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- Jonathan P. Allen
University of San Francisco, School of Management, San Francisco, CA, USA - Jonathan Allen
- Jonathan E. Allen
- Jonathan Parkes Allen
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Publication search results
found 238 matches
- 2024
- Heesung Shim, Jonathan E. Allen, W. F. Drew Bennett:
Enhancing Docking Accuracy with PECAN2, a 3D Atomic Neural Network Trained without Co-Complex Crystal Structures. Mach. Learn. Knowl. Extr. 6(1): 642-657 (2024) - Tom Cunningham, Sana Pandey, Leif Sigerson, Jonathan Stray, Jeff Allen, Bonnie Barrilleaux, Ravi Iyer, Smitha Milli, Mohit Kothari, Behnam Rezaei:
What We Know About Using Non-Engagement Signals in Content Ranking. CoRR abs/2402.06831 (2024) - Jacky Liang, Fei Xia, Wenhao Yu, Andy Zeng, Montserrat Gonzalez Arenas, Maria Attarian, Maria Bauzá, Matthew Bennice, Alex Bewley, Adil Dostmohamed, Chuyuan Kelly Fu, Nimrod Gileadi, Marissa Giustina, Keerthana Gopalakrishnan, Leonard Hasenclever, Jan Humplik, Jasmine Hsu, Nikhil J. Joshi, Ben Jyenis, J. Chase Kew, Sean Kirmani, Tsang-Wei Edward Lee, Kuang-Huei Lee, Assaf Hurwitz Michaely, Joss Moore, Ken Oslund, Dushyant Rao, Allen Z. Ren, Baruch Tabanpour, Quan Vuong, Ayzaan Wahid, Ted Xiao, Ying Xu, Vincent Zhuang, Peng Xu, Erik Frey, Ken Caluwaerts, Tingnan Zhang, Brian Ichter, Jonathan Tompson, Leila Takayama, Vincent Vanhoucke, Izhak Shafran, Maja J. Mataric, Dorsa Sadigh, Nicolas Heess, Kanishka Rao, Nik Stewart, Jie Tan, Carolina Parada:
Learning to Learn Faster from Human Feedback with Language Model Predictive Control. CoRR abs/2402.11450 (2024) - 2023
- Tanja Magoc, Katie S. Allen, Cara McDonnell, Jean-Paul Russo, Jonathan Cummins, Joshua R. Vest, Christopher A. Harle:
Generalizability and portability of natural language processing system to extract individual social risk factors. Int. J. Medical Informatics 177: 105115 (2023) - Garrett A. Stevenson, Dan Kirshner, Brian J. Bennion, Yue Yang, Xiaohua Zhang, Adam T. Zemla, Marisa W. Torres, Aidan Epstein, Derek Jones, Hyojin Kim, W. F. Drew Bennett, Sergio Ernesto Wong, Jonathan E. Allen, Felice C. Lightstone:
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method. J. Chem. Inf. Model. 63(21): 6655-6666 (2023) - Fergal J. Martin, M. Ridwan Amode, Alisha Aneja, Olanrewaju Austine-Orimoloye, Andrey G. Azov, If Barnes, Arne Becker, Ruth Bennett, Andrew E. Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Alexandra Bignell, Sanjay Boddu, Paulo R. B. Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Mehrnaz Charkhchi, Alexander Cockburn, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Jayantilal Dodiya, Sarah M. Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos García-Girón, Thiago Augusto Lopes Genez, Gurpreet S. Ghattaoraya, Jose Gonzalez Martinez, Cristi Guijarro, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike P. Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Diego Marques-Coelho, José Carlos Marugán, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N. Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Pilizota, Irina Prosovetskaia, José G. Pérez-Silva, Ahamed Imran Abdul Salam, Nuno Saraiva-Agostinho, Helen Schuilenburg, Dan Sheppard, Swati Sinha, Botond Sipos, William Stark, Emily Steed, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Michal Szpak, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A. Walsh, Brandon Walts, Elizabeth Wass, Natalie L. Willhoft, Jamie Allen, Jorge Álvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jane E. Loveland, Benjamin Moore, Jonathan M. Mudge, John G. Tate, David Thybert, Stephen J. Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E. Hunt, Magali Ruffier, Fiona Cunningham, Sarah Dyer, Robert D. Finn, Kevin L. Howe, Peter W. Harrison, Andrew D. Yates, Paul Flicek:
Ensembl 2023. Nucleic Acids Res. 51(D1): 933-941 (2023) - Jonathan W. Stallrich, Katherine Allen-Moyer, Bradley Jones:
D - and A -Optimal Screening Designs. Technometrics 65(4): 492-501 (2023) - Jonathan Ting, Sujata Basyal, Brendon C. Allen:
Robust Control of a Nonsmooth or Switched Control Affine Uncertain Nonlinear System Using a Novel RISE-Inspired Approach. ACC 2023: 4253-4257 - David A. Smith, Jacob Murel, Jonathan Parkes Allen, Matthew Thomas Miller:
Automatic Collation for Diversifying Corpora: Commonly Copied Texts as Distant Supervision for Handwritten Text Recognition. CHR 2023: 206-221 - Jonathan A. Kelner, Jerry Li, Allen Liu, Aaron Sidford, Kevin Tian:
Semi-Random Sparse Recovery in Nearly-Linear Time. COLT 2023: 2352-2398 - Jonathan A. Kelner, Jerry Li, Allen Liu, Aaron Sidford, Kevin Tian:
Matrix Completion in Almost-Verification Time. FOCS 2023: 2102-2128 - Jonathan P. Allen:
Digital Innovation Systems and the Rejection of the Terrestrial. IFIPJWC 2023: 50-54 - Derek Jones, Jonathan E. Allen, Xiaohua Zhang, Behnam Khaleghi, Jaeyoung Kang, Weihong Xu, Niema Moshiri, Tajana Simunic Rosing:
HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations. CoRR abs/2303.15604 (2023) - Fabricio Arend Torres, Marcello Massimo Negri, Marco Inversi, Jonathan Aellen, Volker Roth:
Lagrangian Flow Networks for Conservation Laws. CoRR abs/2305.16846 (2023) - Jonathan A. Kelner, Jerry Li, Allen Liu, Aaron Sidford, Kevin Tian:
Matrix Completion in Almost-Verification Time. CoRR abs/2308.03661 (2023) - 2022
- Fangfang Xia, Jonathan E. Allen, Prasanna Balaprakash, Thomas S. Brettin, Cristina Garcia-Cardona, Austin Clyde, Judith D. Cohn, James H. Doroshow, Xiaotian Duan, Veronika Dubinkina, Yvonne A. Evrard, Ya Ju Fan, Jason Gans, Stewart He, Pinyi Lu, Sergei Maslov, Alexander Partin, Maulik Shukla, Eric A. Stahlberg, Justin M. Wozniak, Hyun Seung Yoo, George F. Zaki, Yitan Zhu, Rick Stevens:
A cross-study analysis of drug response prediction in cancer cell lines. Briefings Bioinform. 23(1) (2022) - Vincent Blay, Tijana Radivojevic, Jonathan E. Allen, Corey M. Hudson, Héctor García Martín:
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design. J. Chem. Inf. Model. 62(15): 3551-3564 (2022) - Heesung Shim, Hyojin Kim, Jonathan E. Allen, Heike Wulff:
Pose Classification Using Three-Dimensional Atomic Structure-Based Neural Networks Applied to Ion Channel-Ligand Docking. J. Chem. Inf. Model. 62(10): 2301-2315 (2022) - Fiona Cunningham, James E. Allen, Jamie Allen, Jorge Álvarez-Jarreta, M. Ridwan Amode, Irina M. Armean, Olanrewaju Austine-Orimoloye, Andrey G. Azov, If Barnes, Ruth Bennett, Andrew E. Berry, Jyothish Bhai, Alexandra Bignell, Konstantinos Billis, Sanjay Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla A. Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Jayantilal Dodiya, Sarah M. Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos García-Girón, Thiago A. L. Genez, Jose Gonzalez Martinez, Cristina Guijarro-Clarke, Arthur Gymer, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Thomas Juettemann, Vinay Kaikala, Mike P. Kay, Ilias Lavidas, Tuan Le, Diana Lemos, José Carlos Marugán, Shamika Mohanan, Aleena Mushtaq, Marc Naven, Denye N. Oheh, Anne Parker, Andrew Parton, Malcolm Perry, Ivana Pilizota, Irina Prosovetskaia, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Dan Sheppard, José G. Pérez-Silva, William Stark, Emily Steed, Kyösti Sutinen, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Michal Szpak, Anja Thormann, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A. Walsh, Brandon Walts, Natalie L. Willhoft, Andrea Winterbottom, Elizabeth Wass, Marc Chakiachvili, Bethany Flint, Adam Frankish, Stefano Giorgetti, Leanne Haggerty, Sarah E. Hunt, Garth IIsley, Jane E. Loveland, Fergal J. Martin, Benjamin Moore, Jonathan M. Mudge, Matthieu Muffato, Emily Perry, Magali Ruffier, John G. Tate, David Thybert, Stephen J. Trevanion, Sarah Dyer, Peter W. Harrison, Kevin L. Howe, Andrew D. Yates, Daniel R. Zerbino, Paul Flicek:
Ensembl 2022. Nucleic Acids Res. 50(D1): 988-995 (2022) - Gorka Lasso, Saad Khan, Stephanie A. Allen, Margarette Mariano, Catalina Florez, Erika P. Orner, Jose A. Quiroz, Gregory Quevedo, Aldo Massimi, Aditi Hegde, Ariel S. Wirchnianski, Robert H. Bortz III, Ryan J. Malonis, George I. Georgiev, Karen Tong, Natalia G. Herrera, Nicholas C. Morano, Scott J. Garforth, Avinash Malaviya, Ahmed Khokhar, Ethan Laudermilch, M. Eugenia Dieterle, J. Maximilian Fels, Denise Haslwanter, Rohit K. Jangra, Jason Barnhill, Steven C. Almo, Kartik Chandran, Jonathan R. Lai, Libusha Kelly, Johanna P. Daily, Olivia Vergnolle:
Longitudinally monitored immune biomarkers predict the timing of COVID-19 outcomes. PLoS Comput. Biol. 18(1) (2022) - Dong H. Ahn, Xiaohua Zhang, Jeffrey Mast, Stephen Herbein, Francesco Di Natale, Dan Kirshner, Sam Ade Jacobs, Ian Karlin, Daniel J. Milroy, Bronis R. de Supinski, Brian Van Essen, Jonathan E. Allen, Felice C. Lightstone:
Scalable Composition and Analysis Techniques for Massive Scientific Workflows. e-Science 2022: 32-43 - David Watkins-Valls, Peter K. Allen, Henrique Maia, Madhavan Seshadri, Jonathan Sanabria, Nicholas R. Waytowich, Jacob Varley:
Mobile Manipulation Leveraging Multiple Views. IROS 2022: 4585-4592 - Nikolai Vogler, Jonathan Parkes Allen, Matthew Thomas Miller, Taylor Berg-Kirkpatrick:
Lacuna Reconstruction: Self-Supervised Pre-Training for Low-Resource Historical Document Transcription. NAACL-HLT (Findings) 2022: 206-216 - Jonathan A. Kelner, Jerry Li, Allen Liu, Aaron Sidford, Kevin Tian:
Semi-Random Sparse Recovery in Nearly-Linear Time. CoRR abs/2203.04002 (2022) - Dennis Madsen, Jonathan Aellen, Andreas Morel-Forster, Thomas Vetter, Marcel Lüthi:
GiNGR: Generalized Iterative Non-Rigid Point Cloud and Surface Registration Using Gaussian Process Regression. CoRR abs/2203.09986 (2022) - Ya Ju Fan, Jonathan E. Allen, Kevin S. McLoughlin, Da Shi, Brian J. Bennion, Xiaohua Zhang, Felice C. Lightstone:
Evaluating Point-Prediction Uncertainties in Neural Networks for Drug Discovery. CoRR abs/2210.17043 (2022) - 2021
- Jonathan M. Spring, Eric Hatleback, Allen D. Householder, Art Manion, Deana Shick:
Time to Change the CVSS? IEEE Secur. Priv. 19(2): 74-78 (2021) - Sam Ade Jacobs, Tim Moon, Kevin McLoughlin, Derek Jones, David Hysom, Dong H. Ahn, John C. Gyllenhaal, Pythagoras Watson, Felice C. Lightstone, Jonathan E. Allen, Ian Karlin, Brian Van Essen:
Enabling rapid COVID-19 small molecule drug design through scalable deep learning of generative models. Int. J. High Perform. Comput. Appl. 35(5) (2021) - David Allen Surovik, Kun Wang, Massimo Vespignani, Jonathan Bruce, Kostas E. Bekris:
Adaptive tensegrity locomotion: Controlling a compliant icosahedron with symmetry-reduced reinforcement learning. Int. J. Robotics Res. 40(1) (2021) - Derek Jones, Hyojin Kim, Xiaohua Zhang, Adam T. Zemla, Garrett Stevenson, W. F. Drew Bennett, Daniel A. Kirshner, Sergio Ernesto Wong, Felice C. Lightstone, Jonathan E. Allen:
Improved Protein-Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference. J. Chem. Inf. Model. 61(4): 1583-1592 (2021)
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