{"id":"https://openalex.org/W4411549233","doi":"https://doi.org/10.1021/acs.jcim.5c01037","title":"Distance-Aware Molecular Property Prediction in Nonlinear Structure\u2013Property Space","display_name":"Distance-Aware Molecular Property Prediction in Nonlinear Structure\u2013Property Space","publication_year":2025,"publication_date":"2025-06-23","ids":{"openalex":"https://openalex.org/W4411549233","doi":"https://doi.org/10.1021/acs.jcim.5c01037","pmid":"https://pubmed.ncbi.nlm.nih.gov/40549871"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c01037","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01037","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5100319280","display_name":"Jae Young Kim","orcid":"https://orcid.org/0000-0003-0101-2620"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jae Young Kim","raw_affiliation_strings":["Delaware Energy Institute (DEI), University of Delaware, 221 Academy St., Newark, Delaware 19716, United States","Department of Chemical and Biomolecular Engineering","University of Delaware"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Delaware Energy Institute (DEI), University of Delaware, 221 Academy St., Newark, Delaware 19716, United States","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering","institution_ids":[]},{"raw_affiliation_string":"University of Delaware","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066110304","display_name":"Dionisios G. Vlachos","orcid":"https://orcid.org/0000-0002-6795-8403"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dionisios G. Vlachos","raw_affiliation_strings":["Delaware Energy Institute (DEI), University of Delaware, 221 Academy St., Newark, Delaware 19716, United States","Department of Chemical and Biomolecular Engineering","University of Delaware"],"raw_orcid":"https://orcid.org/0000-0002-6795-8403","affiliations":[{"raw_affiliation_string":"Delaware Energy Institute (DEI), University of Delaware, 221 Academy St., Newark, Delaware 19716, United States","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering","institution_ids":[]},{"raw_affiliation_string":"University of Delaware","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5066110304"],"corresponding_institution_ids":["https://openalex.org/I86501945"],"apc_list":null,"apc_paid":null,"fwci":1.063,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.80302877,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"65","issue":"13","first_page":"6744","last_page":"6756"},"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":0.9943000078201294,"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/T12748","display_name":"Molecular spectroscopy and chirality","score":0.9789000153541565,"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/property","display_name":"Property (philosophy)","score":0.8709401488304138},{"id":"https://openalex.org/keywords/nonlinear-system","display_name":"Nonlinear system","score":0.5897777080535889},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.5352355241775513},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38256847858428955},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.17850524187088013},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.05666729807853699}],"concepts":[{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.8709401488304138},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.5897777080535889},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.5352355241775513},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38256847858428955},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.17850524187088013},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.05666729807853699},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c01037","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01037","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40549871","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40549871","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 chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334046","display_name":"Delaware Biotechnology Institute","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W1604938182","https://openalex.org/W1988270791","https://openalex.org/W1990621008","https://openalex.org/W1992332072","https://openalex.org/W1994854869","https://openalex.org/W2015931265","https://openalex.org/W2037547741","https://openalex.org/W2042820172","https://openalex.org/W2051190954","https://openalex.org/W2051531646","https://openalex.org/W2089049624","https://openalex.org/W2091310925","https://openalex.org/W2091764690","https://openalex.org/W2099071242","https://openalex.org/W2136699148","https://openalex.org/W2140095548","https://openalex.org/W2146060259","https://openalex.org/W2225235469","https://openalex.org/W2295598076","https://openalex.org/W2315837940","https://openalex.org/W2559145072","https://openalex.org/W2562301581","https://openalex.org/W2587942483","https://openalex.org/W2606329443","https://openalex.org/W2612972698","https://openalex.org/W2904495238","https://openalex.org/W2906627336","https://openalex.org/W2912010043","https://openalex.org/W2945385893","https://openalex.org/W2949676527","https://openalex.org/W2964060211","https://openalex.org/W2986369394","https://openalex.org/W3025031475","https://openalex.org/W3044724994","https://openalex.org/W3093152954","https://openalex.org/W3098306883","https://openalex.org/W3120618935","https://openalex.org/W3172204734","https://openalex.org/W4220724626","https://openalex.org/W4220751823","https://openalex.org/W4225597912","https://openalex.org/W4290659046","https://openalex.org/W4309218736","https://openalex.org/W4310222678","https://openalex.org/W4317796304","https://openalex.org/W4362520745","https://openalex.org/W4362717105","https://openalex.org/W4372330430","https://openalex.org/W4381308335","https://openalex.org/W4385806991","https://openalex.org/W4387617009","https://openalex.org/W4388668567","https://openalex.org/W4388852108","https://openalex.org/W4389297375","https://openalex.org/W4392168327","https://openalex.org/W4394890631","https://openalex.org/W4399761055","https://openalex.org/W4399811086","https://openalex.org/W4404645076","https://openalex.org/W4405658563"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Molecular":[0],"property":[1,119],"prediction":[2,21,59,112,124],"with":[3,25,43,58,102],"limited":[4],"data":[5,82,156],"in":[6,30],"novel":[7],"chemical":[8,155],"domains":[9,147],"remains":[10],"challenging.":[11],"We":[12,50],"introduce":[13],"an":[14,31],"approach":[15,122],"based":[16],"on":[17,145],"the":[18],"hypothesis":[19],"that":[20],"difficulty":[22],"increases":[23],"systematically":[24],"distance":[26,110],"from":[27],"well-characterized":[28],"regions":[29],"appropriately":[32],"defined":[33],"structure\u2013property":[34,40,53],"space.":[35],"Our":[36],"framework":[37],"combines":[38],"nonlinear":[39],"space":[41],"embedding":[42,54],"distance-aware":[44,62],"domain":[45],"classification":[46,63],"and":[47,66,70,111,133,137,148,169],"uncertainty":[48,73,150],"quantification.":[49],"create":[51],"a":[52,115,130],"connecting":[55],"molecular":[56,77],"similarity":[57],"difficulty,":[60],"implement":[61],"balancing":[64],"precision":[65],"true":[67],"positive":[68],"rate,":[69],"provide":[71],"distance-based":[72],"estimates":[74,151],"scaled":[75],"by":[76,92,126],"similarity.":[78],"Across":[79],"four":[80],"ecotoxicity":[81],"sets,":[83],"our":[84,121],"local":[85],"models":[86],"reduced":[87,123],"root":[88],"mean":[89],"squared":[90],"error":[91,125],"28\u201348%":[93],"for":[94,152],"truly":[95],"in-domain":[96],"molecules":[97],"compared":[98,128],"to":[99,129],"global":[100,131],"models,":[101],"strong":[103],"correlations":[104],"(":[105],"r":[106],"=":[107],"0.40\u20130.62)":[108],"between":[109],"error.":[113],"In":[114],"biolubricant":[116],"base":[117],"oil":[118],"application,":[120],"29%":[127],"model":[132],"outperformed":[134],"transfer":[135],"learning":[136,140],"standard":[138],"machine":[139],"approaches.":[141],"This":[142],"framework\u2019s":[143],"focus":[144],"relevant":[146],"distance-calibrated":[149],"limited,":[153],"heterogeneous":[154],"makes":[157],"it":[158],"broadly":[159],"applicable":[160],"across":[161],"applications,":[162],"such":[163],"as":[164],"toxicity":[165],"prediction,":[166],"drug":[167],"discovery,":[168],"materials":[170],"design.":[171]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
