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For: Guo J, Ibanez-Lopez AS, Gao H, Quach V, Coley CW, Jensen KF, Barzilay R. Automated Chemical Reaction Extraction from Scientific Literature. J Chem Inf Model 2021;62:2035-2045. [PMID: 34115937 DOI: 10.1021/acs.jcim.1c00284] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Number Cited by Other Article(s)
1
Jeong J, Park T, Song J, Kang S, Won J, Han J, Min K. Integrating Data Mining and Natural Language Processing to Construct a Melting Point Database for Organometallic Compounds. J Chem Inf Model 2024;64:7432-7446. [PMID: 39352375 DOI: 10.1021/acs.jcim.4c01254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
2
Chen LY, Li YP. Machine learning-guided strategies for reaction conditions design and optimization. Beilstein J Org Chem 2024;20:2476-2492. [PMID: 39376489 PMCID: PMC11457048 DOI: 10.3762/bjoc.20.212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 09/19/2024] [Indexed: 10/09/2024]  Open
3
Ai Q, Meng F, Shi J, Pelkie B, Coley CW. Extracting structured data from organic synthesis procedures using a fine-tuned large language model. DIGITAL DISCOVERY 2024;3:1822-1831. [PMID: 39157760 PMCID: PMC11322921 DOI: 10.1039/d4dd00091a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024]
4
Huang Z, Li X, Li A, Yang Y, He L, Zhang Z, Wu S, Wang Y, Cai S, He Y, Liu X. MPNTEXT: An Interactive Platform for Automatically Extracting Metal-Polyphenol Networks and Their Applications from Scientific Literature. J Chem Inf Model 2024. [PMID: 39258795 DOI: 10.1021/acs.jcim.4c01093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
5
Zhang X, Li Y, Li C, Zhu J, Gan Z, Wang L, Sun X, You H. A chemical reaction entity recognition method based on a natural language data augmentation strategy. Chem Commun (Camb) 2024;60:9610-9613. [PMID: 39148332 DOI: 10.1039/d4cc01471e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
6
Rebello NJ, Arora A, Mochigase H, Lin TS, Shi J, Audus DJ, Muckley ES, Osmani A, Olsen BD. The Block Copolymer Phase Behavior Database. J Chem Inf Model 2024;64:6464-6476. [PMID: 39126359 DOI: 10.1021/acs.jcim.4c00242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
7
Su Y, Wang X, Ye Y, Xie Y, Xu Y, Jiang Y, Wang C. Automation and machine learning augmented by large language models in a catalysis study. Chem Sci 2024;15:12200-12233. [PMID: 39118602 PMCID: PMC11304797 DOI: 10.1039/d3sc07012c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 06/21/2024] [Indexed: 08/10/2024]  Open
8
Fan V, Qian Y, Wang A, Wang A, Coley CW, Barzilay R. OpenChemIE: An Information Extraction Toolkit for Chemistry Literature. J Chem Inf Model 2024;64:5521-5534. [PMID: 38950894 DOI: 10.1021/acs.jcim.4c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
9
Zhang W, Wang Q, Kong X, Xiong J, Ni S, Cao D, Niu B, Chen M, Li Y, Zhang R, Wang Y, Zhang L, Li X, Xiong Z, Shi Q, Huang Z, Fu Z, Zheng M. Fine-tuning large language models for chemical text mining. Chem Sci 2024;15:10600-10611. [PMID: 38994403 PMCID: PMC11234886 DOI: 10.1039/d4sc00924j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/02/2024] [Indexed: 07/13/2024]  Open
10
Shaw WJ, Kidder MK, Bare SR, Delferro M, Morris JR, Toma FM, Senanayake SD, Autrey T, Biddinger EJ, Boettcher S, Bowden ME, Britt PF, Brown RC, Bullock RM, Chen JG, Daniel C, Dorhout PK, Efroymson RA, Gaffney KJ, Gagliardi L, Harper AS, Heldebrant DJ, Luca OR, Lyubovsky M, Male JL, Miller DJ, Prozorov T, Rallo R, Rana R, Rioux RM, Sadow AD, Schaidle JA, Schulte LA, Tarpeh WA, Vlachos DG, Vogt BD, Weber RS, Yang JY, Arenholz E, Helms BA, Huang W, Jordahl JL, Karakaya C, Kian KC, Kothandaraman J, Lercher J, Liu P, Malhotra D, Mueller KT, O'Brien CP, Palomino RM, Qi L, Rodriguez JA, Rousseau R, Russell JC, Sarazen ML, Sholl DS, Smith EA, Stevens MB, Surendranath Y, Tassone CJ, Tran B, Tumas W, Walton KS. A US perspective on closing the carbon cycle to defossilize difficult-to-electrify segments of our economy. Nat Rev Chem 2024;8:376-400. [PMID: 38693313 DOI: 10.1038/s41570-024-00587-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2024] [Indexed: 05/03/2024]
11
Bai J, Mosbach S, Taylor CJ, Karan D, Lee KF, Rihm SD, Akroyd J, Lapkin AA, Kraft M. A dynamic knowledge graph approach to distributed self-driving laboratories. Nat Commun 2024;15:462. [PMID: 38263405 PMCID: PMC10805810 DOI: 10.1038/s41467-023-44599-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024]  Open
12
Zhang B, Xiao H, Ye G, Song Z, Han T, Sharman E, Luo M, Cheng A, Zhu Q, Zhao H, Zhang G, Wang S, Jiang J. Label-Free Data Mining of Scientific Literature by Unsupervised Syntactic Distance Analysis. J Phys Chem Lett 2024;15:212-219. [PMID: 38157213 DOI: 10.1021/acs.jpclett.3c03345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
13
Matsumoto Y, Gotoh H. Compound Classification and Consideration of Correlation with Chemical Descriptors from Articles on Antioxidant Capacity Using Natural Language Processing. J Chem Inf Model 2024;64:119-127. [PMID: 38118462 DOI: 10.1021/acs.jcim.3c01826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
14
Zhang Y, Liu C, Liu M, Liu T, Lin H, Huang CB, Ning L. Attention is all you need: utilizing attention in AI-enabled drug discovery. Brief Bioinform 2023;25:bbad467. [PMID: 38189543 PMCID: PMC10772984 DOI: 10.1093/bib/bbad467] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/03/2023] [Accepted: 11/25/2023] [Indexed: 01/09/2024]  Open
15
Machi K, Akiyama S, Nagata Y, Yoshioka M. OSPAR: A Corpus for Extraction of Organic Synthesis Procedures with Argument Roles. J Chem Inf Model 2023;63:6619-6628. [PMID: 37859303 PMCID: PMC10647022 DOI: 10.1021/acs.jcim.3c01449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023]
16
Li S, Zhang Y, Fang Z, Meng K, Tian R, He H, Sun S. Extracting the Synthetic Route of Pd-Based Catalysts in Methanol Steam Reforming from the Scientific Literature. J Chem Inf Model 2023;63:6249-6260. [PMID: 37807535 DOI: 10.1021/acs.jcim.3c01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
17
Jablonka KM, Ai Q, Al-Feghali A, Badhwar S, Bocarsly JD, Bran AM, Bringuier S, Brinson LC, Choudhary K, Circi D, Cox S, de Jong WA, Evans ML, Gastellu N, Genzling J, Gil MV, Gupta AK, Hong Z, Imran A, Kruschwitz S, Labarre A, Lála J, Liu T, Ma S, Majumdar S, Merz GW, Moitessier N, Moubarak E, Mouriño B, Pelkie B, Pieler M, Ramos MC, Ranković B, Rodriques SG, Sanders JN, Schwaller P, Schwarting M, Shi J, Smit B, Smith BE, Van Herck J, Völker C, Ward L, Warren S, Weiser B, Zhang S, Zhang X, Zia GA, Scourtas A, Schmidt KJ, Foster I, White AD, Blaiszik B. 14 examples of how LLMs can transform materials science and chemistry: a reflection on a large language model hackathon. DIGITAL DISCOVERY 2023;2:1233-1250. [PMID: 38013906 PMCID: PMC10561547 DOI: 10.1039/d3dd00113j] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/08/2023] [Indexed: 11/04/2023]
18
Panayi A, Ward K, Benhadji-Schaff A, Ibanez-Lopez AS, Xia A, Barzilay R. Evaluation of a prototype machine learning tool to semi-automate data extraction for systematic literature reviews. Syst Rev 2023;12:187. [PMID: 37803451 PMCID: PMC10557215 DOI: 10.1186/s13643-023-02351-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/13/2023] [Indexed: 10/08/2023]  Open
19
Reid JP, Betinol IO, Kuang Y. Mechanism to model: a physical organic chemistry approach to reaction prediction. Chem Commun (Camb) 2023;59:10711-10721. [PMID: 37552047 DOI: 10.1039/d3cc03229a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
20
Qian Y, Guo J, Tu Z, Coley CW, Barzilay R. RxnScribe: A Sequence Generation Model for Reaction Diagram Parsing. J Chem Inf Model 2023. [PMID: 37368970 DOI: 10.1021/acs.jcim.3c00439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
21
Shetty P, Rajan AC, Kuenneth C, Gupta S, Panchumarti LP, Holm L, Zhang C, Ramprasad R. A general-purpose material property data extraction pipeline from large polymer corpora using natural language processing. NPJ COMPUTATIONAL MATERIALS 2023;9:52. [PMID: 37033291 PMCID: PMC10073792 DOI: 10.1038/s41524-023-01003-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
22
Qian Y, Guo J, Tu Z, Li Z, Coley CW, Barzilay R. MolScribe: Robust Molecular Structure Recognition with Image-to-Graph Generation. J Chem Inf Model 2023;63:1925-1934. [PMID: 36971363 DOI: 10.1021/acs.jcim.2c01480] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
23
Wang W, Liu Y, Wang Z, Hao G, Song B. The way to AI-controlled synthesis: how far do we need to go? Chem Sci 2022;13:12604-12615. [PMID: 36519036 PMCID: PMC9645373 DOI: 10.1039/d2sc04419f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/26/2022] [Indexed: 09/08/2024]  Open
24
Shavalieva G, Papadokonstantakis S, Peters G. Prior Knowledge for Predictive Modeling: The Case of Acute Aquatic Toxicity. J Chem Inf Model 2022;62:4018-4031. [PMID: 35998659 PMCID: PMC9472271 DOI: 10.1021/acs.jcim.1c01079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Indexed: 11/30/2022]
25
Tang C, McInnes BT. Cascade Processes with Micellar Reaction Media: Recent Advances and Future Directions. Molecules 2022;27:molecules27175611. [PMID: 36080376 PMCID: PMC9458028 DOI: 10.3390/molecules27175611] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/26/2022]  Open
26
Gao H, Zhu LT, Luo ZH, Fraga MA, Hsing IM. Machine Learning and Data Science in Chemical Engineering. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.2c01788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
27
Rarey M, Nicklaus MC, Warr W. Special Issue on Reaction Informatics and Chemical Space. J Chem Inf Model 2022;62:2009-2010. [DOI: 10.1021/acs.jcim.2c00390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
28
Zhang L, He M. Prediction of solar cell materials via unsupervised literature learning. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021;34:095902. [PMID: 34844235 DOI: 10.1088/1361-648x/ac3e1e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/29/2021] [Indexed: 06/13/2023]
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