{"id":"https://openalex.org/W4319074048","doi":"https://doi.org/10.1186/s13321-023-00682-3","title":"Explainable uncertainty quantifications for deep learning-based molecular property prediction","display_name":"Explainable uncertainty quantifications for deep learning-based molecular property prediction","publication_year":2023,"publication_date":"2023-02-03","ids":{"openalex":"https://openalex.org/W4319074048","doi":"https://doi.org/10.1186/s13321-023-00682-3","pmid":"https://pubmed.ncbi.nlm.nih.gov/36737786"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-023-00682-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00682-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00682-3","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00682-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078585565","display_name":"Chu-I Yang","orcid":"https://orcid.org/0000-0001-9402-510X"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Chu-I Yang","raw_affiliation_strings":["Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003414479","display_name":"Yi\u2010Pei Li","orcid":"https://orcid.org/0000-0002-1314-3276"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yi-Pei Li","raw_affiliation_strings":["Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan. yipeili@ntu.edu.tw","Taiwan International Graduate Program (TIGP), Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 11529, Taiwan. yipeili@ntu.edu.tw","Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan. yipeili@ntu.edu.tw","institution_ids":[]},{"raw_affiliation_string":"Taiwan International Graduate Program (TIGP), Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 11529, Taiwan. yipeili@ntu.edu.tw","institution_ids":[]},{"raw_affiliation_string":"Department of Chemical Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5078585565"],"corresponding_institution_ids":["https://openalex.org/I16733864"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":11.8702,"has_fulltext":true,"cited_by_count":61,"citation_normalized_percentile":{"value":0.98931262,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"15","issue":"1","first_page":"13","last_page":"13"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9998000264167786,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9379000067710876,"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/uncertainty-quantification","display_name":"Uncertainty quantification","score":0.7752878069877625},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7079099416732788},{"id":"https://openalex.org/keywords/measurement-uncertainty","display_name":"Measurement uncertainty","score":0.6717139482498169},{"id":"https://openalex.org/keywords/calibration","display_name":"Calibration","score":0.6655676364898682},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.6215083599090576},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5770673751831055},{"id":"https://openalex.org/keywords/uncertainty-analysis","display_name":"Uncertainty analysis","score":0.5574740767478943},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5335102081298828},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5266958475112915},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.4819774031639099},{"id":"https://openalex.org/keywords/standard-uncertainty","display_name":"Standard uncertainty","score":0.4712021052837372},{"id":"https://openalex.org/keywords/interval","display_name":"Interval (graph theory)","score":0.42298197746276855},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.14764603972434998},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1418900489807129},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.08092999458312988}],"concepts":[{"id":"https://openalex.org/C32230216","wikidata":"https://www.wikidata.org/wiki/Q7882499","display_name":"Uncertainty quantification","level":2,"score":0.7752878069877625},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7079099416732788},{"id":"https://openalex.org/C137209882","wikidata":"https://www.wikidata.org/wiki/Q1403517","display_name":"Measurement uncertainty","level":2,"score":0.6717139482498169},{"id":"https://openalex.org/C165838908","wikidata":"https://www.wikidata.org/wiki/Q736777","display_name":"Calibration","level":2,"score":0.6655676364898682},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.6215083599090576},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5770673751831055},{"id":"https://openalex.org/C177803969","wikidata":"https://www.wikidata.org/wiki/Q29205","display_name":"Uncertainty analysis","level":2,"score":0.5574740767478943},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5335102081298828},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5266958475112915},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.4819774031639099},{"id":"https://openalex.org/C2994224358","wikidata":"https://www.wikidata.org/wiki/Q13649246","display_name":"Standard uncertainty","level":3,"score":0.4712021052837372},{"id":"https://openalex.org/C2778067643","wikidata":"https://www.wikidata.org/wiki/Q166507","display_name":"Interval (graph theory)","level":2,"score":0.42298197746276855},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.14764603972434998},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1418900489807129},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.08092999458312988},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-023-00682-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00682-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00682-3","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:36737786","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36737786","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9898940","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9898940","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9898940/pdf/13321_2023_Article_682.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:cdd8c8b4fa234e6db1676cf0ae92f7e2","is_oa":true,"landing_page_url":"https://doaj.org/article/cdd8c8b4fa234e6db1676cf0ae92f7e2","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-14 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-023-00682-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00682-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00682-3","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3316197792","display_name":null,"funder_award_id":"111-2636-E-002-025","funder_id":"https://openalex.org/F4320322795","funder_display_name":"Ministry of Science and Technology, Taiwan"}],"funders":[{"id":"https://openalex.org/F4320322795","display_name":"Ministry of Science and Technology, Taiwan","ror":"https://ror.org/02kv4zf79"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4319074048.pdf"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W317957491","https://openalex.org/W806995027","https://openalex.org/W935072310","https://openalex.org/W1511368807","https://openalex.org/W1560021816","https://openalex.org/W1583837637","https://openalex.org/W1757990252","https://openalex.org/W2039698541","https://openalex.org/W2076498053","https://openalex.org/W2080635178","https://openalex.org/W2111959010","https://openalex.org/W2502949459","https://openalex.org/W2580919858","https://openalex.org/W2594183968","https://openalex.org/W2600383743","https://openalex.org/W2607662938","https://openalex.org/W2759315951","https://openalex.org/W2790808809","https://openalex.org/W2892094491","https://openalex.org/W2900090807","https://openalex.org/W2913529346","https://openalex.org/W2914584698","https://openalex.org/W2947216528","https://openalex.org/W2947835681","https://openalex.org/W2948194985","https://openalex.org/W2950501364","https://openalex.org/W2963058055","https://openalex.org/W2963238274","https://openalex.org/W2965563166","https://openalex.org/W2966357564","https://openalex.org/W2975495759","https://openalex.org/W2981731882","https://openalex.org/W3014339631","https://openalex.org/W3014596384","https://openalex.org/W3035711539","https://openalex.org/W3044338806","https://openalex.org/W3044724994","https://openalex.org/W3067819707","https://openalex.org/W3093687066","https://openalex.org/W3093934881","https://openalex.org/W3098465726","https://openalex.org/W3099276598","https://openalex.org/W3108753481","https://openalex.org/W3116286104","https://openalex.org/W3119291344","https://openalex.org/W3130255721","https://openalex.org/W3134774296","https://openalex.org/W3170966572","https://openalex.org/W3173107846","https://openalex.org/W3185456481","https://openalex.org/W3202166349","https://openalex.org/W3216626280","https://openalex.org/W4200071670","https://openalex.org/W4213070269","https://openalex.org/W4297782413","https://openalex.org/W4304184517","https://openalex.org/W4309258819","https://openalex.org/W6601365666"],"related_works":["https://openalex.org/W3130844878","https://openalex.org/W2388898390","https://openalex.org/W3139964550","https://openalex.org/W2387053421","https://openalex.org/W2108853753","https://openalex.org/W2354141393","https://openalex.org/W2605144881","https://openalex.org/W2949799777","https://openalex.org/W2376692293","https://openalex.org/W4205181462"],"abstract_inverted_index":{"Quantifying":[0],"uncertainty":[1,22,52,71,80,89,117,130],"in":[2,7,47],"machine":[3],"learning":[4],"is":[5],"important":[6],"new":[8],"research":[9],"areas":[10],"with":[11,104],"scarce":[12],"high-quality":[13],"data.":[14],"In":[15],"this":[16],"work,":[17],"we":[18,108],"develop":[19],"an":[20,55],"explainable":[21],"quantification":[23],"method":[24,32,53,113],"for":[25,122,136],"deep":[26],"learning-based":[27],"molecular":[28],"property":[29],"prediction.":[30,83],"This":[31,127],"can":[33,67,90],"capture":[34],"aleatoric":[35],"and":[36,40,95,132,139],"epistemic":[37],"uncertainties":[38,43],"separately":[39],"attribute":[41],"the":[42,48,62,75,82,116],"to":[44,61,73,81,114],"atoms":[45],"present":[46],"molecule.":[49],"The":[50],"atom-based":[51],"provides":[54,133],"extra":[56],"layer":[57],"of":[58],"chemical":[59,76,93,97],"insight":[60],"estimated":[63],"uncertainties,":[64],"i.e.,":[65],"one":[66],"analyze":[68],"individual":[69],"atomic":[70,88],"values":[72],"diagnose":[74],"component":[77],"that":[78,87],"introduces":[79],"Our":[84],"experiments":[85],"suggest":[86],"detect":[91],"unseen":[92],"structures":[94],"identify":[96],"species":[98],"whose":[99],"data":[100],"are":[101],"potentially":[102],"associated":[103],"significant":[105],"noise.":[106],"Furthermore,":[107],"propose":[109],"a":[110,134,141],"post-hoc":[111],"calibration":[112,131],"refine":[115],"quantified":[118],"by":[119],"ensemble":[120],"models":[121],"better":[123],"confidence":[124],"interval":[125],"estimates.":[126],"work":[128],"improves":[129],"framework":[135],"assessing":[137],"whether":[138],"why":[140],"prediction":[142],"should":[143],"be":[144],"considered":[145],"unreliable.":[146]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":22},{"year":2024,"cited_by_count":23},{"year":2023,"cited_by_count":9}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}