{"id":"https://openalex.org/W4386862116","doi":"https://doi.org/10.1186/s13321-023-00751-7","title":"Extended study on atomic featurization in graph neural networks for molecular property prediction","display_name":"Extended study on atomic featurization in graph neural networks for molecular property prediction","publication_year":2023,"publication_date":"2023-09-19","ids":{"openalex":"https://openalex.org/W4386862116","doi":"https://doi.org/10.1186/s13321-023-00751-7","pmid":"https://pubmed.ncbi.nlm.nih.gov/37726841"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-023-00751-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00751-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00751-7","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/s13321-023-00751-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080267354","display_name":"Agnieszka Wojtuch","orcid":"https://orcid.org/0000-0002-3112-2049"},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Agnieszka Wojtuch","raw_affiliation_strings":["Faculty of Mathematics and Computer Science, Jagiellonian University, \u0141ojasiewicza 6, 30-348, Krak\u00f3w, Poland. agnieszka.wojtuch@alumni.uj.edu.pl","Faculty of Mathematics and Computer Science, Jagiellonian University, \u0141ojasiewicza 6, 30-348, Krak\u00f3w, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Computer Science, Jagiellonian University, \u0141ojasiewicza 6, 30-348, Krak\u00f3w, Poland. agnieszka.wojtuch@alumni.uj.edu.pl","institution_ids":[]},{"raw_affiliation_string":"Faculty of Mathematics and Computer Science, Jagiellonian University, \u0141ojasiewicza 6, 30-348, Krak\u00f3w, Poland","institution_ids":["https://openalex.org/I126596746"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078152358","display_name":"Tomasz Danel","orcid":"https://orcid.org/0000-0001-6053-0028"},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Tomasz Danel","raw_affiliation_strings":["Faculty of Mathematics and Computer Science, Jagiellonian University, \u0141ojasiewicza 6, 30-348, Krak\u00f3w, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Computer Science, Jagiellonian University, \u0141ojasiewicza 6, 30-348, Krak\u00f3w, Poland","institution_ids":["https://openalex.org/I126596746"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059858209","display_name":"Sabina Podlewska","orcid":"https://orcid.org/0000-0002-2891-5603"},"institutions":[{"id":"https://openalex.org/I99542240","display_name":"Polish Academy of Sciences","ror":"https://ror.org/01dr6c206","country_code":"PL","type":"funder","lineage":["https://openalex.org/I99542240"]},{"id":"https://openalex.org/I4210120768","display_name":"Maj Institute of Pharmacology","ror":"https://ror.org/0288swk05","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210120768","https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Sabina Podlewska","raw_affiliation_strings":["Maj Institute of Pharmacology, Polish Academy of Sciences, Sm\u0119tna 12, 31-343, Krak\u00f3w, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Maj Institute of Pharmacology, Polish Academy of Sciences, Sm\u0119tna 12, 31-343, Krak\u00f3w, Poland","institution_ids":["https://openalex.org/I4210120768","https://openalex.org/I99542240"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025532190","display_name":"\u0141ukasz Maziarka","orcid":"https://orcid.org/0000-0001-6947-8131"},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"\u0141ukasz Maziarka","raw_affiliation_strings":["Faculty of Mathematics and Computer Science, Jagiellonian University, \u0141ojasiewicza 6, 30-348, Krak\u00f3w, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Computer Science, Jagiellonian University, \u0141ojasiewicza 6, 30-348, Krak\u00f3w, Poland","institution_ids":["https://openalex.org/I126596746"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5080267354"],"corresponding_institution_ids":["https://openalex.org/I126596746"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":3.1089,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.93084592,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"15","issue":"1","first_page":"81","last_page":"81"},"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":0.9988999962806702,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9368000030517578,"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":0.6883029341697693},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.6106435060501099},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5404556393623352},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.515763521194458},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42108261585235596},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4107745289802551},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3484058976173401},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3268429636955261}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6883029341697693},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.6106435060501099},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5404556393623352},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.515763521194458},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42108261585235596},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4107745289802551},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3484058976173401},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3268429636955261},{"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":5,"locations":[{"id":"doi:10.1186/s13321-023-00751-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00751-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00751-7","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:37726841","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37726841","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:ruj.uj.edu.pl:item/320866","is_oa":true,"landing_page_url":"https://ruj.uj.edu.pl/xmlui/handle/item/320866","pdf_url":"http://ruj.uj.edu.pl/bitstreams/fc503d0f-efc5-4ab9-b980-660c4b028f43/download","source":{"id":"https://openalex.org/S4306401249","display_name":"Jagiellonian University Repository (Jagiellonian University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I126596746","host_organization_name":"Jagiellonian University","host_organization_lineage":["https://openalex.org/I126596746"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10507875","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10507875","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10507875/pdf/13321_2023_Article_751.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:fd17a7dd86344f909f5397f815e16f8c","is_oa":true,"landing_page_url":"https://doaj.org/article/fd17a7dd86344f909f5397f815e16f8c","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 1-27 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-023-00751-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00751-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00751-7","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":[{"display_name":"Affordable and clean energy","score":0.5899999737739563,"id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G4532590350","display_name":null,"funder_award_id":"2019/35/N/ST6/02125","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"},{"id":"https://openalex.org/G7188852973","display_name":null,"funder_award_id":"2020/37/N/ST6/02728","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386862116.pdf"},"referenced_works_count":72,"referenced_works":["https://openalex.org/W1738019091","https://openalex.org/W1904365287","https://openalex.org/W1964513093","https://openalex.org/W1975147762","https://openalex.org/W1988037271","https://openalex.org/W2011703862","https://openalex.org/W2031650516","https://openalex.org/W2060531713","https://openalex.org/W2076498053","https://openalex.org/W2107081909","https://openalex.org/W2114704115","https://openalex.org/W2170973067","https://openalex.org/W2179414561","https://openalex.org/W2290847742","https://openalex.org/W2295598076","https://openalex.org/W2473190403","https://openalex.org/W2529996553","https://openalex.org/W2562257444","https://openalex.org/W2594183968","https://openalex.org/W2606780347","https://openalex.org/W2610148085","https://openalex.org/W2612690371","https://openalex.org/W2735246657","https://openalex.org/W2754490690","https://openalex.org/W2773987374","https://openalex.org/W2794301983","https://openalex.org/W2794474109","https://openalex.org/W2805404971","https://openalex.org/W2806547269","https://openalex.org/W2895744665","https://openalex.org/W2896457183","https://openalex.org/W2913099012","https://openalex.org/W2913351693","https://openalex.org/W2957050889","https://openalex.org/W2964015378","https://openalex.org/W2964121744","https://openalex.org/W2966357564","https://openalex.org/W2967052368","https://openalex.org/W2970119293","https://openalex.org/W2972741532","https://openalex.org/W2973114758","https://openalex.org/W2986232138","https://openalex.org/W2992525328","https://openalex.org/W3007488165","https://openalex.org/W3009970748","https://openalex.org/W3010220451","https://openalex.org/W3023204497","https://openalex.org/W3034516664","https://openalex.org/W3081574977","https://openalex.org/W3093934881","https://openalex.org/W3094502228","https://openalex.org/W3098269892","https://openalex.org/W3100157108","https://openalex.org/W3100751385","https://openalex.org/W3104850868","https://openalex.org/W3109493217","https://openalex.org/W3116202926","https://openalex.org/W3199234580","https://openalex.org/W3201677331","https://openalex.org/W3203569367","https://openalex.org/W3217253223","https://openalex.org/W4213233019","https://openalex.org/W4224004818","https://openalex.org/W4284969772","https://openalex.org/W4286487916","https://openalex.org/W4287828570","https://openalex.org/W4297733535","https://openalex.org/W4306889137","https://openalex.org/W4310222865","https://openalex.org/W4362520745","https://openalex.org/W4382239609","https://openalex.org/W4394665502"],"related_works":["https://openalex.org/W2582753012","https://openalex.org/W2961085424","https://openalex.org/W2391251536","https://openalex.org/W4300101497","https://openalex.org/W2362198218","https://openalex.org/W1982750869","https://openalex.org/W2019521278","https://openalex.org/W1984922432","https://openalex.org/W2375008505","https://openalex.org/W2085756966"],"abstract_inverted_index":{"Graph":[0],"neural":[1,42],"networks":[2],"have":[3],"recently":[4],"become":[5],"a":[6,98,165],"standard":[7],"method":[8],"for":[9],"analyzing":[10],"chemical":[11],"compounds.":[12],"In":[13],"the":[14,20,30,44,55,59,76,92,106,136,141,162,174,177,186],"field":[15],"of":[16,32,46,54,78,94,109,138,143,176],"molecular":[17],"property":[18],"prediction,":[19],"emphasis":[21],"is":[22,35,111],"now":[23],"on":[24,75,101,168],"designing":[25],"new":[26],"model":[27,102,169],"architectures,":[28,118],"and":[29,82,104,154],"importance":[31],"atom":[33,70,95,132,155],"featurization":[34],"oftentimes":[36],"belittled.":[37],"When":[38],"contrasting":[39],"two":[40],"graph":[41,86,120],"networks,":[43],"use":[45],"different":[47],"representations":[48,71],"possibly":[49],"leads":[50],"to":[51,58,180],"incorrect":[52],"attribution":[53],"results":[56],"solely":[57],"network":[60],"architecture.":[61],"To":[62],"better":[63,181],"understand":[64,182],"this":[65],"issue,":[66],"we":[67,126,172],"compare":[68],"multiple":[69],"by":[72],"evaluating":[73],"them":[74],"prediction":[77],"free":[79],"energy,":[80],"solubility,":[81],"metabolic":[83],"stability":[84],"using":[85,149],"convolutional":[87],"networks.":[88],"We":[89],"discover":[90],"that":[91,105,128],"choice":[93],"representation":[96,163],"has":[97,164],"significant":[99],"impact":[100,167],"performance":[103],"optimal":[107],"subset":[108],"features":[110],"task-specific.":[112],"Additional":[113],"experiments":[114],"involving":[115],"more":[116],"sophisticated":[117],"including":[119],"transformers,":[121],"support":[122],"these":[123],"findings.":[124],"Moreover,":[125],"demonstrate":[127],"some":[129],"commonly":[130],"used":[131],"features,":[133],"such":[134],"as":[135],"number":[137,142],"neighbors":[139],"or":[140],"hydrogens,":[144],"can":[145],"be":[146],"easily":[147],"predicted":[148],"only":[150],"information":[151],"about":[152],"bonds":[153],"type,":[156],"yet":[157],"their":[158],"explicit":[159],"inclusion":[160],"in":[161],"positive":[166],"performance.":[170],"Finally,":[171],"explain":[173],"predictions":[175],"best-performing":[178],"models":[179],"how":[183],"they":[184],"utilize":[185],"available":[187],"atomic":[188],"features.":[189]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":6}],"updated_date":"2026-04-30T09:15:22.047038","created_date":"2025-10-10T00:00:00"}
