{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T08:11:43Z","timestamp":1778919103016,"version":"3.51.4"},"reference-count":76,"publisher":"American Chemical Society (ACS)","issue":"9","license":[{"start":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T00:00:00Z","timestamp":1777075200000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP25ama121026"],"award-info":[{"award-number":["JP25ama121026"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP24H01760"],"award-info":[{"award-number":["JP24H01760"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP25H01574"],"award-info":[{"award-number":["JP25H01574"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2026,5,11]]},"DOI":"10.1021\/acs.jcim.6c00181","type":"journal-article","created":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T13:01:53Z","timestamp":1777122113000},"page":"5101-5111","source":"Crossref","is-referenced-by-count":0,"title":["A Transformer for Reaction-Aware Compound Explorations with GFlowNet in QSAR-Guided Molecular Design"],"prefix":"10.1021","volume":"66","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-6071-2755","authenticated-orcid":true,"given":"Shogo","family":"Nakamura","sequence":"first","affiliation":[{"name":"Department of Life Science and Technology","place":["Yokohama, Japan"]},{"name":"Institute of Science Tokyo","place":["Yokohama, Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3114-7895","authenticated-orcid":true,"given":"Nobuaki","family":"Yasuo","sequence":"additional","affiliation":[{"name":"Tokyo Tech Academy for Convergence of Materials and Informatics (TAC-MI)","place":["Tokyo, Japan"]},{"name":"Institute of Science Tokyo","place":["Tokyo, Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3806-9535","authenticated-orcid":true,"given":"Masakazu","family":"Sekijima","sequence":"additional","affiliation":[{"name":"Department of Computing","place":["Yokohama, Japan"]},{"name":"Institute of Science Tokyo","place":["Yokohama, Japan"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"316","published-online":{"date-parts":[[2026,4,25]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhealeco.2016.01.012"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2020.1166"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1021\/acsmedchemlett.2c00375"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1111\/j.1476-5381.2010.01127.x"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1038\/nrd1086"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1021\/acsomega.3c01314"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1038\/s42256-020-00236-4"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1021\/ci00057a005"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c01496"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1080\/14686996.2017.1401424"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1021\/acsomega.3c05430"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-024-00812-5"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.4c00759"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1021\/acscentsci.7b00572"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-018-0286-7"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-79682-4"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1021\/acscentsci.9b00576"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.2c01618"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.4c01107"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1038\/s43588-024-00737-x"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1039\/D4SC05894A"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.2c00177"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.4c00842"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-47011-2"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.4c01385"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1002\/anie.201814681"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1186\/1758-2946-1-8"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2023.102658"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1002\/anie.199104553"},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.1021\/acscentsci.7b00064"},{"key":"ref31\/cit31","doi-asserted-by":"publisher","DOI":"10.1021\/acssynbio.4c00091"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1608"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.4c00338"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1021\/co300096q"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2020.101681"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002380"},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1021\/jm030809x"},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-020-00429-4"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1038\/s42256-019-0067-7"},{"key":"ref40\/cit40","unstructured":"Gao, W.; Mercado, R.; Coley, C. W. In\n                      Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design\n                      , International Conference on Learning Representations; ICLR, 2022."},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1063\/5.0076749"},{"key":"ref42\/cit42","unstructured":"Noh, J.; Jeong, D.W.; Kim, K.; Han, S.; Lee, M.; Lee, H.; Jung, Y. In\n                      Path-Aware and Structure-Preserving Generation of Synthetically Accessible Molecules\n                      , Proceedings of the 39th International Conference on Machine Learning; ICML, 2022; pp 16952\u201316968."},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.4c01214"},{"key":"ref44\/cit44","unstructured":"Gottipati, S. K.; Sattarov, B.; Niu, S.; Pathak, Y.; Wei, H.; Liu, S.; Blackburn, S.; Thomas, K.; Coley, C.; Tang, J. In\n                      Learning to Navigate the Synthetically Accessible Chemical Space Using Reinforcement Learning\n                      , International Conference on Machine Learning; ICML, 2020; pp 3668\u20133679."},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.1021\/acsomega.0c04153"},{"key":"ref46\/cit46","unstructured":"Bengio, E.; Jain, M.; Korablyov, M.; Precup, D.; Bengio, Y. In\n                      Flow Network Based Generative Models for Non-Iterative Diverse Candidate Generation\n                      , Advances in Neural Information Processing Systems; NeurIPS, 2021; pp 27381\u201327394."},{"key":"ref47\/cit47","first-page":"1","volume":"24","author":"Bengio Y.","year":"2023","journal-title":"J. Mach. Learn. Res."},{"key":"ref48\/cit48","unstructured":"Zhu, Y.; Wu, J.; Hu, C.; Yan, J.; Hsieh, C.Y.; Hou, T.; Wu, J. In\n                      Sample-Efficient Multi-Objective Molecular Optimization with GFlowNets\n                      , Thirty-Seventh Conference on Neural Information Processing Systems; NIPS, 2023."},{"key":"ref49\/cit49","unstructured":"Kim, H.; Kim, M.; Choi, S.; Park, J. In\n                      Genetic-Guided GFlowNets for Sample Efficient Molecular Optimization\n                      , Thirty-Eighth Annual Conference on Neural Information Processing Systems; NIPS, 2024."},{"key":"ref50\/cit50","unstructured":"Jain, M.; Raparthy, S. C.; Hern\u00e1ndez-Garc\u00eda, A.; Rector-Brooks, J.; Bengio, Y.; Miret, S.; Bengio, E. Multi-Objective GFlowNets, 2023. https:\/\/openreview.net\/forum?id\/3z1Ws6GEYV4."},{"key":"ref51\/cit51","unstructured":"Shen, T.; Seo, S.; Lee, G.; Pandey, M.; Smith, J. R.; Cherkasov, A.; Kim, W. Y.; Ester, M. In\n                      TacoGFN: Target-Conditioned GFlowNet for Structure-Based Drug Design\n                      , Transactions on Machine Learning Research; MLR, 2024."},{"key":"ref52\/cit52","unstructured":"Koziarski, M.; Rekesh, A.; Shevchuk, D.; van der Sloot, A. M.; Gai\u0144ski, P.; Bengio, Y.; Liu, C.H.; Tyers, M.; Batey, R. A. In\n                      RGFN: Synthesizable Molecular Generation Using GFlowNets\n                      , Thirty-Eighth Annual Conference on Neural Information Processing Systems; NIPS, 2024."},{"key":"ref53\/cit53","unstructured":"Cretu, M.; Harris, C.; Roy, J.; Bengio, E.; Li\u00f2, P. In\n                      Synflownet: Towards Molecule Design with Guaranteed Synthesis Pathways\n                      , ICLR 2024 Workshop on Generative and Experimental Perspectives for Biomolecular Design; ICLR, 2024."},{"key":"ref54\/cit54","unstructured":"Seo, S.; Kim, M.; Shen, T.; Ester, M.; Park, J.; Ahn, S.; Kim, W. Y. In\n                      Generative Flows on Synthetic Pathway for Drug Design\n                      , Thirteenth International Conference on Learning Representations; ICLR, 2025."},{"key":"ref55\/cit55","unstructured":"Shen, T.; Seo, S.; Irwin, R.; Didi, K.; Olsson, S.; Kim, W. Y.; Ester, M. Compositional Flows for 3D Molecule and Synthesis Pathway Co-design, arXiv:2504.08051. arXiv.org e-Print archive, 2025 https:\/\/arxiv.org\/abs\/2504.08051."},{"key":"ref56\/cit56","unstructured":"Bradshaw, J.; Paige, B.; Kusner, M. J.; Segler, M.; Hern\u00e1ndez-Lobato, J. M. In\n                      A Model to Search for Synthesizable Molecules\n                      , Advances in Neural Information Processing Systems; NeurIPS, 2019; pp 12000\u201312010."},{"key":"ref57\/cit57","unstructured":"Bradshaw, J.; Paige, B.; Kusner, M. J.; Segler, M.; Hern\u00e1ndez-Lobato, J. M. In\n                      Barking Up the Right Tree: An Approach to Search over molecule Synthesis Dags\n                      , Advances in Neural Information Processing Systems; NeurIPS, 2020; pp 6852\u20136866."},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.1038\/s42004-025-01437-x"},{"key":"ref59\/cit59","doi-asserted-by":"publisher","DOI":"10.1038\/s42256-020-00284-w"},{"key":"ref60\/cit60","doi-asserted-by":"crossref","unstructured":"Akiba, T.; Sano, S.; Yanase, T.; Ohta, T.; Koyama, M. In\n                      Optuna: A Next-Generation Hyperparameter Optimization Framework\n                      , Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining; ACM, 2019; pp 2623\u20132631.","DOI":"10.1145\/3292500.3330701"},{"key":"ref61\/cit61","unstructured":"Lowe, D. Chemical reactions from U.S. patents (1976-Sep2016) 2017 https:\/\/figshare.com\/articles\/dataset\/Chemical_reactions_from_US_patents_1976-Sep2016_\/5104873."},{"key":"ref62\/cit62","unstructured":"Vaswani, A.; Shazeer, N.; Parmar, N.; Uszkoreit, J.; Jones, L.; Gomez, A. N.; Kaiser, \u0141.; Polosukhin, I. In\n                      Attention is All You Need\n                      , Advances in Neural Information Processing Systems; NeurIPS, 2017."},{"key":"ref63\/cit63","doi-asserted-by":"crossref","unstructured":"Malkin, N.; Jain, M.; Bengio, E.; Sun, C.; Bengio, Y. In\n                      Trajectory Balance: Improved Credit Assignment in GFlowNets\n                      , Advances in Neural Information Processing Systems; NeurIPS, 2022; pp 5955\u20135967.","DOI":"10.52202\/068431-0431"},{"key":"ref64\/cit64","unstructured":"Madan, K.; Rector-Brooks, J.; Korablyov, M.; Bengio, E.; Jain, M.; Nica, A. C.; Bosc, T.; Bengio, Y.; Malkin, N. In\n                      Learning GFlowNets from Partial Episodes for Improved Convergence and Stability\n                      , International Conference on Machine Learning; ICML, 2023; pp 23467\u201323483."},{"key":"ref65\/cit65","doi-asserted-by":"publisher","DOI":"10.1021\/jm300687e"},{"key":"ref66\/cit66","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-017-0203-5"},{"key":"ref67\/cit67","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad1004"},{"key":"ref68\/cit68","doi-asserted-by":"publisher","DOI":"10.1021\/jm4004285"},{"key":"ref69\/cit69","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.8b00234"},{"key":"ref70\/cit70","doi-asserted-by":"publisher","DOI":"10.3389\/fphar.2020.565644"},{"key":"ref71\/cit71","unstructured":"Landrum, G. RDKit: Open-source cheminformatics, 2026. http:\/\/www.rdkit.org, accessed February 21, 2026."},{"key":"ref72\/cit72","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-020-00472-1"},{"key":"ref73\/cit73","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00174"},{"key":"ref74\/cit74","doi-asserted-by":"publisher","DOI":"10.1021\/jm1011116"},{"key":"ref75\/cit75","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejmech.2018.02.042"},{"key":"ref76\/cit76","unstructured":"Zindell, R. M.; Riether, D.; Thomson, D. S.; Wu, L.; World Intellectual Property Organization (WIPO). Compounds which modulate the CB2 receptor. WO Patent, WO2007\/118041A1, 2007 https:\/\/worldwide.espacenet.com\/patent\/search\/family\/038198564\/publication\/WO2007118041A1. Published Oct 18, 2007."}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.6c00181","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.6c00181","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T07:38:54Z","timestamp":1778917134000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.6c00181"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,25]]},"references-count":76,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,5,11]]}},"alternative-id":["10.1021\/acs.jcim.6c00181"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.6c00181","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,25]]}}}