{"id":"https://openalex.org/W2161005172","doi":"https://doi.org/10.1186/1758-2946-3-s1-o8","title":"Graph kernels for chemoinformatics \u2013 a critical discussion","display_name":"Graph kernels for chemoinformatics \u2013 a critical discussion","publication_year":2011,"publication_date":"2011-04-19","ids":{"openalex":"https://openalex.org/W2161005172","doi":"https://doi.org/10.1186/1758-2946-3-s1-o8","mag":"2161005172"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-3-s1-o8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-o8","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-O8","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"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-O8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020780798","display_name":"Matthias Rupp","orcid":"https://orcid.org/0000-0002-2934-2958"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Matthias Rupp","raw_affiliation_strings":["Helmholtz Zentrum M\u00fcnchen, Deutsches Forschungszentrum f\u00fcr Umwelt & Gesundheit, Ingolst\u00e4dter Landstr. 1, 85764, Neuherberg, Germany"],"affiliations":[{"raw_affiliation_string":"Helmholtz Zentrum M\u00fcnchen, Deutsches Forschungszentrum f\u00fcr Umwelt & Gesundheit, Ingolst\u00e4dter Landstr. 1, 85764, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5020780798"],"corresponding_institution_ids":["https://openalex.org/I3018134672"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.3255,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.64013267,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"3","issue":"S1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9955000281333923,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.9782000184059143,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.8197964429855347},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6688622832298279},{"id":"https://openalex.org/keywords/graph-kernel","display_name":"Graph kernel","score":0.6126030087471008},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.47516340017318726},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.45529818534851074},{"id":"https://openalex.org/keywords/kernel-method","display_name":"Kernel method","score":0.3049752116203308},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2788969576358795},{"id":"https://openalex.org/keywords/polynomial-kernel","display_name":"Polynomial kernel","score":0.20242366194725037},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.14171037077903748},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.12889710068702698}],"concepts":[{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.8197964429855347},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6688622832298279},{"id":"https://openalex.org/C100595998","wikidata":"https://www.wikidata.org/wiki/Q11731931","display_name":"Graph kernel","level":5,"score":0.6126030087471008},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.47516340017318726},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.45529818534851074},{"id":"https://openalex.org/C122280245","wikidata":"https://www.wikidata.org/wiki/Q620622","display_name":"Kernel method","level":3,"score":0.3049752116203308},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2788969576358795},{"id":"https://openalex.org/C160446489","wikidata":"https://www.wikidata.org/wiki/Q7226642","display_name":"Polynomial kernel","level":4,"score":0.20242366194725037},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.14171037077903748},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.12889710068702698},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-3-s1-o8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-o8","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-O8","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":"pmh:oai:doaj.org/article:05c458e31a114650a155c474e90d92e7","is_oa":true,"landing_page_url":"https://doaj.org/article/05c458e31a114650a155c474e90d92e7","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-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 3, Iss Suppl 1, p O8 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2091941","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3083561","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-3-s1-o8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-o8","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-O8","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":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2161005172.pdf","grobid_xml":"https://content.openalex.org/works/W2161005172.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1592371672","https://openalex.org/W1963645901","https://openalex.org/W2043964180","https://openalex.org/W2097745317","https://openalex.org/W2118143246","https://openalex.org/W2168029744","https://openalex.org/W3101749733"],"related_works":["https://openalex.org/W2118143246","https://openalex.org/W2058413069","https://openalex.org/W942849820","https://openalex.org/W2492149513","https://openalex.org/W1580611036","https://openalex.org/W1592261055","https://openalex.org/W4290802792","https://openalex.org/W2078320823","https://openalex.org/W2043334680","https://openalex.org/W4285213554"],"abstract_inverted_index":{"We":[0],"analyze":[1],"the":[2,59,65,89,110,145,206,250,261,273,282],"use,":[3],"advantages,":[4],"and":[5,43,75,99,119,136,173,193,209,236,292],"drawbacks":[6],"of":[7,15,25,67,86,113,131,147,249,263,269,272,284],"graph":[8,46,70,226],"kernels":[9,47,54,150,227],"in":[10,33,39,129,144,205],"chemoin-formatics,":[11],"including":[12],"a":[13,50,95,216,237],"comparison":[14,262],"kernel-based":[16],"approaches":[17],"with":[18,79],"other":[19],"methodology,":[20],"as":[21,23,107,109,117],"well":[22,108],"examples":[24],"applications.\r\n\r\nKernel-based":[26],"machine":[27],"learning":[28,81],"[1],":[29],"now":[30],"widely":[31],"applied":[32],"chemoinformatics,":[34],"delivers":[35],"state-of-the-art":[36],"performance":[37],"[2]":[38],"tasks":[40],"like":[41],"classification":[42],"regression.":[44],"Molecular":[45,175],"[3]":[48,151],"are":[49,55,126,139,152,164,188,197,223,228,231],"recent":[51],"development":[52],"where":[53],"defined":[56,156],"directly":[57,157],"on":[58,158,166],"molecular":[60,293],"structure":[61,73,176,234,265],"graph.":[62],"This":[63],"allows":[64,93],"adaptation":[66],"methods":[68],"from":[69],"theory":[71],"to":[72,133],"graphs":[74,177],"their":[76,210],"direct":[77,111],"use":[78,112],"kernel":[91],"algorithms.":[82],"The":[83,160,267],"main":[84],"advantage":[85],"learning,":[88],"so-called":[90],"trick,":[92],"for":[94,104,200,233,243,260],"systematic,":[96],"computationally":[97],"feasible,":[98],"often":[100,203],"globally":[101],"optimal":[102,171,253],"search":[103],"non-linear":[105],"patterns,":[106,170],"non-numerical":[114],"inputs":[115],"such":[116],"strings":[118],"graphs.":[120,159],"A":[121],"drawback":[122],"is":[123,213],"that":[124,138,181],"solutions":[125],"expressed":[127],"indirectly":[128],"terms":[130],"similarity":[132,252],"training":[134,148],"samples,":[135],"runtimes":[137],"typically":[140],"quadratic":[141],"or":[142],"cubic":[143],"number":[146],"samples.\r\n\r\nGraph":[149],"positive":[153],"semidefinite":[154],"functions":[155],"most":[161],"important":[162],"types":[163],"based":[165],"random":[167],"walks,":[168],"subgraph":[169],"assignments,":[172],"graphlets.":[174],"have":[178,190,239],"strong":[179],"properties":[180],"can":[182],"be":[183],"exploited":[184],"[4],":[185],"e.g.,":[186],"they":[187,222],"undirected,":[189],"no":[191,194],"self-loops":[192],"multiple":[195],"edges,":[196],"connected":[198],"(except":[199],"salts),":[201],"annotated,":[202],"planar":[204],"graph-theoretic":[207],"sense,":[208],"vertex":[211],"degree":[212],"bounded":[214],"by":[215],"small":[217,264],"constant.":[218],"In":[219],"many":[220],"applications,":[221],"small.":[224],"Many":[225],"general-purpose,":[229],"some":[230],"suitable":[232],"graphs,":[235],"few":[238],"been":[240],"explicitly":[241],"designed":[242,259],"them.\r\n\r\nWe":[244],"present":[245],"three":[246],"exemplary":[247],"applications":[248],"iterative":[251],"assignment":[254],"[5],":[256],"which":[257],"was":[258],"graphs:":[266],"discovery":[268],"novel":[270],"agonists":[271],"peroxisome":[274],"proliferator-activated":[275],"receptor":[276],"\u03b3":[277],"[6]":[278],"(ligand-based":[279],"virtual":[280],"screening),":[281],"estimation":[283],"acid":[285],"dissociation":[286],"constants":[287],"[7]":[288],"(quantitative":[289],"structure-property":[290],"relationships),":[291],"de":[294],"novo":[295],"design":[296],"[8].":[297]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2016-06-24T00:00:00"}
