{"id":"https://openalex.org/W4408842983","doi":"https://doi.org/10.1186/s13321-025-00966-w","title":"A unified approach to inferring chemical compounds with the desired aqueous solubility","display_name":"A unified approach to inferring chemical compounds with the desired aqueous solubility","publication_year":2025,"publication_date":"2025-03-26","ids":{"openalex":"https://openalex.org/W4408842983","doi":"https://doi.org/10.1186/s13321-025-00966-w","pmid":"https://pubmed.ncbi.nlm.nih.gov/40140978"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-00966-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00966-w","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00966-w","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/s13321-025-00966-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Muniba Batool","orcid":null},"institutions":[{"id":"https://openalex.org/I12469534","display_name":"Quaid-i-Azam University","ror":"https://ror.org/04s9hft57","country_code":"PK","type":"education","lineage":["https://openalex.org/I12469534"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Muniba Batool","raw_affiliation_strings":["Discrete Mathematics and Computational Intelligence Laboratory, Department of Mathematics, Quaid-i-Azam University, Islamabad, Pakistan","Discrete Mathematics and Computational Intelligence Laboratory, Department of Mathematics,  Quaid-i-Azam University, \nIslamabad, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Discrete Mathematics and Computational Intelligence Laboratory, Department of Mathematics, Quaid-i-Azam University, Islamabad, Pakistan","institution_ids":["https://openalex.org/I12469534"]},{"raw_affiliation_string":"Discrete Mathematics and Computational Intelligence Laboratory, Department of Mathematics,  Quaid-i-Azam University, \nIslamabad, Pakistan","institution_ids":["https://openalex.org/I12469534"]}]},{"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/I12469534","display_name":"Quaid-i-Azam University","ror":"https://ror.org/04s9hft57","country_code":"PK","type":"education","lineage":["https://openalex.org/I12469534"]}],"countries":["PK"],"is_corresponding":true,"raw_author_name":"Naveed Ahmed Azam","raw_affiliation_strings":["Discrete Mathematics and Computational Intelligence Laboratory, Department of Mathematics, Quaid-i-Azam University, Islamabad, Pakistan. naveedazam@qau.edu.pk","Discrete Mathematics and Computational Intelligence Laboratory, Department of Mathematics,  Quaid-i-Azam University, \nIslamabad, Pakistan"],"raw_orcid":"https://orcid.org/0000-0002-7941-3419","affiliations":[{"raw_affiliation_string":"Discrete Mathematics and Computational Intelligence Laboratory, Department of Mathematics, Quaid-i-Azam University, Islamabad, Pakistan. naveedazam@qau.edu.pk","institution_ids":["https://openalex.org/I12469534"]},{"raw_affiliation_string":"Discrete Mathematics and Computational Intelligence Laboratory, Department of Mathematics,  Quaid-i-Azam University, \nIslamabad, Pakistan","institution_ids":["https://openalex.org/I12469534"]}]},{"author_position":"middle","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":false,"raw_author_name":"Jianshen Zhu","raw_affiliation_strings":["Discrete Mathematics Laboratory, Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, 606-8501, Kyoto, Japan"],"raw_orcid":"https://orcid.org/0000-0002-1287-9572","affiliations":[{"raw_affiliation_string":"Discrete Mathematics Laboratory, Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, 606-8501, 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":["Discrete Mathematics Laboratory, Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, 606-8501, Kyoto, Japan"],"raw_orcid":"https://orcid.org/0000-0002-2479-3135","affiliations":[{"raw_affiliation_string":"Discrete Mathematics Laboratory, Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, 606-8501, 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, 606-8306, Kyoto, Japan"],"raw_orcid":"https://orcid.org/0000-0003-0869-7896","affiliations":[{"raw_affiliation_string":"Graduate School of Advanced Integrated Studies in Human Survivability (Shishu-Kan), Kyoto University, 606-8306, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016330265","display_name":"Tatsuya Akutsu","orcid":"https://orcid.org/0000-0001-9763-797X"},"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, 611-0011, Uji, Japan"],"raw_orcid":"https://orcid.org/0000-0001-9763-797X","affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, 611-0011, Uji, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5069120004"],"corresponding_institution_ids":["https://openalex.org/I12469534"],"apc_list":{"value":2190,"currency":"USD","value_usd":2190},"apc_paid":{"value":2190,"currency":"USD","value_usd":2190},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.05883842,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"1","first_page":"37","last_page":"37"},"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":0.9972000122070312,"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":0.9620000123977661,"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":0.7155086398124695},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5599991083145142},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.49557673931121826},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.49384742975234985},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.4745693504810333},{"id":"https://openalex.org/keywords/regression","display_name":"Regression","score":0.46547931432724},{"id":"https://openalex.org/keywords/linear-regression","display_name":"Linear regression","score":0.44995787739753723},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4004679322242737},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38241350650787354},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3428192436695099},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.25999146699905396},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1907612681388855}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7155086398124695},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5599991083145142},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.49557673931121826},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.49384742975234985},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.4745693504810333},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.46547931432724},{"id":"https://openalex.org/C48921125","wikidata":"https://www.wikidata.org/wiki/Q10861030","display_name":"Linear regression","level":2,"score":0.44995787739753723},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4004679322242737},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38241350650787354},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3428192436695099},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.25999146699905396},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1907612681388855},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"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/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-00966-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00966-w","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00966-w","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:40140978","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40140978","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:doaj.org/article:33ed0e1ca87d4662a487b72b12144821","is_oa":true,"landing_page_url":"https://doaj.org/article/33ed0e1ca87d4662a487b72b12144821","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"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 17, Iss 1, Pp 1-15 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11938699","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11938699","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-00966-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00966-w","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00966-w","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/G2652498698","display_name":"Analysis and Control of Steady States of Multiple Biological Networks","funder_award_id":"22K19830","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6460038971","display_name":"Advanced Studies and Developments on Discrete Preimage Problems","funder_award_id":"22H00532","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":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4408842983.pdf"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W2009307057","https://openalex.org/W2041392558","https://openalex.org/W2120919910","https://openalex.org/W2123862598","https://openalex.org/W2135046866","https://openalex.org/W2146060259","https://openalex.org/W2267384021","https://openalex.org/W2502759836","https://openalex.org/W2754233385","https://openalex.org/W2937726486","https://openalex.org/W3018495986","https://openalex.org/W3098530784","https://openalex.org/W3133969611","https://openalex.org/W3135980175","https://openalex.org/W3164427032","https://openalex.org/W3194348808","https://openalex.org/W4214817272","https://openalex.org/W4214885680","https://openalex.org/W4220785481","https://openalex.org/W4226189398","https://openalex.org/W4308548134","https://openalex.org/W4319662043","https://openalex.org/W4323294421","https://openalex.org/W4367553744","https://openalex.org/W4387740953","https://openalex.org/W4401747077"],"related_works":["https://openalex.org/W2382521049","https://openalex.org/W1585007175","https://openalex.org/W2144385241","https://openalex.org/W4300101996","https://openalex.org/W2165950148","https://openalex.org/W31220157","https://openalex.org/W2288557197","https://openalex.org/W4233024177","https://openalex.org/W2101914902","https://openalex.org/W3174613421"],"abstract_inverted_index":{"Aqueous":[0],"solubility":[1],"(AS)":[2],"is":[3,178],"a":[4,10,21,55,116,126,142],"key":[5],"physiochemical":[6],"property":[7],"that":[8,161],"plays":[9],"crucial":[11],"role":[12],"in":[13,78,115],"drug":[14],"discovery":[15],"and":[16,27,45,91,100,109,134,156,165],"material":[17],"design.":[18],"We":[19],"report":[20],"novel":[22],"unified":[23],"approach":[24,177],"to":[25,65,72,111,141,168],"predict":[26],"infer":[28],"chemical":[29,154],"compounds":[30,102],"with":[31,103],"the":[32,60,73,79,104,130,135,175],"desired":[33,105],"AS":[34,136,147],"based":[35,53],"on":[36,54,150],"simple":[37,131],"deterministic":[38],"graph-theoretic":[39,132],"descriptors,":[40],"multiple":[41],"linear":[42,48],"regression":[43,62],"(MLR),":[44],"mixed":[46],"integer":[47],"programming":[49],"(MILP).":[50],"Selected":[51],"descriptors":[52,90,133,155],"forward":[56],"stepwise":[57],"procedure":[58],"enabled":[59],"simplest":[61],"model,":[63],"MLR,":[64],"achieve":[66],"significantly":[67],"good":[68],"prediction":[69],"accuracy":[70,77],"compared":[71],"existing":[74],"approaches,":[75],"achieving":[76],"range":[80,119],"[0.7191,":[81],"0.9377]":[82],"for":[83,170],"29":[84],"diverse":[85],"datasets.":[86],"By":[87],"simulating":[88],"these":[89],"learning":[92,159],"models":[93,160],"as":[94],"MILPs,":[95],"we":[96],"inferred":[97],"mathematically":[98],"exact":[99],"optimal":[101],"AS,":[106],"prescribed":[107],"structures,":[108],"up":[110],"50":[112],"non-hydrogen":[113],"atoms":[114],"reasonable":[117],"time":[118],"[6,":[120],"1166]":[121],"seconds.":[122],"These":[123],"findings":[124],"indicate":[125],"strong":[127],"correlation":[128],"between":[129],"of":[137,145,174],"compounds,":[138],"potentially":[139],"leading":[140],"deeper":[143],"understanding":[144],"their":[146],"without":[148],"relying":[149],"widely":[151],"used":[152],"complicated":[153],"complex":[157],"machine":[158],"are":[162],"computationally":[163],"expensive,":[164],"therefore":[166],"difficult":[167],"use":[169],"inference.":[171],"An":[172],"implementation":[173],"proposed":[176],"available":[179],"at":[180],"https://github.com/ku-dml/mol-infer/tree/master/AqSol":[181],".":[182]},"counts_by_year":[],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
