{"id":"https://openalex.org/W7138902578","doi":"https://doi.org/10.1145/3801737","title":"Interpretable Machine Learning for Protein Science: Structure, Function, and Interactions","display_name":"Interpretable Machine Learning for Protein Science: Structure, Function, and Interactions","publication_year":2026,"publication_date":"2026-03-18","ids":{"openalex":"https://openalex.org/W7138902578","doi":"https://doi.org/10.1145/3801737"},"language":"en","primary_location":{"id":"doi:10.1145/3801737","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3801737","pdf_url":null,"source":{"id":"https://openalex.org/S157921468","display_name":"ACM Computing Surveys","issn_l":"0360-0300","issn":["0360-0300","1557-7341"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Computing Surveys","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1145/3801737","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057428816","display_name":"Luiz Felipe Vecchietti","orcid":"https://orcid.org/0000-0003-2862-6200"},"institutions":[{"id":"https://openalex.org/I4210096592","display_name":"Max Planck Institute for Security and Privacy","ror":"https://ror.org/00bj0r217","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210096592"]},{"id":"https://openalex.org/I4210104335","display_name":"Institute for Basic Science","ror":"https://ror.org/00y0zf565","country_code":"KR","type":"facility","lineage":["https://openalex.org/I4210104335"]}],"countries":["DE","KR"],"is_corresponding":false,"raw_author_name":"Luiz Felipe Vecchietti","raw_affiliation_strings":["Institute for Basic Science","Max Planck Institute for Security and Privacy"],"raw_orcid":"https://orcid.org/0000-0003-2862-6200","affiliations":[{"raw_affiliation_string":"Institute for Basic Science","institution_ids":["https://openalex.org/I4210104335"]},{"raw_affiliation_string":"Max Planck Institute for Security and Privacy","institution_ids":["https://openalex.org/I4210096592"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066329655","display_name":"Minji Lee","orcid":"https://orcid.org/0000-0001-5293-8904"},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]},{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["KR","US"],"is_corresponding":false,"raw_author_name":"Minji Lee","raw_affiliation_strings":["Columbia University","Korea Advanced Institute of Science and Technology"],"raw_orcid":"https://orcid.org/0000-0001-5293-8904","affiliations":[{"raw_affiliation_string":"Columbia University","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Korea Advanced Institute of Science and Technology","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114418892","display_name":"Begench Hangeldiyev","orcid":null},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Begench Hangeldiyev","raw_affiliation_strings":["Korea Advanced Institute of Science and Technology"],"raw_orcid":"https://orcid.org/0009-0008-2614-8843","affiliations":[{"raw_affiliation_string":"Korea Advanced Institute of Science and Technology","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119012920","display_name":"Bryan Nathanael Wijaya","orcid":null},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]},{"id":"https://openalex.org/I4210096592","display_name":"Max Planck Institute for Security and Privacy","ror":"https://ror.org/00bj0r217","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210096592"]},{"id":"https://openalex.org/I4210104335","display_name":"Institute for Basic Science","ror":"https://ror.org/00y0zf565","country_code":"KR","type":"facility","lineage":["https://openalex.org/I4210104335"]}],"countries":["DE","KR"],"is_corresponding":false,"raw_author_name":"Bryan Nathanael Wijaya","raw_affiliation_strings":["Institute for Basic Science","Korea Advanced Institute of Science and Technology","Max Planck Institute for Security and Privacy"],"raw_orcid":"https://orcid.org/0009-0007-3509-0519","affiliations":[{"raw_affiliation_string":"Institute for Basic Science","institution_ids":["https://openalex.org/I4210104335"]},{"raw_affiliation_string":"Korea Advanced Institute of Science and Technology","institution_ids":["https://openalex.org/I157485424"]},{"raw_affiliation_string":"Max Planck Institute for Security and Privacy","institution_ids":["https://openalex.org/I4210096592"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101369548","display_name":"Hyunkyu Jung","orcid":null},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]},{"id":"https://openalex.org/I4210104335","display_name":"Institute for Basic Science","ror":"https://ror.org/00y0zf565","country_code":"KR","type":"facility","lineage":["https://openalex.org/I4210104335"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Hyunkyu Jung","raw_affiliation_strings":["Institute for Basic Science","Korea Advanced Institute of Science and Technology"],"raw_orcid":"https://orcid.org/0009-0005-3725-4092","affiliations":[{"raw_affiliation_string":"Institute for Basic Science","institution_ids":["https://openalex.org/I4210104335"]},{"raw_affiliation_string":"Korea Advanced Institute of Science and Technology","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011280743","display_name":"Hahnbeom Park","orcid":"https://orcid.org/0000-0002-7129-1912"},"institutions":[{"id":"https://openalex.org/I58716616","display_name":"Korea Institute of Science and Technology","ror":"https://ror.org/05kzfa883","country_code":"KR","type":"facility","lineage":["https://openalex.org/I27494661","https://openalex.org/I2801339556","https://openalex.org/I2801339556","https://openalex.org/I4210144908","https://openalex.org/I4387152098","https://openalex.org/I4387152098","https://openalex.org/I58716616"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Hahnbeom Park","raw_affiliation_strings":["Korea Institute of Science and Technology"],"raw_orcid":"https://orcid.org/0000-0002-7129-1912","affiliations":[{"raw_affiliation_string":"Korea Institute of Science and Technology","institution_ids":["https://openalex.org/I58716616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100653784","display_name":"Tae\u2010Kyun Kim","orcid":"https://orcid.org/0000-0002-7587-6053"},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Tae-Kyun Kim","raw_affiliation_strings":["Korea Advanced Institute of Science and Technology"],"raw_orcid":"https://orcid.org/0000-0002-7587-6053","affiliations":[{"raw_affiliation_string":"Korea Advanced Institute of Science and Technology","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129999412","display_name":"Meeyoung Cha","orcid":null},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]},{"id":"https://openalex.org/I4210096592","display_name":"Max Planck Institute for Security and Privacy","ror":"https://ror.org/00bj0r217","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210096592"]},{"id":"https://openalex.org/I4210104335","display_name":"Institute for Basic Science","ror":"https://ror.org/00y0zf565","country_code":"KR","type":"facility","lineage":["https://openalex.org/I4210104335"]}],"countries":["DE","KR"],"is_corresponding":false,"raw_author_name":"Meeyoung Cha","raw_affiliation_strings":["Institute for Basic Science","Korea Advanced Institute of Science and Technology","Max Planck Institute for Security and Privacy"],"raw_orcid":"https://orcid.org/0000-0003-4085-9648","affiliations":[{"raw_affiliation_string":"Institute for Basic Science","institution_ids":["https://openalex.org/I4210104335"]},{"raw_affiliation_string":"Korea Advanced Institute of Science and Technology","institution_ids":["https://openalex.org/I157485424"]},{"raw_affiliation_string":"Max Planck Institute for Security and Privacy","institution_ids":["https://openalex.org/I4210096592"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5130158656","display_name":"Ho Min Kim","orcid":null},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]},{"id":"https://openalex.org/I4210104335","display_name":"Institute for Basic Science","ror":"https://ror.org/00y0zf565","country_code":"KR","type":"facility","lineage":["https://openalex.org/I4210104335"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Ho Min Kim","raw_affiliation_strings":["Institute for Basic Science","Korea Advanced Institute of Science and Technology"],"raw_orcid":"https://orcid.org/0000-0003-0029-3643","affiliations":[{"raw_affiliation_string":"Institute for Basic Science","institution_ids":["https://openalex.org/I4210104335"]},{"raw_affiliation_string":"Korea Advanced Institute of Science and Technology","institution_ids":["https://openalex.org/I157485424"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.22319206,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"58","issue":"11","first_page":"1","last_page":"24"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.26980000734329224,"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":0.26980000734329224,"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/T12026","display_name":"Explainable Artificial Intelligence (XAI)","score":0.10279999673366547,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.08470000326633453,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.9265000224113464},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6642000079154968},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.6353999972343445},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5098000168800354},{"id":"https://openalex.org/keywords/structured-prediction","display_name":"Structured prediction","score":0.41909998655319214},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.37869998812675476}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.9265000224113464},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8287000060081482},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7759000062942505},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.7705000042915344},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6642000079154968},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.6353999972343445},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5098000168800354},{"id":"https://openalex.org/C22367795","wikidata":"https://www.wikidata.org/wiki/Q7625208","display_name":"Structured prediction","level":2,"score":0.41909998655319214},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.37869998812675476},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.3366999924182892},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.30399999022483826},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.26759999990463257},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.25920000672340393},{"id":"https://openalex.org/C84525736","wikidata":"https://www.wikidata.org/wiki/Q831366","display_name":"Decision tree","level":2,"score":0.2572000026702881}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3801737","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3801737","pdf_url":null,"source":{"id":"https://openalex.org/S157921468","display_name":"ACM Computing Surveys","issn_l":"0360-0300","issn":["0360-0300","1557-7341"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Computing Surveys","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1145/3801737","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3801737","pdf_url":null,"source":{"id":"https://openalex.org/S157921468","display_name":"ACM Computing Surveys","issn_l":"0360-0300","issn":["0360-0300","1557-7341"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Computing Surveys","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W2001923477","https://openalex.org/W2047544230","https://openalex.org/W2103017472","https://openalex.org/W2110314310","https://openalex.org/W2111973517","https://openalex.org/W2113403117","https://openalex.org/W2295598076","https://openalex.org/W2379594833","https://openalex.org/W2910705748","https://openalex.org/W2945976633","https://openalex.org/W2962858109","https://openalex.org/W2963021451","https://openalex.org/W2964449086","https://openalex.org/W2992752586","https://openalex.org/W2997234557","https://openalex.org/W3005086430","https://openalex.org/W3005669732","https://openalex.org/W3007590609","https://openalex.org/W3033892090","https://openalex.org/W3083406432","https://openalex.org/W3132153121","https://openalex.org/W3146944767","https://openalex.org/W3157473273","https://openalex.org/W3164046276","https://openalex.org/W3185671814","https://openalex.org/W3207298831","https://openalex.org/W4210997669","https://openalex.org/W4224939843","https://openalex.org/W4229031603","https://openalex.org/W4280497806","https://openalex.org/W4281790889","https://openalex.org/W4288066876","https://openalex.org/W4293434244","https://openalex.org/W4311181469","https://openalex.org/W4321851522","https://openalex.org/W4366279959","https://openalex.org/W4375856225","https://openalex.org/W4382631247","https://openalex.org/W4388024559","https://openalex.org/W4389174567","https://openalex.org/W4390754450","https://openalex.org/W4396721167","https://openalex.org/W4396895148","https://openalex.org/W4400448758","https://openalex.org/W4400656170","https://openalex.org/W4410291869","https://openalex.org/W4412086768","https://openalex.org/W4413759428","https://openalex.org/W7133208181"],"related_works":[],"abstract_inverted_index":{"Recent":[0],"advancements":[1],"in":[2],"machine":[3],"learning":[4],"(ML)":[5],"are":[6],"transforming":[7],"the":[8,39,45,51,103],"field":[9],"of":[10,32,53,105],"structural":[11],"biology.":[12],"For":[13],"example,":[14],"AlphaFold,":[15],"a":[16],"groundbreaking":[17],"neural":[18,40],"network":[19,41],"for":[20,71,111],"protein":[21,73,92,94,113,134],"structure":[22],"prediction,":[23],"has":[24,56],"been":[25],"widely":[26],"adopted":[27],"by":[28],"researchers.":[29],"The":[30],"availability":[31],"easy-to-use":[33],"interfaces":[34],"and":[35,80,96,107,118,133],"interpretable":[36,83,123],"outcomes":[37],"from":[38,76],"architecture,":[42],"such":[43,89,122],"as":[44,90],"confidence":[46],"scores":[47],"used":[48],"to":[49,61,78,126],"assess":[50],"quality":[52],"predicted":[54],"structures,":[55,93],"made":[57],"AlphaFold":[58],"accessible":[59],"even":[60],"non-ML":[62],"experts.":[63],"In":[64],"this":[65],"article,":[66],"we":[67],"present":[68],"various":[69],"methods":[70,85],"representing":[72],"3D":[74],"structures":[75],"low-":[77],"high-resolution,":[79],"show":[81],"how":[82],"ML":[84],"can":[86],"support":[87],"tasks":[88],"predicting":[91],"functions,":[95],"protein-protein":[97],"interactions.":[98],"This":[99],"survey":[100],"also":[101],"emphasizes":[102],"significance":[104],"interpreting":[106],"visualizing":[108],"ML-based":[109],"inference":[110],"structure-based":[112],"representations":[114],"that":[115],"enhance":[116],"interpretability":[117],"knowledge":[119],"discovery.":[120],"Developing":[121],"approaches":[124],"promises":[125],"further":[127],"accelerate":[128],"fields,":[129],"including":[130],"drug":[131],"development":[132],"design.":[135]},"counts_by_year":[],"updated_date":"2026-08-12T21:12:35.861297","created_date":"2026-03-20T00:00:00"}
