{"id":"https://openalex.org/W4409652897","doi":"https://doi.org/10.1186/s13321-025-01003-6","title":"GESim: ultrafast graph-based molecular similarity calculation via von Neumann graph entropy","display_name":"GESim: ultrafast graph-based molecular similarity calculation via von Neumann graph entropy","publication_year":2025,"publication_date":"2025-04-22","ids":{"openalex":"https://openalex.org/W4409652897","doi":"https://doi.org/10.1186/s13321-025-01003-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/40264225"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01003-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01003-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01003-6","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/s13321-025-01003-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041427242","display_name":"Hiroaki Shiokawa","orcid":"https://orcid.org/0000-0002-8530-2651"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]},{"id":"https://openalex.org/I41802502","display_name":"Kanagawa University","ror":"https://ror.org/02j6c0d67","country_code":"JP","type":"education","lineage":["https://openalex.org/I41802502"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Hiroaki Shiokawa","raw_affiliation_strings":["Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan. shiokawa@cs.tsukuba.ac.jp","MolNavi LLC, #402 Wizard building 1-4-3 Sengen-cho Nishi-ku, Yokohama, Kanagawa, 220-0072, Japan. shiokawa@cs.tsukuba.ac.jp"],"affiliations":[{"raw_affiliation_string":"Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan. shiokawa@cs.tsukuba.ac.jp","institution_ids":["https://openalex.org/I146399215"]},{"raw_affiliation_string":"MolNavi LLC, #402 Wizard building 1-4-3 Sengen-cho Nishi-ku, Yokohama, Kanagawa, 220-0072, Japan. shiokawa@cs.tsukuba.ac.jp","institution_ids":["https://openalex.org/I41802502"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023231952","display_name":"Shoichi Ishida","orcid":"https://orcid.org/0000-0002-5638-3579"},"institutions":[{"id":"https://openalex.org/I164131854","display_name":"Yokohama University of Pharmacy","ror":"https://ror.org/05s0z8a66","country_code":"JP","type":"education","lineage":["https://openalex.org/I164131854"]},{"id":"https://openalex.org/I89630735","display_name":"Yokohama City University","ror":"https://ror.org/0135d1r83","country_code":"JP","type":"education","lineage":["https://openalex.org/I89630735"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Shoichi Ishida","raw_affiliation_strings":["Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. ishida.sho.nm@yokohama-cu.ac.jp","MolNavi LLC, #402 Wizard building 1-4-3 Sengen-cho Nishi-ku, Yokohama, Kanagawa, 220-0072, Japan. ishida.sho.nm@yokohama-cu.ac.jp"],"affiliations":[{"raw_affiliation_string":"Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. ishida.sho.nm@yokohama-cu.ac.jp","institution_ids":["https://openalex.org/I89630735"]},{"raw_affiliation_string":"MolNavi LLC, #402 Wizard building 1-4-3 Sengen-cho Nishi-ku, Yokohama, Kanagawa, 220-0072, Japan. ishida.sho.nm@yokohama-cu.ac.jp","institution_ids":["https://openalex.org/I164131854"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072608872","display_name":"Kei Terayama","orcid":"https://orcid.org/0000-0003-3914-248X"},"institutions":[{"id":"https://openalex.org/I2802180866","display_name":"Yokohama City University Medical Center","ror":"https://ror.org/03k95ve17","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I2802180866"]},{"id":"https://openalex.org/I860314941","display_name":"JGC (Japan)","ror":"https://ror.org/023s2h905","country_code":"JP","type":"company","lineage":["https://openalex.org/I860314941"]},{"id":"https://openalex.org/I89630735","display_name":"Yokohama City University","ror":"https://ror.org/0135d1r83","country_code":"JP","type":"education","lineage":["https://openalex.org/I89630735"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kei Terayama","raw_affiliation_strings":["Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. terayama@yokohama-cu.ac.jp","MolNavi LLC, #402 Wizard building 1-4-3 Sengen-cho Nishi-ku, Yokohama, Kanagawa, 220-0072, Japan. terayama@yokohama-cu.ac.jp"],"affiliations":[{"raw_affiliation_string":"Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. terayama@yokohama-cu.ac.jp","institution_ids":["https://openalex.org/I89630735","https://openalex.org/I2802180866"]},{"raw_affiliation_string":"MolNavi LLC, #402 Wizard building 1-4-3 Sengen-cho Nishi-ku, Yokohama, Kanagawa, 220-0072, Japan. terayama@yokohama-cu.ac.jp","institution_ids":["https://openalex.org/I860314941"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5041427242"],"corresponding_institution_ids":["https://openalex.org/I146399215","https://openalex.org/I41802502"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":2.8264,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.90360215,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"17","issue":"1","first_page":"57","last_page":"57"},"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":0.9987999796867371,"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":0.9929999709129333,"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/molecular-graph","display_name":"Molecular graph","score":0.7335841655731201},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.672179102897644},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.48351505398750305},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4830377995967865},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.45989683270454407},{"id":"https://openalex.org/keywords/von-neumann-entropy","display_name":"Von Neumann entropy","score":0.4208480715751648},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33710891008377075},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15730935335159302},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07298877835273743}],"concepts":[{"id":"https://openalex.org/C2780022179","wikidata":"https://www.wikidata.org/wiki/Q1986794","display_name":"Molecular graph","level":3,"score":0.7335841655731201},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.672179102897644},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.48351505398750305},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4830377995967865},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.45989683270454407},{"id":"https://openalex.org/C101973423","wikidata":"https://www.wikidata.org/wiki/Q6961323","display_name":"Von Neumann entropy","level":4,"score":0.4208480715751648},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33710891008377075},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15730935335159302},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07298877835273743},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C84114770","wikidata":"https://www.wikidata.org/wiki/Q46344","display_name":"Quantum","level":2,"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/C121040770","wikidata":"https://www.wikidata.org/wiki/Q215675","display_name":"Quantum entanglement","level":3,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-01003-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01003-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01003-6","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:40264225","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40264225","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:pubmedcentral.nih.gov:12013028","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12013028","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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:ad8399595dab45efa59f35813fb9be89","is_oa":true,"landing_page_url":"https://doaj.org/article/ad8399595dab45efa59f35813fb9be89","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 17, Iss 1, Pp 1-13 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-01003-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01003-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01003-6","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":[{"id":"https://openalex.org/G1096714137","display_name":"\u8a0e\u5e55\u601d\u60f3\u306e\u5f62\u6210\u904e\u7a0b\u306e\u7814\u7a76\u2015\u771f\u6728\u548c\u6cc9\u5b88\u306e\u5834\u5408\u2015","funder_award_id":"12102","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G122773906","display_name":"\u30b5\u30f3\u30d5\u30e9\u30f3\u30b7\u30b9\u30b3\u8b1b\u548c\u4f53\u5236\u306e\u5f62\u6210\u3068\u65e5\u672c\u306e\u56fd\u969b\u74b0\u5883","funder_award_id":"010111","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G12401395","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G1709759425","display_name":null,"funder_award_id":"JPMXP1020230120","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G2438688473","display_name":null,"funder_award_id":"JP23nk0101111","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G3291250701","display_name":null,"funder_award_id":"KAKENHI","funder_id":"https://openalex.org/F4320338111","funder_display_name":"Precursory Research for Embryonic Science and Technology"},{"id":"https://openalex.org/G4158682752","display_name":"\u5730\u57df\u958b\u767a\u306b\u8d77\u56e0\u3059\u308b\u6c34\u707d\u5bb3\u3068\u305d\u306e\u5236\u5fa1\u306b\u95a2\u3059\u308b\u57fa\u790e\u7684\u7814\u7a76","funder_award_id":"102023","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4170161455","display_name":null,"funder_award_id":"PRESTO","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4494870512","display_name":null,"funder_award_id":"JPMJPR2033","funder_id":"https://openalex.org/F4320338111","funder_display_name":"Precursory Research for Embryonic Science and Technology"},{"id":"https://openalex.org/G4883608640","display_name":null,"funder_award_id":"JP22ama121023","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G5321753864","display_name":null,"funder_award_id":"JP23nk0101111, JP22ama121023","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G5506242249","display_name":null,"funder_award_id":"22K17894","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5518604981","display_name":null,"funder_award_id":"PREST","funder_id":"https://openalex.org/F4320338111","funder_display_name":"Precursory Research for Embryonic Science and Technology"},{"id":"https://openalex.org/G6606258880","display_name":"\u4e0a\u6749\u85e9\u5211\u6cd5\u306e\u7814\u7a76","funder_award_id":"21023","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7148736649","display_name":null,"funder_award_id":"PRESTO","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G7482275571","display_name":null,"funder_award_id":"Ministry of Education, Culture, Sports, Science and Technology","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7752643416","display_name":null,"funder_award_id":"Japan","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7904330859","display_name":"\u5ddd\u5d0e\u5e02\u5468\u8fba\u306b\u304a\u3051\u308b\u5927\u6c17\u6c5a\u67d3\u306e\u7814\u7a76","funder_award_id":"23012","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8044579487","display_name":null,"funder_award_id":"Japan","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G948027561","display_name":null,"funder_award_id":"JPMJCR23U2, JPMJPR2033, JPMJFR232P, JPMJFR232U","funder_id":"https://openalex.org/F4320334789","funder_display_name":"Japan Science and Technology Agency"},{"id":"https://openalex.org/G975188225","display_name":null,"funder_award_id":"KAKENHI","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"}],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"},{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320334789","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19"},{"id":"https://openalex.org/F4320338111","display_name":"Precursory Research for Embryonic Science and Technology","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409652897.pdf","grobid_xml":"https://content.openalex.org/works/W4409652897.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1583837637","https://openalex.org/W1964513093","https://openalex.org/W1980090013","https://openalex.org/W1988037271","https://openalex.org/W2016979469","https://openalex.org/W2021748110","https://openalex.org/W2027065525","https://openalex.org/W2034306513","https://openalex.org/W2039749139","https://openalex.org/W2056899820","https://openalex.org/W2081266727","https://openalex.org/W2096541451","https://openalex.org/W2119512897","https://openalex.org/W2123583562","https://openalex.org/W2142799844","https://openalex.org/W2145546477","https://openalex.org/W2151697120","https://openalex.org/W2152618599","https://openalex.org/W2297764176","https://openalex.org/W2338678442","https://openalex.org/W2472085920","https://openalex.org/W2609826536","https://openalex.org/W2615384791","https://openalex.org/W2765831819","https://openalex.org/W2930082324","https://openalex.org/W2963728299","https://openalex.org/W2991279511","https://openalex.org/W3072176192","https://openalex.org/W3094640617","https://openalex.org/W3103148916","https://openalex.org/W3191852652","https://openalex.org/W3204360269","https://openalex.org/W4213070269","https://openalex.org/W4220699355","https://openalex.org/W4220701080","https://openalex.org/W4230962939","https://openalex.org/W4240773179","https://openalex.org/W4253863064","https://openalex.org/W4309908854","https://openalex.org/W4310273071","https://openalex.org/W4388455891","https://openalex.org/W4401024471"],"related_works":["https://openalex.org/W2140915619","https://openalex.org/W2069578873","https://openalex.org/W2963628562","https://openalex.org/W4394636362","https://openalex.org/W4301054890","https://openalex.org/W2376164644","https://openalex.org/W3102577252","https://openalex.org/W2001712202","https://openalex.org/W2013842271","https://openalex.org/W2808877228"],"abstract_inverted_index":{"Representing":[0],"molecules":[1],"as":[2,16,20,28,124],"graphs":[3],"is":[4,122],"a":[5],"natural":[6],"approach":[7],"for":[8,36,50,67,94],"capturing":[9],"their":[10,119],"structural":[11],"information,":[12],"with":[13],"atoms":[14],"depicted":[15],"nodes":[17],"and":[18,46,89],"bonds":[19],"edges.":[21],"Although":[22],"graph-based":[23,65],"similarity":[24,70,82,96],"calculation":[25],"approaches,":[26],"such":[27],"the":[29,72,101],"graph":[30,77],"edit":[31],"distance,":[32],"have":[33],"been":[34],"proposed":[35],"calculating":[37,68],"molecular":[38,69,81,87,95],"similarity,":[39],"these":[40],"approaches":[41],"are":[42],"nondeterministic":[43],"polynomial":[44],"(NP)-hard":[45],"thus":[47],"computationally":[48],"infeasible":[49],"routine":[51],"use,":[52],"unlike":[53],"fingerprint-based":[54],"methods.":[55],"To":[56],"address":[57],"this":[58],"limitation,":[59],"we":[60],"developed":[61],"GESim,":[62],"an":[63,125],"ultrafast":[64],"method":[66],"on":[71,128],"basis":[73],"of":[74],"von":[75],"Neumann":[76],"entropy.":[78],"GESim":[79,99,121],"enables":[80],"calculations":[83],"by":[84],"considering":[85],"entire":[86],"graphs,":[88],"evaluations":[90],"using":[91],"two":[92],"benchmarks":[93],"suggest":[97],"that":[98],"has":[100],"ability":[102],"to":[103,116],"differentiate":[104],"between":[105],"highly":[106],"similar":[107],"molecules,":[108],"even":[109],"in":[110],"cases":[111],"where":[112],"other":[113],"methods":[114],"fail":[115],"effectively":[117],"distinguish":[118],"similarity.":[120],"provided":[123],"open-source":[126],"package":[127],"GitHub":[129],"at":[130],"https://github.com/LazyShion/GESim":[131],".":[132]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
