{"id":"https://openalex.org/W4221151630","doi":"https://doi.org/10.1186/s13321-022-00648-x","title":"Improving VAE based molecular representations for compound property prediction","display_name":"Improving VAE based molecular representations for compound property prediction","publication_year":2022,"publication_date":"2022-10-14","ids":{"openalex":"https://openalex.org/W4221151630","doi":"https://doi.org/10.1186/s13321-022-00648-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/36242073"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-022-00648-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00648-x","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00648-x","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/s13321-022-00648-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053167026","display_name":"Ani Tevosyan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ani Tevosyan","raw_affiliation_strings":["YerevaNN, Charents str. 20, 0025, Yerevan, Armenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"YerevaNN, Charents str. 20, 0025, Yerevan, Armenia","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013131159","display_name":"Lusine Khondkaryan","orcid":"https://orcid.org/0000-0003-0578-0758"},"institutions":[{"id":"https://openalex.org/I4210133976","display_name":"Institute of Molecular Biology","ror":"https://ror.org/03t8mqd25","country_code":"AM","type":"facility","lineage":["https://openalex.org/I4210133976","https://openalex.org/I99064381"]},{"id":"https://openalex.org/I99064381","display_name":"National Academy of Sciences of Armenia","ror":"https://ror.org/04mczx267","country_code":"AM","type":"government","lineage":["https://openalex.org/I99064381"]}],"countries":["AM"],"is_corresponding":false,"raw_author_name":"Lusine Khondkaryan","raw_affiliation_strings":["Laboratory of Cell Technologies, Institute of Molecular Biology, National Academy of Sciences of RA, Hasratyan str. 7, 0014, Yerevan, Armenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Cell Technologies, Institute of Molecular Biology, National Academy of Sciences of RA, Hasratyan str. 7, 0014, Yerevan, Armenia","institution_ids":["https://openalex.org/I4210133976","https://openalex.org/I99064381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005769994","display_name":"Hrant Khachatrian","orcid":"https://orcid.org/0000-0002-1544-5649"},"institutions":[{"id":"https://openalex.org/I196551433","display_name":"Yerevan State University","ror":"https://ror.org/00s8vne50","country_code":"AM","type":"education","lineage":["https://openalex.org/I196551433"]}],"countries":["AM"],"is_corresponding":false,"raw_author_name":"Hrant Khachatrian","raw_affiliation_strings":["YerevaNN, Charents str. 20, 0025, Yerevan, Armenia","Yerevan State University, Alex Manoogian str. 1, 0025, Yerevan, Armenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"YerevaNN, Charents str. 20, 0025, Yerevan, Armenia","institution_ids":[]},{"raw_affiliation_string":"Yerevan State University, Alex Manoogian str. 1, 0025, Yerevan, Armenia","institution_ids":["https://openalex.org/I196551433"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080974052","display_name":"Gohar Tadevosyan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210133976","display_name":"Institute of Molecular Biology","ror":"https://ror.org/03t8mqd25","country_code":"AM","type":"facility","lineage":["https://openalex.org/I4210133976","https://openalex.org/I99064381"]},{"id":"https://openalex.org/I99064381","display_name":"National Academy of Sciences of Armenia","ror":"https://ror.org/04mczx267","country_code":"AM","type":"government","lineage":["https://openalex.org/I99064381"]}],"countries":["AM"],"is_corresponding":false,"raw_author_name":"Gohar Tadevosyan","raw_affiliation_strings":["Laboratory of Cell Technologies, Institute of Molecular Biology, National Academy of Sciences of RA, Hasratyan str. 7, 0014, Yerevan, Armenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Cell Technologies, Institute of Molecular Biology, National Academy of Sciences of RA, Hasratyan str. 7, 0014, Yerevan, Armenia","institution_ids":["https://openalex.org/I4210133976","https://openalex.org/I99064381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028792014","display_name":"Lilit Apresyan","orcid":"https://orcid.org/0000-0003-4564-5446"},"institutions":[{"id":"https://openalex.org/I4210133976","display_name":"Institute of Molecular Biology","ror":"https://ror.org/03t8mqd25","country_code":"AM","type":"facility","lineage":["https://openalex.org/I4210133976","https://openalex.org/I99064381"]},{"id":"https://openalex.org/I99064381","display_name":"National Academy of Sciences of Armenia","ror":"https://ror.org/04mczx267","country_code":"AM","type":"government","lineage":["https://openalex.org/I99064381"]}],"countries":["AM"],"is_corresponding":false,"raw_author_name":"Lilit Apresyan","raw_affiliation_strings":["Laboratory of Cell Technologies, Institute of Molecular Biology, National Academy of Sciences of RA, Hasratyan str. 7, 0014, Yerevan, Armenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Cell Technologies, Institute of Molecular Biology, National Academy of Sciences of RA, Hasratyan str. 7, 0014, Yerevan, Armenia","institution_ids":["https://openalex.org/I4210133976","https://openalex.org/I99064381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050797011","display_name":"Nelly Babayan","orcid":"https://orcid.org/0000-0001-9205-7693"},"institutions":[{"id":"https://openalex.org/I4210094371","display_name":"Scientific Center of Zoology and Hydroecology","ror":"https://ror.org/00t5ymp38","country_code":"AM","type":"facility","lineage":["https://openalex.org/I4210094371","https://openalex.org/I99064381"]},{"id":"https://openalex.org/I4210133976","display_name":"Institute of Molecular Biology","ror":"https://ror.org/03t8mqd25","country_code":"AM","type":"facility","lineage":["https://openalex.org/I4210133976","https://openalex.org/I99064381"]},{"id":"https://openalex.org/I99064381","display_name":"National Academy of Sciences of Armenia","ror":"https://ror.org/04mczx267","country_code":"AM","type":"government","lineage":["https://openalex.org/I99064381"]}],"countries":["AM"],"is_corresponding":false,"raw_author_name":"Nelly Babayan","raw_affiliation_strings":[", Toxometris.ai, Sarmen str. 7, 0009, Yerevan, Armenia","Laboratory of Cell Technologies, Institute of Molecular Biology, National Academy of Sciences of RA, Hasratyan str. 7, 0014, Yerevan, Armenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":", Toxometris.ai, Sarmen str. 7, 0009, Yerevan, Armenia","institution_ids":["https://openalex.org/I4210094371"]},{"raw_affiliation_string":"Laboratory of Cell Technologies, Institute of Molecular Biology, National Academy of Sciences of RA, Hasratyan str. 7, 0014, Yerevan, Armenia","institution_ids":["https://openalex.org/I4210133976","https://openalex.org/I99064381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014325801","display_name":"Helga Stopper","orcid":"https://orcid.org/0000-0003-4168-8211"},"institutions":[{"id":"https://openalex.org/I25974101","display_name":"University of W\u00fcrzburg","ror":"https://ror.org/00fbnyb24","country_code":"DE","type":"education","lineage":["https://openalex.org/I25974101"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Helga Stopper","raw_affiliation_strings":["Department of Toxicology, Institute of Pharmacology and Toxicology, University of W\u00fcrzburg, Versbacher str. 9, 97078, W\u00fcrzburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Toxicology, Institute of Pharmacology and Toxicology, University of W\u00fcrzburg, Versbacher str. 9, 97078, W\u00fcrzburg, Germany","institution_ids":["https://openalex.org/I25974101"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011162032","display_name":"Zaven Navoyan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210094371","display_name":"Scientific Center of Zoology and Hydroecology","ror":"https://ror.org/00t5ymp38","country_code":"AM","type":"facility","lineage":["https://openalex.org/I4210094371","https://openalex.org/I99064381"]}],"countries":["AM"],"is_corresponding":true,"raw_author_name":"Zaven Navoyan","raw_affiliation_strings":[", Toxometris.ai, Sarmen str. 7, 0009, Yerevan, Armenia. znavoyan@gmail.com","Toxometris.ai, Sarmen str. 7, 0009, Yerevan, Armenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":", Toxometris.ai, Sarmen str. 7, 0009, Yerevan, Armenia. znavoyan@gmail.com","institution_ids":["https://openalex.org/I4210094371"]},{"raw_affiliation_string":"Toxometris.ai, Sarmen str. 7, 0009, Yerevan, Armenia","institution_ids":["https://openalex.org/I4210094371"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5011162032"],"corresponding_institution_ids":["https://openalex.org/I4210094371"],"apc_list":{"value":2390,"currency":"USD","value_usd":2390},"apc_paid":{"value":2390,"currency":"USD","value_usd":2390},"fwci":1.8638,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.86854744,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"14","issue":"1","first_page":"69","last_page":"69"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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":0.9994999766349792,"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":0.9754999876022339,"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/computer-science","display_name":"Computer science","score":0.674815833568573},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.6392923593521118},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.48542413115501404},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.33551326394081116}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.674815833568573},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.6392923593521118},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48542413115501404},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.33551326394081116},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","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":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-022-00648-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00648-x","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00648-x","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:36242073","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36242073","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9569108","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9569108","pdf_url":null,"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:080560541e4c4c8aba31578c3dbfaf0c","is_oa":true,"landing_page_url":"https://doaj.org/article/080560541e4c4c8aba31578c3dbfaf0c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 14, Iss 1, Pp 1-14 (2022)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-022-00648-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00648-x","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00648-x","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":[],"funders":[{"id":"https://openalex.org/F4320324101","display_name":"State Committee of Science","ror":"https://ror.org/01ptpr676"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4221151630.pdf","grobid_xml":"https://content.openalex.org/works/W4221151630.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1757990252","https://openalex.org/W1988037271","https://openalex.org/W2033757486","https://openalex.org/W2034368206","https://openalex.org/W2128245586","https://openalex.org/W2157331557","https://openalex.org/W2165698076","https://openalex.org/W2171639300","https://openalex.org/W2294345429","https://openalex.org/W2315837940","https://openalex.org/W2395579298","https://openalex.org/W2406943157","https://openalex.org/W2529996553","https://openalex.org/W2566440510","https://openalex.org/W2594183968","https://openalex.org/W2735246657","https://openalex.org/W2751756351","https://openalex.org/W2786565076","https://openalex.org/W2786722833","https://openalex.org/W2789796452","https://openalex.org/W2791713605","https://openalex.org/W2887113605","https://openalex.org/W2887447356","https://openalex.org/W2903198840","https://openalex.org/W2904147875","https://openalex.org/W2914757825","https://openalex.org/W2914870491","https://openalex.org/W2922073769","https://openalex.org/W2943018619","https://openalex.org/W2946928580","https://openalex.org/W2950128007","https://openalex.org/W2962764460","https://openalex.org/W2994728899","https://openalex.org/W3006187295","https://openalex.org/W3018495986","https://openalex.org/W3032781902","https://openalex.org/W3098269892","https://openalex.org/W3171159608","https://openalex.org/W3187366930","https://openalex.org/W3196929030","https://openalex.org/W3215689235","https://openalex.org/W4238056312","https://openalex.org/W4294285719","https://openalex.org/W4311415873"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"Collecting":[0],"labeled":[1],"data":[2],"for":[3,64],"many":[4],"important":[5],"tasks":[6,45],"in":[7,99,162],"chemoinformatics":[8],"is":[9],"time":[10],"consuming":[11],"and":[12,36,69,129,150,157],"requires":[13],"expensive":[14],"experiments.":[15],"In":[16,73],"recent":[17],"years,":[18],"machine":[19,88],"learning":[20,89],"has":[21],"been":[22,58],"used":[23],"to":[24,40,60,81],"learn":[25],"rich":[26],"representations":[27,101],"of":[28,53,87,119,122,134,146],"molecules":[29],"using":[30],"large":[31],"scale":[32],"unlabeled":[33,160],"molecular":[34,70,97],"datasets":[35,136],"transfer":[37,63],"the":[38,42,54,62,100,108,117,120,127,130,135,141,144,151,158,163],"knowledge":[39],"solve":[41],"more":[43],"challenging":[44],"with":[46],"limited":[47],"datasets.":[48],"Variational":[49],"autoencoders":[50],"are":[51],"one":[52],"tools":[55],"that":[56],"have":[57],"proposed":[59],"perform":[61],"both":[65],"chemical":[66,83],"property":[67,84,112,147,154],"prediction":[68,85,113,148,155],"generation":[71],"tasks.":[72,114],"this":[74],"work":[75],"we":[76,139],"propose":[77],"a":[78],"simple":[79],"method":[80,109],"improve":[82],"performance":[86,145],"models":[90,149],"by":[91,103],"incorporating":[92],"additional":[93],"information":[94],"on":[95,110],"correlated":[96],"descriptors":[98,128],"learned":[102],"variational":[104],"autoencoders.":[105],"We":[106,115],"verify":[107],"three":[111],"explore":[116],"impact":[118],"number":[121],"incorporated":[123],"descriptors,":[124],"correlation":[125],"between":[126,143,153],"target":[131],"properties,":[132],"sizes":[133],"etc.":[137],"Finally,":[138],"show":[140],"relation":[142],"distance":[152],"dataset":[156,161],"larger":[159],"representation":[164],"space.":[165]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":3}],"updated_date":"2026-08-25T07:29:55.448023","created_date":"2025-10-10T00:00:00"}