{"id":"https://openalex.org/W3199818698","doi":"https://doi.org/10.1109/tcbb.2021.3112598","title":"A Novel Method for Inferring Chemical Compounds With Prescribed Topological Substructures Based on Integer Programming","display_name":"A Novel Method for Inferring Chemical Compounds With Prescribed Topological Substructures Based on Integer Programming","publication_year":2021,"publication_date":"2021-09-14","ids":{"openalex":"https://openalex.org/W3199818698","doi":"https://doi.org/10.1109/tcbb.2021.3112598","mag":"3199818698","pmid":"https://pubmed.ncbi.nlm.nih.gov/34520360"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3112598","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3112598","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","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/A5038066385","display_name":"Jianshen Zhu","orcid":"https://orcid.org/0000-0002-1287-9572"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Jianshen Zhu","raw_affiliation_strings":["Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Kyoto, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069120004","display_name":"Naveed Ahmed Azam","orcid":"https://orcid.org/0000-0002-7941-3419"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Naveed Ahmed Azam","raw_affiliation_strings":["Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Kyoto, Japan"],"raw_orcid":"https://orcid.org/0000-0002-7941-3419","affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100403369","display_name":"Fan Zhang","orcid":"https://orcid.org/0000-0001-5391-2749"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Fan Zhang","raw_affiliation_strings":["Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Kyoto, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084691948","display_name":"Aleksandar Shurbevski","orcid":"https://orcid.org/0000-0001-9224-6929"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Aleksandar Shurbevski","raw_affiliation_strings":["Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Kyoto, Japan"],"raw_orcid":"https://orcid.org/0000-0001-9224-6929","affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073751548","display_name":"Kazuya Haraguchi","orcid":"https://orcid.org/0000-0002-2479-3135"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kazuya Haraguchi","raw_affiliation_strings":["Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Kyoto, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075053640","display_name":"Liang Zhao","orcid":"https://orcid.org/0000-0003-0869-7896"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Liang Zhao","raw_affiliation_strings":["Graduate School of Advanced Integrated Studies in Human Survivability (Shishu-Kan), Kyoto University, Kyoto, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Advanced Integrated Studies in Human Survivability (Shishu-Kan), Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073738140","display_name":"Hiroshi Nagamochi","orcid":"https://orcid.org/0000-0002-8332-1517"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroshi Nagamochi","raw_affiliation_strings":["Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Kyoto, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016330265","display_name":"Tatsuya Akutsu","orcid":null},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tatsuya Akutsu","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Japan"],"raw_orcid":"https://orcid.org/0000-0001-9763-797X","affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5038066385"],"corresponding_institution_ids":["https://openalex.org/I22299242"],"apc_list":null,"apc_paid":null,"fwci":0.757,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.76028685,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"19","issue":"6","first_page":"3233","last_page":"3245"},"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9710000157356262,"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"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9631999731063843,"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":0.5534831285476685},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.5525453686714172},{"id":"https://openalex.org/keywords/substructure","display_name":"Substructure","score":0.5146937966346741},{"id":"https://openalex.org/keywords/integer","display_name":"Integer (computer science)","score":0.4363633096218109},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.40053319931030273},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3588562607765198},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.3531268835067749},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2938545048236847},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.19513460993766785}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5534831285476685},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.5525453686714172},{"id":"https://openalex.org/C99679407","wikidata":"https://www.wikidata.org/wiki/Q56761637","display_name":"Substructure","level":2,"score":0.5146937966346741},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.4363633096218109},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.40053319931030273},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3588562607765198},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.3531268835067749},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2938545048236847},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.19513460993766785},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"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/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","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":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2021.3112598","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3112598","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34520360","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34520360","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7285770518","display_name":null,"funder_award_id":"#18H04113","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1982792699","https://openalex.org/W1992156271","https://openalex.org/W2017254234","https://openalex.org/W2032179189","https://openalex.org/W2133756602","https://openalex.org/W2267384021","https://openalex.org/W2529996553","https://openalex.org/W2549411284","https://openalex.org/W2578240541","https://openalex.org/W2592262780","https://openalex.org/W2763220183","https://openalex.org/W2802872171","https://openalex.org/W2806351858","https://openalex.org/W2963676163","https://openalex.org/W2994860160","https://openalex.org/W3016636888","https://openalex.org/W3023125360","https://openalex.org/W3024970380","https://openalex.org/W3027161112","https://openalex.org/W3080596191","https://openalex.org/W3083232557","https://openalex.org/W3092965201","https://openalex.org/W3097145107","https://openalex.org/W3192862300","https://openalex.org/W3194348808","https://openalex.org/W4288346884","https://openalex.org/W4297951436","https://openalex.org/W6733974131","https://openalex.org/W6771848067","https://openalex.org/W6776458850","https://openalex.org/W6784846323","https://openalex.org/W6800511363","https://openalex.org/W6840818090"],"related_works":["https://openalex.org/W3092057765","https://openalex.org/W1925942709","https://openalex.org/W1530057402","https://openalex.org/W2047683846","https://openalex.org/W303980170","https://openalex.org/W2351491280","https://openalex.org/W4300951706","https://openalex.org/W2086440213","https://openalex.org/W2589814023","https://openalex.org/W4226030601"],"abstract_inverted_index":{"Drug":[0],"discovery":[1],"is":[2,56,76,94],"one":[3],"of":[4,8,23,41,91,111,163,169,180],"the":[5,21,51,65,84,109,139,142,153,185],"major":[6],"goals":[7],"computational":[9,181],"biology":[10],"and":[11,32,45,87,124,165,172],"bioinformatics.":[12],"A":[13],"novel":[14],"framework":[15,154],"has":[16],"recently":[17],"been":[18,115],"proposed":[19,186],"for":[20],"design":[22],"chemical":[24,62,71,92,112,170,190],"graphs":[25,113,125,164,191],"using":[26,58],"both":[27],"artificial":[28],"neural":[29],"networks":[30],"(ANNs)":[31],"mixed":[33],"integer":[34],"linear":[35],"programming":[36],"(MILP).":[37],"This":[38],"method":[39,151],"consists":[40],"a":[42,69,73,89,97,127,147,160,166,175],"prediction":[43,48],"phase":[44],"an":[46,54,80],"inverse":[47],"phase.":[49],"In":[50,64],"first":[52],"phase,":[53,67],"ANN":[55,86],"trained":[57,85],"data":[59],"on":[60,141],"existing":[61],"compounds.":[63],"second":[66],"given":[68],"target":[70,176],"property,":[72],"feature":[74],"vector":[75],"inferred":[77],"by":[78,96,106],"solving":[79],"MILP":[81],"formulated":[82],"from":[83],"then":[88],"set":[90],"structures":[93],"enumerated":[95],"graph":[98],"enumeration":[99],"algorithm.":[100],"Although":[101],"exact":[102],"solutions":[103],"are":[104],"guaranteed":[105],"this":[107],"framework,":[108],"types":[110],"have":[114],"restricted":[116],"to":[117,135,152,174,195],"such":[118],"classes":[119],"as":[120],"trees,":[121],"monocyclic":[122],"graphs,":[123],"with":[126,131,192],"specified":[128],"polymer":[129],"topology":[130],"cycle":[132],"index":[133],"up":[134,194],"2.":[136],"To":[137],"overcome":[138],"limitation":[140],"topological":[143,161],"structure,":[144],"we":[145,157],"propose":[146],"new":[148],"flexible":[149],"modeling":[150],"so":[155],"that":[156,184],"can":[158,188],"specify":[159],"substructure":[162],"partial":[167],"assignment":[168],"elements":[171],"bond-multiplicity":[173],"graph.":[177],"The":[178],"results":[179],"experiments":[182],"suggest":[183],"system":[187],"infer":[189],"around":[193],"50":[196],"non-hydrogen":[197],"atoms.":[198]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}