{"id":"https://openalex.org/W2984339599","doi":"https://doi.org/10.1093/bib/bbz125","title":"A novel molecular representation with BiGRU neural networks for learning atom","display_name":"A novel molecular representation with BiGRU neural networks for learning atom","publication_year":2019,"publication_date":"2019-09-11","ids":{"openalex":"https://openalex.org/W2984339599","doi":"https://doi.org/10.1093/bib/bbz125","mag":"2984339599","pmid":"https://pubmed.ncbi.nlm.nih.gov/31729524"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbz125","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbz125","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027410770","display_name":"Xuan Lin","orcid":"https://orcid.org/0000-0001-7216-1821"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuan Lin","raw_affiliation_strings":["College of Computer Science and Technology, Hunan University, Changsha, 410082, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Hunan University, Changsha, 410082, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021932264","display_name":"Zhe Quan","orcid":"https://orcid.org/0000-0003-2669-9190"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhe Quan","raw_affiliation_strings":["College of Computer Science and Technology, Hunan University, Changsha, 410082, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Hunan University, Changsha, 410082, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037730132","display_name":"Zhi-Jie Wang","orcid":"https://orcid.org/0000-0002-6865-7899"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhi-Jie Wang","raw_affiliation_strings":["College of Computer Science and Technology, Hunan University, Changsha, 410082, China"],"raw_orcid":"https://orcid.org/0000-0002-6865-7899","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Hunan University, Changsha, 410082, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100340333","display_name":"Huang Huang","orcid":"https://orcid.org/0000-0002-5950-4698"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huang Huang","raw_affiliation_strings":["College of Computer, National University of Defense Technology, Changsha, 410073,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer, National University of Defense Technology, Changsha, 410073,China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027286013","display_name":"Xiangxiang Zeng","orcid":"https://orcid.org/0000-0003-1081-7658"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangxiang Zeng","raw_affiliation_strings":["College of Computer Science and Technology, Hunan University, Changsha, 410082, China","School of Data and Computer Science, Sun Yat-sen University, Guangzhou, 510275, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Hunan University, Changsha, 410082, China","institution_ids":["https://openalex.org/I16609230"]},{"raw_affiliation_string":"School of Data and Computer Science, Sun Yat-sen University, Guangzhou, 510275, China","institution_ids":["https://openalex.org/I157773358"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5037730132"],"corresponding_institution_ids":["https://openalex.org/I16609230"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":4.3464,"has_fulltext":false,"cited_by_count":165,"citation_normalized_percentile":{"value":0.95670421,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"21","issue":"6","first_page":"2099","last_page":"2111"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9994000196456909,"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"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9994000196456909,"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/T12613","display_name":"X-ray Diffraction in Crystallography","score":0.9769999980926514,"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/T12285","display_name":"Surface Chemistry and Catalysis","score":0.9442999958992004,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6611052751541138},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5621985793113708},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.513650119304657},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.49584946036338806},{"id":"https://openalex.org/keywords/atom","display_name":"Atom (system on chip)","score":0.43915417790412903},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.32010960578918457}],"concepts":[{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6611052751541138},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5621985793113708},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.513650119304657},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.49584946036338806},{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.43915417790412903},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32010960578918457},{"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/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbz125","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbz125","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31729524","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31729524","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1941139581","display_name":null,"funder_award_id":"U1611264","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2428490243","display_name":null,"funder_award_id":"U1711262","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4044104431","display_name":null,"funder_award_id":"U1401256","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4862241317","display_name":"\u5f02\u6784\u5185\u5b58\u8ba1\u7b97\u7cfb\u7edf\u7684\u6269\u5c55\u6027\u95ee\u9898\u7814\u7a76","funder_award_id":"61772183","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5007580677","display_name":"\u9762\u5411\u969c\u788d\u7a7a\u95f4\u7684\u79fb\u52a8\u5bf9\u8c61\u67e5\u8be2\u5904\u7406\u6280\u672f\u7814\u7a76","funder_award_id":"61972425","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6840496190","display_name":null,"funder_award_id":"U1811264","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7385024857","display_name":null,"funder_award_id":"2018YFB0204100","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7660082681","display_name":null,"funder_award_id":"U1711261","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8282194463","display_name":null,"funder_award_id":"61602166","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8698608195","display_name":null,"funder_award_id":"U1501252","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":84,"referenced_works":["https://openalex.org/W84368778","https://openalex.org/W569478347","https://openalex.org/W1522301498","https://openalex.org/W1553469512","https://openalex.org/W1583837637","https://openalex.org/W1614298861","https://openalex.org/W1924770834","https://openalex.org/W1975147762","https://openalex.org/W1988037271","https://openalex.org/W1998056319","https://openalex.org/W1999798000","https://openalex.org/W2006868936","https://openalex.org/W2014858249","https://openalex.org/W2251189452","https://openalex.org/W2290145898","https://openalex.org/W2290847742","https://openalex.org/W2333144702","https://openalex.org/W2343107734","https://openalex.org/W2382467334","https://openalex.org/W2406943157","https://openalex.org/W2461470610","https://openalex.org/W2461620095","https://openalex.org/W2473190403","https://openalex.org/W2521476646","https://openalex.org/W2529996553","https://openalex.org/W2551117563","https://openalex.org/W2559655401","https://openalex.org/W2565185351","https://openalex.org/W2565684601","https://openalex.org/W2594183968","https://openalex.org/W2597601064","https://openalex.org/W2604272474","https://openalex.org/W2607662938","https://openalex.org/W2612708909","https://openalex.org/W2613712744","https://openalex.org/W2620564586","https://openalex.org/W2622612680","https://openalex.org/W2756203131","https://openalex.org/W2765131766","https://openalex.org/W2789254732","https://openalex.org/W2790808809","https://openalex.org/W2793643126","https://openalex.org/W2795631711","https://openalex.org/W2799900537","https://openalex.org/W2809953005","https://openalex.org/W2810731239","https://openalex.org/W2913293259","https://openalex.org/W2913617083","https://openalex.org/W2919115771","https://openalex.org/W2922229918","https://openalex.org/W2946099214","https://openalex.org/W2950729596","https://openalex.org/W2964121744","https://openalex.org/W2964199361","https://openalex.org/W2999905431","https://openalex.org/W3098254076","https://openalex.org/W3098269892","https://openalex.org/W3100157108","https://openalex.org/W3103720336","https://openalex.org/W6623726160","https://openalex.org/W6631190155","https://openalex.org/W6636510571","https://openalex.org/W6636825548","https://openalex.org/W6637178625","https://openalex.org/W6638824847","https://openalex.org/W6640212811","https://openalex.org/W6679565970","https://openalex.org/W6682652786","https://openalex.org/W6684191040","https://openalex.org/W6685350579","https://openalex.org/W6713001283","https://openalex.org/W6713134421","https://openalex.org/W6720006811","https://openalex.org/W6733974131","https://openalex.org/W6736177006","https://openalex.org/W6736336676","https://openalex.org/W6736685754","https://openalex.org/W6738509884","https://openalex.org/W6741972917","https://openalex.org/W6747927160","https://openalex.org/W6747954111","https://openalex.org/W6748524405","https://openalex.org/W6751367952","https://openalex.org/W6763608733"],"related_works":["https://openalex.org/W2062195135","https://openalex.org/W2795079307","https://openalex.org/W2391251536","https://openalex.org/W2793058541","https://openalex.org/W2362198218","https://openalex.org/W1983629434","https://openalex.org/W1982750869","https://openalex.org/W2019521278","https://openalex.org/W2033914206","https://openalex.org/W2042327336"],"abstract_inverted_index":{"Molecular":[0],"representations":[1,38,146],"play":[2],"critical":[3],"roles":[4],"in":[5,18,27,94,108,118],"researching":[6],"drug":[7,28,98],"design":[8],"and":[9,11,23,44,54,85,89,104,128,162,182],"properties,":[10],"effective":[12],"methods":[13],"are":[14,39,51,101],"beneficial":[15],"to":[16],"assisting":[17],"the":[19,35,87,95,102,115,119,133,180],"calculation":[20],"of":[21,34,97,125,184],"molecules":[22],"solving":[24,86],"related":[25],"problem":[26],"discovery.":[29],"In":[30,69],"previous":[31],"years,":[32],"most":[33],"traditional":[36],"molecular":[37,148],"based":[40],"on":[41,47,66,154,175],"hand-crafted":[42],"features":[43],"rely":[45],"heavily":[46],"biological":[48],"experimentations,":[49],"which":[50,100,142],"often":[52],"costly":[53],"time":[55],"consuming.":[56],"However,":[57],"recent":[58],"researches":[59],"achieve":[60,172],"promising":[61],"results":[62,166],"using":[63],"machine":[64],"learning":[65,83],"various":[67],"domains.":[68],"this":[70,109],"article,":[71],"we":[72],"present":[73],"a":[74,123],"novel":[75],"method":[76],"named":[77],"Smi2Vec-BiGRU":[78],"that":[79,168],"is":[80],"designed":[81],"for":[82,140,147],"atoms":[84],"single-":[88],"multitask":[90],"binary":[91],"classification":[92],"problems":[93,107],"field":[96],"discovery,":[99],"basic":[103],"also":[105],"key":[106],"field.":[110],"Specifically,":[111],"our":[112,169,185],"approach":[113,170],"transforms":[114],"molecule":[116],"data":[117],"SMILES":[120],"format":[121],"into":[122,132],"set":[124],"sample":[126],"vectors":[127],"then":[129],"feeds":[130],"them":[131],"bidirectional":[134],"gated":[135],"recurrent":[136],"unit":[137],"neural":[138],"networks":[139],"training,":[141],"learns":[143],"low-dimensional":[144],"vector":[145],"drug.":[149],"We":[150],"conduct":[151],"extensive":[152],"experiments":[153],"several":[155],"widely":[156],"used":[157],"benchmarks":[158],"including":[159],"Tox21,":[160],"SIDER":[161],"ClinTox.":[163],"The":[164],"experimental":[165],"show":[167],"can":[171],"state-of-the-art":[173],"performance":[174],"these":[176],"benchmarking":[177],"datasets,":[178],"demonstrating":[179],"feasibility":[181],"competitiveness":[183],"proposed":[186],"approach.":[187]},"counts_by_year":[{"year":2026,"cited_by_count":13},{"year":2025,"cited_by_count":36},{"year":2024,"cited_by_count":37},{"year":2023,"cited_by_count":30},{"year":2022,"cited_by_count":16},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
