{"id":"https://openalex.org/W3198470722","doi":"https://doi.org/10.1093/bib/bbab367","title":"A general optimization protocol for molecular property prediction using a deep learning network","display_name":"A general optimization protocol for molecular property prediction using a deep learning network","publication_year":2021,"publication_date":"2021-09-08","ids":{"openalex":"https://openalex.org/W3198470722","doi":"https://doi.org/10.1093/bib/bbab367","mag":"3198470722","pmid":"https://pubmed.ncbi.nlm.nih.gov/34498673"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab367","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab367","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab367/42229720/bbab367.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab367/42229720/bbab367.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066147862","display_name":"Jen\u2010Hao Chen","orcid":null},"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"]},{"id":"https://openalex.org/I92172085","display_name":"Chunghwa Telecom (Taiwan)","ror":"https://ror.org/04f786589","country_code":"TW","type":"company","lineage":["https://openalex.org/I92172085"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jen-Hao Chen","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Taiwan University, and he is an engineer with Chunghwa Telecom Co., Ltd., Taipei, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Taiwan University, and he is an engineer with Chunghwa Telecom Co., Ltd., Taipei, Taiwan","institution_ids":["https://openalex.org/I92172085","https://openalex.org/I16733864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021255582","display_name":"Yufeng Jane Tseng","orcid":"https://orcid.org/0000-0002-8461-6181"},"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":"Yufeng Jane Tseng","raw_affiliation_strings":["Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5021255582"],"corresponding_institution_ids":["https://openalex.org/I16733864"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.8176,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.87269437,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"23","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9991000294685364,"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/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9930999875068665,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/hyperparameter","display_name":"Hyperparameter","score":0.726836085319519},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7253772020339966},{"id":"https://openalex.org/keywords/bayesian-optimization","display_name":"Bayesian optimization","score":0.6731830835342407},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5606621503829956},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4679746925830841},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.45761600136756897},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4394940733909607},{"id":"https://openalex.org/keywords/bayesian-network","display_name":"Bayesian network","score":0.42624929547309875},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.4135803282260895}],"concepts":[{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.726836085319519},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7253772020339966},{"id":"https://openalex.org/C2778049539","wikidata":"https://www.wikidata.org/wiki/Q17002908","display_name":"Bayesian optimization","level":2,"score":0.6731830835342407},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5606621503829956},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4679746925830841},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.45761600136756897},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4394940733909607},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.42624929547309875},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.4135803282260895},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012995","descriptor_name":"Solubility","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012995","descriptor_name":"Solubility","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012995","descriptor_name":"Solubility","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012995","descriptor_name":"Solubility","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbab367","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab367","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab367/42229720/bbab367.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34498673","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34498673","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8769690","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8769690","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbab367","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab367","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab367/42229720/bbab367.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/6","score":0.44999998807907104,"display_name":"Clean water and sanitation"}],"awards":[{"id":"https://openalex.org/G2665147884","display_name":null,"funder_award_id":"NTU-CC-110L890803, NTU-110L8809","funder_id":"https://openalex.org/F4320323900","funder_display_name":"National Taiwan University"},{"id":"https://openalex.org/G3126255160","display_name":null,"funder_award_id":"NTU-CC-110L890803","funder_id":"https://openalex.org/F4320323900","funder_display_name":"National Taiwan University"},{"id":"https://openalex.org/G3274393671","display_name":null,"funder_award_id":"MOHW110-FDA-D-114-000611","funder_id":"https://openalex.org/F4320325348","funder_display_name":"Taiwan Foundation for Democracy"},{"id":"https://openalex.org/G6321830578","display_name":null,"funder_award_id":"MOST 109-2823-8-002-010-CV","funder_id":"https://openalex.org/F4320309618","funder_display_name":"Ministry of Science and Technology"},{"id":"https://openalex.org/G6386056370","display_name":null,"funder_award_id":"NTU-110L8809","funder_id":"https://openalex.org/F4320323900","funder_display_name":"National Taiwan University"},{"id":"https://openalex.org/G6886464011","display_name":null,"funder_award_id":"NTU-CC-110L890803","funder_id":"https://openalex.org/F4320311701","funder_display_name":"Nottingham Trent University"},{"id":"https://openalex.org/G8158657852","display_name":null,"funder_award_id":"109-2320-B-002-040-","funder_id":"https://openalex.org/F4320309618","funder_display_name":"Ministry of Science and Technology"},{"id":"https://openalex.org/G8860217947","display_name":null,"funder_award_id":"NTU-110L8809","funder_id":"https://openalex.org/F4320311701","funder_display_name":"Nottingham Trent University"}],"funders":[{"id":"https://openalex.org/F4320309618","display_name":"Ministry of Science and Technology","ror":"https://ror.org/02b207r52"},{"id":"https://openalex.org/F4320311701","display_name":"Nottingham Trent University","ror":"https://ror.org/04xyxjd90"},{"id":"https://openalex.org/F4320323900","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95"},{"id":"https://openalex.org/F4320325348","display_name":"Taiwan Foundation for Democracy","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3198470722.pdf","grobid_xml":"https://content.openalex.org/works/W3198470722.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1966716734","https://openalex.org/W2046589863","https://openalex.org/W2097998348","https://openalex.org/W2157331557","https://openalex.org/W2192203593","https://openalex.org/W2524365899","https://openalex.org/W2559655401","https://openalex.org/W2560674852","https://openalex.org/W2594183968","https://openalex.org/W2604272474","https://openalex.org/W2604296437","https://openalex.org/W2613904329","https://openalex.org/W2735246657","https://openalex.org/W2769423117","https://openalex.org/W2775795276","https://openalex.org/W2790808809","https://openalex.org/W2896457183","https://openalex.org/W2911964244","https://openalex.org/W2914611487","https://openalex.org/W2962764460","https://openalex.org/W2964015378","https://openalex.org/W2966357564","https://openalex.org/W2989615256","https://openalex.org/W3000953558","https://openalex.org/W3003771069","https://openalex.org/W3005552578","https://openalex.org/W3032963903","https://openalex.org/W3103092523","https://openalex.org/W3210732293","https://openalex.org/W4234552385","https://openalex.org/W4241677786","https://openalex.org/W4289292158","https://openalex.org/W4293508416","https://openalex.org/W6674385629","https://openalex.org/W6726873649","https://openalex.org/W6728047685","https://openalex.org/W6736161267","https://openalex.org/W6737778391","https://openalex.org/W6746779403","https://openalex.org/W6747218270","https://openalex.org/W6755207826","https://openalex.org/W6756302984","https://openalex.org/W6759047552","https://openalex.org/W6772452955","https://openalex.org/W6779326878"],"related_works":["https://openalex.org/W4233965824","https://openalex.org/W2607442583","https://openalex.org/W3199199693","https://openalex.org/W4286970057","https://openalex.org/W2967237190","https://openalex.org/W3028852288","https://openalex.org/W4323366554","https://openalex.org/W2405673391","https://openalex.org/W4292388060","https://openalex.org/W2200000192"],"abstract_inverted_index":{"The":[0,97],"key":[1],"to":[2,14,69],"generating":[3,88],"the":[4,30,37,63,101,111,120,141,172,177,181],"best":[5,182],"deep":[6],"learning":[7,127],"model":[8,38,72,124,178,183],"for":[9,87,106,118],"predicting":[10],"molecular":[11,143,151],"property":[12],"is":[13],"test":[15],"and":[16,51,79,125,163,179],"apply":[17],"various":[18],"optimization":[19,23,60,117,190],"methods.":[20],"While":[21],"individual":[22],"methods":[24,50,61],"from":[25,74,187],"different":[26,93,107,150],"past":[27],"works":[28],"outside":[29],"pharmaceutical":[31],"domain":[32],"each":[33,170],"succeeded":[34],"in":[35,62,83],"improving":[36],"performance,":[39],"better":[40],"improvement":[41],"may":[42],"be":[43],"achieved":[44],"when":[45],"specific":[46],"combinations":[47],"of":[48,95,110,114,122,148,171],"these":[49],"practices":[52],"are":[53,77,100,138,165],"applied.":[54],"In":[55],"this":[56],"work,":[57],"three":[58,98,173],"high-performance":[59],"literature":[64],"that":[65],"have":[66],"been":[67],"shown":[68],"dramatically":[70],"improve":[71],"performance":[73],"other":[75],"fields":[76],"used":[78],"discussed,":[80],"eventually":[81],"resulting":[82],"a":[84,123,133],"general":[85],"procedure":[86],"optimized":[89],"CNN":[90],"models":[91],"on":[92],"properties":[94,152],"molecules.":[96],"techniques":[99,174],"dynamic":[102,193],"batch":[103,194],"size":[104,195],"strategy":[105],"enumeration":[108],"ratios":[109],"SMILES":[112],"representation":[113],"compounds,":[115],"Bayesian":[116,189],"selecting":[119],"hyperparameters":[121],"feature":[126,144],"using":[128,188],"chemical":[129],"features":[130],"obtained":[131],"by":[132],"feedforward":[134],"neural":[135],"network,":[136],"which":[137],"concatenated":[139],"with":[140,192],"learned":[142],"vector.":[145],"A":[146],"total":[147],"seven":[149],"(water":[153],"solubility,":[154],"lipophilicity,":[155],"hydration":[156],"energy,":[157],"electronic":[158],"properties,":[159],"blood-brain":[160],"barrier":[161],"permeability":[162],"inhibition)":[164],"used.":[166],"We":[167],"demonstrate":[168],"how":[169,180],"can":[175,184],"affect":[176],"generally":[185],"benefit":[186],"combined":[191],"tuning.":[196]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
