305},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3781000077724457},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.34549999237060547},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3434999883174896},{"id":"https://openalex.org/C153701036","wikidata":"https://www.wikidata.org/wiki/Q659974","display_name":"Trustworthiness","level":2,"score":0.32589998841285706},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.3160000145435333},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3102000057697296},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.28189998865127563},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.27970001101493835},{"id":"https://openalex.org/C111364199","wikidata":"https://www.wikidata.org/wiki/Q2915896","display_name":"Protein methods","level":4,"score":0.27709999680519104},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.27489998936653137},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.27459999918937683},{"id":"https://openalex.org/C114073186","wikidata":"https://www.wikidata.org/wiki/Q2631895","display_name":"Automated planning and scheduling","level":2,"score":0.2687000036239624},{"id":"https://openalex.org/C2780148112","wikidata":"https://www.wikidata.org/wiki/Q1432581","display_name":"Proxy (statistics)","level":2,"score":0.2632000148296356},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.26019999384880066},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.25929999351501465}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:oasis.library.unlv.edu:thesesdissertations-6539","doi":null,"is_oa":false,"landing_page_url":"https://oasis.library.unlv.edu/thesesdissertations/5534","pdf_url":null,"source":{"id":"https://openalex.org/S4377196371","display_name":"Digital Scholarship - UNLV (University of Nevada Reno)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I134113660","host_organization_name":"University of Nevada, Reno","host_organization_lineage":["https://openalex.org/I134113660"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"UNLV Theses, Dissertations, Professional Papers, and Capstones","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4407275359","https://openalex.org/W7126209807","https://openalex.org/W4388891993","https://openalex.org/W7124994589","https://openalex.org/W7171502437","https://openalex.org/W4406317514","https://openalex.org/W7162686567","https://openalex.org/W4412807054","https://openalex.org/W2766352633","https://openalex.org/W4409118940"],"abstract_inverted_index":{"Trustworthy":[0],"prediction":[1,37,53,145],"of":[2,54,87,99],"enzyme":[3,32,35,132,190,217],"function":[4,36],"from":[5,38,131],"protein":[6],"sequences":[7,150],"remains":[8],"a":[9,88,122,138,152,225],"central":[10],"challenge":[11],"in":[12,233],"computational":[13,231],"biology,":[14],"particularly":[15],"when":[16],"annotated":[17,149],"data":[18],"are":[19],"limited,":[20],"imbalanced,":[21],"or":[22],"incomplete.":[23],"This":[24,209],"dissertation":[25,95],"develops":[26,136],"interpretable":[27,47,140,200],"deep":[28,213],"learning":[29,214],"methods":[30,173],"for":[31,51,106,142,180,216,228],"discovery":[33,83,218],"and":[34,60,77,80,84,121,164,201,219,223,235],"amino":[39],"acid":[40],"sequences.":[41,133],"First,":[42],"it":[43,135],"introduces":[44],"PEPIC,":[45],"an":[46],"convolutional":[48],"neural":[49],"network":[50],"substrate-level":[52],"hydrolytic":[55],"plastic-degrading":[56],"enzymes.":[57],"Using":[58],"curated":[59],"expanded":[61],"sequence":[62,72],"datasets,":[63],"PEPIC":[64],"improved":[65,115],"predictive":[66,116,196],"performance":[67,117,197],"over":[68],"benchmark":[69,162],"methods,":[70],"identified":[71],"regions":[73],"aligned":[74],"with":[75],"catalytic":[76],"substrate-binding":[78],"residues,":[79],"supported":[81],"the":[82,97],"experimental":[85],"validation":[86],"previously":[89],"uncharacterized":[90],"PET-degrading":[91],"enzyme.":[92],"Second,":[93],"this":[94],"investigates":[96],"integration":[98],"Kolmogorov-Arnold":[100],"Networks":[101],"(KANs)":[102],"into":[103],"state-of-the-art":[104,172],"models":[105],"Enzyme":[107],"Commission":[108],"(EC)":[109],"number":[110,144,221],"prediction.":[111],"KAN":[112],"modules":[113],"consistently":[114,169],"across":[118,157],"multiple":[119],"architectures,":[120],"dedicated":[123],"interpretation":[124],"method":[125],"recovered":[126],"biologically":[127,177],"meaningful":[128],"motif":[129],"sites":[130],"Third,":[134],"HIT-EC,":[137],"hierarchical":[139],"transformer":[141],"EC":[143,220],"that":[146,188,204],"incorporates":[147],"incompletely":[148],"through":[151],"masked":[153],"loss":[154],"objective.":[155],"Evaluated":[156],"repeated":[158],"hold-out":[159],"experiments,":[160],"external":[161],"data,":[163],"microbial":[165],"genome":[166],"analyses,":[167],"HIT-EC":[168],"outperformed":[170],"current":[171],"while":[174],"providing":[175],"trustworthy,":[176],"grounded":[178],"evidence":[179,203],"its":[181],"predictions.":[182],"Taken":[183],"together,":[184],"these":[185],"studies":[186],"show":[187],"accurate":[189],"annotation":[191,232],"requires":[192],"not":[193],"only":[194],"strong":[195],"but":[198],"also":[199],"reliable":[202],"can":[205],"guide":[206],"biological":[207],"validation.":[208],"work":[210],"advances":[211],"sequence-based":[212],"strategies":[215],"prediction,":[222],"provides":[224],"practical":[226],"foundation":[227],"more":[229],"transparent":[230],"enzymology":[234],"proteomics.":[236]},"counts_by_year":[],"updated_date":"2026-08-29T07:29:34.045763","created_date":"2026-08-29T00:00:00"}
