Search Results - "Kearnes, Steven"

Optimization of Molecules via Deep Reinforcement Learning by Zhou, Zhenpeng, Kearnes, Steven, Li, Li, Zare, Richard N., Riley, Patrick

“…We present a framework, which we call Molecule Deep Q -Networks (MolDQN), for molecule optimization by combining domain knowledge of chemistry and…”
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The Open Reaction Database by Kearnes, Steven M, Maser, Michael R, Wleklinski, Michael, Kast, Anton, Doyle, Abigail G, Dreher, Spencer D, Hawkins, Joel M, Jensen, Klavs F, Coley, Connor W

“…Chemical reaction data in journal articles, patents, and even electronic laboratory notebooks are currently stored in various formats, often unstructured,…”
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Prediction Errors of Molecular Machine Learning Models Lower than Hybrid DFT Error by Faber, Felix A, Hutchison, Luke, Huang, Bing, Gilmer, Justin, Schoenholz, Samuel S, Dahl, George E, Vinyals, Oriol, Kearnes, Steven, Riley, Patrick F, von Lilienfeld, O. Anatole

“…We investigate the impact of choosing regressors and molecular representations for the construction of fast machine learning (ML) models of 13 electronic…”
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Data Sharing in Chemistry: Lessons Learned and a Case for Mandating Structured Reaction Data by Mercado, Rocío, Kearnes, Steven M., Coley, Connor W.

“…The past decade has seen a number of impressive developments in predictive chemistry and reaction informatics driven by machine learning applications to…”
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A Targeted Computational Screen of the SWEETLEAD Database Reveals FDA-Approved Compounds with Anti-Dengue Viral Activity by Moshiri, Jasmine, Constant, David A, Liu, Bowen, Mateo, Roberto, Kearnes, Steven, Novick, Paul, Prasad, Ritika, Nagamine, Claude, Pande, Vijay, Kirkegaard, Karla

“…Affordable and effective antiviral therapies are needed worldwide, especially against agents such as dengue virus that are endemic in underserved regions. Many…”
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SCISSORS: Practical Considerations by Kearnes, Steven M, Haque, Imran S, Pande, Vijay S

“…Molecular similarity has been effectively applied to many problems in cheminformatics and computational drug discovery, but modern methods can be prohibitively…”
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Molecular graph convolutions: moving beyond fingerprints by Kearnes, Steven, McCloskey, Kevin, Berndl, Marc, Pande, Vijay, Riley, Patrick

“…Molecular “fingerprints” encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However,…”
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ROCS-derived features for virtual screening by Kearnes, Steven, Pande, Vijay

“…Rapid overlay of chemical structures (ROCS) is a standard tool for the calculation of 3D shape and chemical (“color”) similarity. ROCS uses unweighted sums to…”
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Artificial Intelligence in Drug Discovery: Into the Great Wide Open by Bajorath, Jürgen, Kearnes, Steven, Walters, W Patrick, Meanwell, Nicholas A, Georg, Gunda I, Wang, Shaomeng

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Machine Learning on DNA-Encoded Libraries: A New Paradigm for Hit Finding by McCloskey, Kevin, Sigel, Eric A, Kearnes, Steven, Xue, Ling, Tian, Xia, Moccia, Dennis, Gikunju, Diana, Bazzaz, Sana, Chan, Betty, Clark, Matthew A, Cuozzo, John W, Guié, Marie-Aude, Guilinger, John P, Huguet, Christelle, Hupp, Christopher D, Keefe, Anthony D, Mulhern, Christopher J, Zhang, Ying, Riley, Patrick

“…DNA-encoded small molecule libraries (DELs) have enabled discovery of novel inhibitors for many distinct protein targets of therapeutic value. We demonstrate a…”
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Author Correction: Optimization of Molecules via Deep Reinforcement Learning by Zhou, Zhenpeng, Kearnes, Steven, Li, Li, Zare, Richard N., Riley, Patrick

“…An amendment to this paper has been published and can be accessed via a link at the top of the paper…”
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Defining Levels of Automated Chemical Design by Goldman, Brian, Kearnes, Steven, Kramer, Trevor, Riley, Patrick, Walters, W. Patrick

“…One application area of computational methods in drug discovery is the automated design of small molecules. Despite the large number of publications describing…”
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The Future Is Now: Artificial Intelligence in Drug Discovery by Bajorath, Jürgen, Kearnes, Steven, Walters, W. Patrick, Georg, Gunda I, Wang, Shaomeng

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A Target Class Ligandability Evaluation of WD40 Repeat-Containing Proteins by Ackloo, Suzanne, Li, Fengling, Szewczyk, Magda, Seitova, Almagul, Loppnau, Peter, Zeng, Hong, Xu, Jin, Ahmad, Shabbir, Arnautova, Yelena A, Baghaie, A. J., Beldar, Serap, Bolotokova, Albina, Centrella, Paolo A., Chau, Irene, Clark, Matthew A., Cuozzo, John W., Dehghani-Tafti, Saba, Disch, Jeremy S., Dong, Aiping, Dumas, Antoine, Feng, Jianwen A., Ghiabi, Pegah, Gibson, Elisa, Gilmer, Justin, Goldman, Brian, Green, Stuart R, Guié, Marie-Aude, Guilinger, John P., Harms, Nathan, Herasymenko, Oleksandra, Houliston, Scott, Hutchinson, Ashley, Kearnes, Steven, Keefe, Anthony D., Kimani, Serah W., Kramer, Trevor, Kutera, Maria, Kwak, Haejin A., Lento, Cristina, Li, Yanjun, Liu, Jenny, Loup, Joachim, Machado, Raquel A. C., Mulhern, Christopher J., Perveen, Sumera, Righetto, Germanna L., Riley, Patrick, Shrestha, Suman, Sigel, Eric A., Silva, Madhushika, Sintchak, Michael D., Slakman, Belinda L., Taylor, Rhys D., Thompson, James, Torng, Wen, Underkoffler, Carl, von Rechenberg, Moritz, Walsh, Ryan T., Watson, Ian, Wilson, Derek J., Wolf, Esther, Yadav, Manisha, Yazdi, Aliakbar K., Zhang, Junyi, Zhang, Ying, Santhakumar, Vijayaratnam, Edwards, Aled M., Barsyte-Lovejoy, Dalia, Schapira, Matthieu, Brown, Peter J., Halabelian, Levon, Arrowsmith, Cheryl H.

“…Target class-focused drug discovery has a strong track record in pharmaceutical research, yet public domain data indicate that many members of protein families…”
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Pursuing a Prospective Perspective by Kearnes, Steven

“…Retrospective testing of predictive models does not consider the real-world context in which models are deployed. Prospective validation, on the other hand,…”
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Structure-Activity Relationships of Influenza a M2 Inhibitors by Kearnes, Steven M., Herron, Steven, Busath, David D.

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Finding Needles in a Haystack: Molecular Similarity and Machine Learning for Drug Discovery Applications by Kearnes, Steven Michael

“…We are in the midst of a machine learning revolution. From self-driving cars to clinical diagnostics, machine learning promises to change the way we live our…”
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Osprey: Hyperparameter Optimization for Machine Learning by T. McGibbon, Robert, X. Hernández, Carlos, P. Harrigan, Matthew, Kearnes, Steven, M. Sultan, Mohammad, Jastrzebski, Stanislaw, E. Husic, Brooke, S. Pande, Vijay

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ROCS-Derived Features for Virtual Screening by Kearnes, Steven, Pande, Vijay

“…Rapid overlay of chemical structures (ROCS) is a standard tool for the calculation of 3D shape and chemical ("color") similarity. ROCS uses unweighted sums to…”
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Decoding Molecular Graph Embeddings with Reinforcement Learning by Kearnes, Steven, Li, Li, Riley, Patrick

“…We present RL-VAE, a graph-to-graph variational autoencoder that uses reinforcement learning to decode molecular graphs from latent embeddings. Methods have…”
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