{"id":"https://openalex.org/W3093834826","doi":"https://doi.org/10.1021/acs.jcim.0c00393","title":"Benchmark on Indexing Algorithms for Accelerating Molecular Similarity Search","display_name":"Benchmark on Indexing Algorithms for Accelerating Molecular Similarity Search","publication_year":2020,"publication_date":"2020-10-23","ids":{"openalex":"https://openalex.org/W3093834826","doi":"https://doi.org/10.1021/acs.jcim.0c00393","mag":"3093834826","pmid":"https://pubmed.ncbi.nlm.nih.gov/33095006"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c00393","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00393","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/A5055242074","display_name":"Chunjiang Zhu","orcid":"https://orcid.org/0000-0002-5227-3575"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chun Jiang Zhu","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States"],"raw_orcid":"https://orcid.org/0000-0002-5227-3575","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079583126","display_name":"Minghu Song","orcid":"https://orcid.org/0000-0003-0887-0767"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Minghu Song","raw_affiliation_strings":["Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, United States"],"raw_orcid":"https://orcid.org/0000-0003-0887-0767","affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, United States","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077976494","display_name":"Qinqing Liu","orcid":"https://orcid.org/0000-0003-2973-852X"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qinqing Liu","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029107626","display_name":"Chlo\u00e9 Becquey","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chlo\u00e9 Becquey","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051393532","display_name":"Jinbo Bi","orcid":"https://orcid.org/0000-0001-6996-4092"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jinbo Bi","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut 06269, United States","institution_ids":["https://openalex.org/I140172145"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5079583126"],"corresponding_institution_ids":["https://openalex.org/I140172145"],"apc_list":null,"apc_paid":null,"fwci":0.289,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.64152511,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"60","issue":"12","first_page":"6167","last_page":"6184"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9973000288009644,"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":0.9973000288009644,"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/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9955999851226807,"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"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9940000176429749,"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":0.8169453740119934},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.8156009316444397},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.8153342008590698},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7000970840454102},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5945186018943787},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5164006352424622},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5030516982078552},{"id":"https://openalex.org/keywords/nearest-neighbor-search","display_name":"Nearest neighbor search","score":0.4537990987300873},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4128819704055786},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4074726998806},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3781468868255615},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.36292093992233276},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22637265920639038},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1096494197845459}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8169453740119934},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.8156009316444397},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.8153342008590698},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7000970840454102},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5945186018943787},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5164006352424622},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5030516982078552},{"id":"https://openalex.org/C116738811","wikidata":"https://www.wikidata.org/wiki/Q608751","display_name":"Nearest neighbor search","level":2,"score":0.4537990987300873},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4128819704055786},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4074726998806},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3781468868255615},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.36292093992233276},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22637265920639038},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1096494197845459},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"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/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"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":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.0c00393","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00393","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:33095006","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33095006","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":[{"display_name":"Industry, innovation and infrastructure","score":0.5,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":65,"referenced_works":["https://openalex.org/W145388748","https://openalex.org/W1554174647","https://openalex.org/W1605923270","https://openalex.org/W1736726159","https://openalex.org/W1985067238","https://openalex.org/W1988037271","https://openalex.org/W1990451437","https://openalex.org/W1994529543","https://openalex.org/W2004106830","https://openalex.org/W2008999889","https://openalex.org/W2019538911","https://openalex.org/W2046441184","https://openalex.org/W2049644877","https://openalex.org/W2050576295","https://openalex.org/W2071541305","https://openalex.org/W2086179657","https://openalex.org/W2087134511","https://openalex.org/W2092276439","https://openalex.org/W2096635897","https://openalex.org/W2097921974","https://openalex.org/W2101234009","https://openalex.org/W2110026675","https://openalex.org/W2116013009","https://openalex.org/W2118353525","https://openalex.org/W2123256336","https://openalex.org/W2123838366","https://openalex.org/W2132069633","https://openalex.org/W2146592462","https://openalex.org/W2147717514","https://openalex.org/W2148781362","https://openalex.org/W2153168552","https://openalex.org/W2157133710","https://openalex.org/W2176720124","https://openalex.org/W2200017991","https://openalex.org/W2296335794","https://openalex.org/W2412446857","https://openalex.org/W2472085920","https://openalex.org/W2523268797","https://openalex.org/W2593864460","https://openalex.org/W2612836460","https://openalex.org/W2613409207","https://openalex.org/W2735218636","https://openalex.org/W2757662681","https://openalex.org/W2838874902","https://openalex.org/W2895805257","https://openalex.org/W2899837977","https://openalex.org/W2900090807","https://openalex.org/W2900694120","https://openalex.org/W2903425689","https://openalex.org/W2905012389","https://openalex.org/W2937935913","https://openalex.org/W2949985202","https://openalex.org/W2951624434","https://openalex.org/W2953128081","https://openalex.org/W2963469388","https://openalex.org/W2979013754","https://openalex.org/W2991756646","https://openalex.org/W2994270865","https://openalex.org/W2998589874","https://openalex.org/W3003257820","https://openalex.org/W3004954215","https://openalex.org/W3035302862","https://openalex.org/W3103145119","https://openalex.org/W4242599275","https://openalex.org/W4243209889"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W1949910768","https://openalex.org/W1480566255","https://openalex.org/W2254397067","https://openalex.org/W2013685631","https://openalex.org/W1882921205"],"abstract_inverted_index":{"Structurally":[0],"similar":[1],"analogues":[2],"of":[3,30,65,113,129,229],"given":[4],"query":[5],"compounds":[6],"can":[7,44,234],"be":[8,36,53,235],"rapidly":[9],"retrieved":[10],"from":[11,237],"chemical":[12],"databases":[13],"by":[14],"the":[15,21,26,40,48,63,82,111,124,136,167,176,180,207,217,230],"molecular":[16,57,125],"similarity":[17,28,58,67,84,126],"search":[18,29,49,59,85],"approaches.":[19],"However,":[20],"computational":[22,102,115],"cost":[23],"associated":[24],"with":[25],"exhaustive":[27],"a":[31,120,159],"large":[32],"compound":[33],"database":[34],"will":[35],"quite":[37],"high.":[38],"Although":[39],"latest":[41],"indexing":[42,89,132,193],"algorithms":[43],"greatly":[45],"speed":[46],"up":[47],"process,":[50],"they":[51],"cannot":[52],"readily":[54],"applicable":[55],"to":[56,62,80,104,109,122,189],"problems":[60],"due":[61],"lack":[64],"Tanimoto":[66,83],"metric":[68],"implementation.":[69],"In":[70],"this":[71],"paper,":[72],"we":[73,118],"first":[74],"implement":[75],"Python":[76],"or":[77,179],"C++":[78],"codes":[79],"enable":[81],"via":[86],"several":[87],"recent":[88,131],"algorithms,":[90,194],"such":[91,210],"as":[92,211],"Hnsw":[93,212],"and":[94,153,172,198,213,223],"Onng.":[95],"Moreover,":[96],"there":[97],"are":[98,144,187],"increasing":[99],"interests":[100],"in":[101],"communities":[103],"develop":[105],"robust":[106],"benchmarking":[107,185,195],"systems":[108,233],"access":[110],"performance":[112,128],"various":[114],"algorithms.":[116,133],"Here,":[117],"provide":[119],"benchmark":[121,232],"evaluate":[123],"searching":[127,221,224],"these":[130],"To":[134],"avoid":[135],"potential":[137],"package":[138],"dependency":[139],"issues,":[140],"two":[141],"separate":[142],"benchmarks":[143],"built":[145],"based":[146],"on":[147],"currently":[148],"popular":[149],"container":[150,157,162],"technologies,":[151],"Docker":[152],"Singularity.":[154],"The":[155,226],"Singularity":[156],"is":[158],"rather":[160],"new":[161,192],"framework":[163],"specifically":[164],"designed":[165],"for":[166],"high-performance":[168],"computing":[169],"(HPC)":[170],"platform":[171],"does":[173],"not":[174],"need":[175],"privileged":[177],"permissions":[178],"separated":[181],"daemon":[182],"process.":[183],"Both":[184],"methods":[186],"extensible":[188],"incorporate":[190],"other":[191],"data":[196],"sets,":[197],"different":[199],"customized":[200],"parameter":[201],"settings.":[202],"Our":[203],"results":[204],"demonstrate":[205],"that":[206],"graph-based":[208],"methods,":[209],"Onng,":[214],"consistently":[215],"achieve":[216],"best":[218],"trade-off":[219],"between":[220],"effectiveness":[222],"efficiencies.":[225],"source":[227],"code":[228],"entire":[231],"downloaded":[236],"https://github.uconn.edu/mldrugdiscovery/MssBenchmark.":[238]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
