{"id":"https://openalex.org/W2049237203","doi":"https://doi.org/10.1021/ci400403w","title":"Atom Environment Kernels on Molecules","display_name":"Atom Environment Kernels on Molecules","publication_year":2014,"publication_date":"2014-05-06","ids":{"openalex":"https://openalex.org/W2049237203","doi":"https://doi.org/10.1021/ci400403w","mag":"2049237203","pmid":"https://pubmed.ncbi.nlm.nih.gov/24802375"},"language":"en","primary_location":{"id":"doi:10.1021/ci400403w","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci400403w","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/A5055876250","display_name":"Hiroshi Yamashita","orcid":"https://orcid.org/0000-0002-6731-7673"},"institutions":[{"id":"https://openalex.org/I200475212","display_name":"The Graduate University for Advanced Studies, SOKENDAI","ror":"https://ror.org/0516ah480","country_code":"JP","type":"education","lineage":["https://openalex.org/I200475212"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Hiroshi Yamashita","raw_affiliation_strings":["The Graduate University for Advanced Studies, 10-3 Midori-cho, Tachikawa,\rTokyo 190-8562, Japan","The Graduate University for Advanced Studies , 10-3 Midori-cho, Tachikawa, Tokyo 190-8562, Japan"],"affiliations":[{"raw_affiliation_string":"The Graduate University for Advanced Studies, 10-3 Midori-cho, Tachikawa,\rTokyo 190-8562, Japan","institution_ids":["https://openalex.org/I200475212"]},{"raw_affiliation_string":"The Graduate University for Advanced Studies , 10-3 Midori-cho, Tachikawa, Tokyo 190-8562, Japan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062020503","display_name":"Tomoyuki Higuchi","orcid":"https://orcid.org/0000-0003-3021-3173"},"institutions":[{"id":"https://openalex.org/I4210134673","display_name":"The Institute of Statistical Mathematics","ror":"https://ror.org/03jcejr58","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210134673","https://openalex.org/I4210158934"]},{"id":"https://openalex.org/I200475212","display_name":"The Graduate University for Advanced Studies, SOKENDAI","ror":"https://ror.org/0516ah480","country_code":"JP","type":"education","lineage":["https://openalex.org/I200475212"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tomoyuki Higuchi","raw_affiliation_strings":["The Graduate University for Advanced Studies, 10-3 Midori-cho, Tachikawa,\rTokyo 190-8562, Japan","The Institute of Statistical Mathematics, 10-3 Midori-cho, Tachikawa, Tokyo 190-8562, Japan","The Graduate University for Advanced Studies, 10-3 Midori-cho, Tachikawa,#R#Tokyo 190-8562, Japan"],"affiliations":[{"raw_affiliation_string":"The Graduate University for Advanced Studies, 10-3 Midori-cho, Tachikawa,\rTokyo 190-8562, Japan","institution_ids":["https://openalex.org/I200475212"]},{"raw_affiliation_string":"The Institute of Statistical Mathematics, 10-3 Midori-cho, Tachikawa, Tokyo 190-8562, Japan","institution_ids":["https://openalex.org/I4210134673"]},{"raw_affiliation_string":"The Graduate University for Advanced Studies, 10-3 Midori-cho, Tachikawa,#R#Tokyo 190-8562, Japan","institution_ids":["https://openalex.org/I200475212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031629643","display_name":"Ryo Yoshida","orcid":"https://orcid.org/0000-0001-8092-0162"},"institutions":[{"id":"https://openalex.org/I4210134673","display_name":"The Institute of Statistical Mathematics","ror":"https://ror.org/03jcejr58","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210134673","https://openalex.org/I4210158934"]},{"id":"https://openalex.org/I4210086780","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19","country_code":"JP","type":"government","lineage":["https://openalex.org/I4210086780"]},{"id":"https://openalex.org/I200475212","display_name":"The Graduate University for Advanced Studies, SOKENDAI","ror":"https://ror.org/0516ah480","country_code":"JP","type":"education","lineage":["https://openalex.org/I200475212"]},{"id":"https://openalex.org/I46980622","display_name":"Kyoto Seika University","ror":"https://ror.org/05g4f0342","country_code":"JP","type":"education","lineage":["https://openalex.org/I46980622"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ryo Yoshida","raw_affiliation_strings":["JST CREST, 10-3 Midori-cho, Tachikawa,\rTokyo 190-8562, Japan","JST ERATO, 2-2-2 Hikaridai, Seika-cho,\rSoraku-gun, Kyoto 619-0288, Japan","The Graduate University for Advanced Studies, 10-3 Midori-cho, Tachikawa,\rTokyo 190-8562, Japan","The Institute of Statistical Mathematics, 10-3 Midori-cho, Tachikawa, Tokyo 190-8562, Japan","The Graduate University for Advanced Studies, 10-3 Midori-cho, Tachikawa,#R#Tokyo 190-8562, Japan"],"affiliations":[{"raw_affiliation_string":"JST CREST, 10-3 Midori-cho, Tachikawa,\rTokyo 190-8562, Japan","institution_ids":["https://openalex.org/I4210086780"]},{"raw_affiliation_string":"JST ERATO, 2-2-2 Hikaridai, Seika-cho,\rSoraku-gun, Kyoto 619-0288, Japan","institution_ids":["https://openalex.org/I46980622"]},{"raw_affiliation_string":"The Graduate University for Advanced Studies, 10-3 Midori-cho, Tachikawa,\rTokyo 190-8562, Japan","institution_ids":["https://openalex.org/I200475212"]},{"raw_affiliation_string":"The Institute of Statistical Mathematics, 10-3 Midori-cho, Tachikawa, Tokyo 190-8562, Japan","institution_ids":["https://openalex.org/I4210134673"]},{"raw_affiliation_string":"The Graduate University for Advanced Studies, 10-3 Midori-cho, Tachikawa,#R#Tokyo 190-8562, Japan","institution_ids":["https://openalex.org/I200475212"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5055876250"],"corresponding_institution_ids":["https://openalex.org/I200475212"],"apc_list":null,"apc_paid":null,"fwci":1.0682,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.77700529,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"54","issue":"5","first_page":"1289","last_page":"1300"},"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":0.9947999715805054,"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":0.9879000186920166,"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":0.654711902141571},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.626198947429657},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.5984370708465576},{"id":"https://openalex.org/keywords/graph-kernel","display_name":"Graph kernel","score":0.597160816192627},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5508142709732056},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5466868877410889},{"id":"https://openalex.org/keywords/kernel-method","display_name":"Kernel method","score":0.45036742091178894},{"id":"https://openalex.org/keywords/extension","display_name":"Extension (predicate logic)","score":0.43557021021842957},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4337659478187561},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.43126603960990906},{"id":"https://openalex.org/keywords/tree-kernel","display_name":"Tree kernel","score":0.4198117256164551},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32433781027793884},{"id":"https://openalex.org/keywords/polynomial-kernel","display_name":"Polynomial kernel","score":0.29711413383483887},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.28128141164779663},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.26770421862602234},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.17893683910369873},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.0917932391166687}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.654711902141571},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.626198947429657},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.5984370708465576},{"id":"https://openalex.org/C100595998","wikidata":"https://www.wikidata.org/wiki/Q11731931","display_name":"Graph kernel","level":5,"score":0.597160816192627},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5508142709732056},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5466868877410889},{"id":"https://openalex.org/C122280245","wikidata":"https://www.wikidata.org/wiki/Q620622","display_name":"Kernel method","level":3,"score":0.45036742091178894},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.43557021021842957},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4337659478187561},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.43126603960990906},{"id":"https://openalex.org/C140417398","wikidata":"https://www.wikidata.org/wiki/Q16933942","display_name":"Tree kernel","level":5,"score":0.4198117256164551},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32433781027793884},{"id":"https://openalex.org/C160446489","wikidata":"https://www.wikidata.org/wiki/Q7226642","display_name":"Polynomial kernel","level":4,"score":0.29711413383483887},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.28128141164779663},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.26770421862602234},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.17893683910369873},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0917932391166687},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci400403w","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci400403w","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:24802375","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24802375","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":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W179694669","https://openalex.org/W1487233798","https://openalex.org/W1510073064","https://openalex.org/W1576213419","https://openalex.org/W1605923270","https://openalex.org/W1968414728","https://openalex.org/W1988037271","https://openalex.org/W1989451208","https://openalex.org/W1996824494","https://openalex.org/W2017091502","https://openalex.org/W2017398555","https://openalex.org/W2026265322","https://openalex.org/W2026625220","https://openalex.org/W2035366345","https://openalex.org/W2039472955","https://openalex.org/W2040389962","https://openalex.org/W2044834685","https://openalex.org/W2049334526","https://openalex.org/W2070505319","https://openalex.org/W2081301924","https://openalex.org/W2098930828","https://openalex.org/W2127689830","https://openalex.org/W2129893339","https://openalex.org/W2136507529","https://openalex.org/W2147286743","https://openalex.org/W2153635508","https://openalex.org/W2154904274","https://openalex.org/W2161616234","https://openalex.org/W2221103459","https://openalex.org/W2560674852","https://openalex.org/W2606092111","https://openalex.org/W2903296288","https://openalex.org/W4213151958"],"related_works":["https://openalex.org/W2089892314","https://openalex.org/W1983263273","https://openalex.org/W2179275589","https://openalex.org/W2096302783","https://openalex.org/W2974741803","https://openalex.org/W1558903433","https://openalex.org/W2189183545","https://openalex.org/W2170018389","https://openalex.org/W2121506664","https://openalex.org/W2093878082"],"abstract_inverted_index":{"The":[0,99],"measurement":[1],"of":[2,9,34,61,88,156,161],"molecular":[3,39,165],"similarity":[4,21],"is":[5,52,141],"an":[6,86,103,127],"essential":[7],"part":[8],"various":[10],"machine":[11],"learning":[12],"tasks":[13,155],"in":[14,37,54],"chemical":[15],"informatics.":[16],"Graph":[17],"kernels":[18,27],"provide":[19],"good":[20],"measures":[22],"between":[23,106,111],"molecules.":[24],"Conventional":[25],"graph":[26,83],"are":[28,149],"based":[29],"on":[30],"counting":[31,56],"common":[32],"subgraphs":[33,63,107],"specific":[35],"types":[36],"the":[38,55,62,76,89,119,135,138],"graphs.":[40],"This":[41],"approach":[42],"has":[43],"two":[44],"primary":[45],"limitations:":[46],"(i)":[47],"only":[48],"exact":[49],"subgraph":[50,132],"matching":[51,110],"considered":[53],"operation,":[57],"and":[58,96,153],"(ii)":[59],"most":[60],"will":[64],"be":[65],"less":[66],"relevant":[67],"to":[68,74,125,130,134,137],"a":[69,81,123,144,158],"given":[70],"task.":[71],"In":[72,117],"order":[73],"address":[75],"above-mentioned":[77],"limitations,":[78],"we":[79],"propose":[80],"new":[82],"kernel":[84,91,101,121],"as":[85],"extension":[87],"subtree":[90],"initially":[92],"proposed":[93,100,120],"by":[94,108,143],"Ramon":[95],"G\u00e4rtner":[97],"(2003).":[98],"tolerates":[102],"inexact":[104],"match":[105],"allowing":[109],"atoms":[112],"with":[113,167],"similar":[114],"local":[115],"environments.":[116],"addition,":[118],"provides":[122],"method":[124],"assign":[126],"importance":[128],"weight":[129],"each":[131],"according":[133],"relevance":[136],"task,":[139],"which":[140],"predetermined":[142],"statistical":[145],"test.":[146],"These":[147],"extensions":[148],"evaluated":[150],"for":[151],"classification":[152],"regression":[154],"predicting":[157],"wide":[159],"range":[160],"pharmaceutical":[162],"properties":[163],"from":[164],"structures,":[166],"promising":[168],"results.":[169]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
