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Rick Stevens
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- affiliation: Argonne National Laboratory, Lemont, Illinois, USA
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2020 – today
- 2024
[c66]Xuefeng Liu, Takuma Yoneda, Rick Stevens, Matthew R. Walter, Yuxin Chen:
Blending Imitation and Reinforcement Learning for Robust Policy Improvement. ICLR 2024- [c65]Xuefeng Liu, Chih-chan Tien, Peng Ding, Songhao Jiang, Rick L. Stevens:
Entropy-Reinforced Planning with Large Language Models for Drug Discovery. ICML 2024 - [c64]Archit Vasan, Ozan Gökdemir, Alexander Brace, Arvind Ramanathan, Thomas S. Brettin, Rick Stevens, Venkatram Vishwanath:
High Performance Binding Affinity Prediction with a Transformer-Based Surrogate Model. IPDPS (Workshops) 2024: 571-580 - [i27]Nathaniel Hudson, J. Gregory Pauloski, Matt Baughman, Alok Kamatar, Mansi Sakarvadia, Logan T. Ward, Ryan Chard, André Bauer, Maksim Levental, Wenyi Wang, Will Engler, Owen Price Skelly, Ben Blaiszik, Rick Stevens, Kyle Chard, Ian T. Foster:
Trillion Parameter AI Serving Infrastructure for Scientific Discovery: A Survey and Vision. CoRR abs/2402.03480 (2024) - [i26]Ashka Shah, Adela DePavia, Nathaniel Hudson, Ian T. Foster, Rick Stevens:
Causal Discovery over High-Dimensional Structured Hypothesis Spaces with Causal Graph Partitioning. CoRR abs/2406.06348 (2024) - [i25]Xuefeng Liu, Chih-chan Tien, Peng Ding, Songhao Jiang, Rick L. Stevens:
Entropy-Reinforced Planning with Large Language Models for Drug Discovery. CoRR abs/2406.07025 (2024) - 2023
- [j51]Bharat Kale
, Austin Clyde, Maoyuan Sun, Arvind Ramanathan, Rick Stevens, Michael E. Papka:
ChemoGraph: Interactive Visual Exploration of the Chemical Space. Comput. Graph. Forum 42(3): 13-24 (2023) - [j50]Maxim Zvyagin, Alexander Brace, Kyle Hippe, Yuntian Deng, Bin Zhang, Cindy Orozco Bohorquez, Austin Clyde, Bharat Kale, Danilo Perez-Rivera, Heng Ma, Carla M. Mann, Michael W. Irvin, Defne G. Ozgulbas, Natalia Vassilieva, J. Gregory Pauloski, Logan T. Ward, Valérie Hayot-Sasson, Murali Emani, Sam Foreman, Zhen Xie, Diangen Lin, Maulik Shukla, Weili Nie, Josh Romero, Christian Dallago, Arash Vahdat, Chaowei Xiao, Thomas Gibbs, Ian T. Foster, James J. Davis, Michael E. Papka, Thomas S. Brettin, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, Arvind Ramanathan:
GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics. Int. J. High Perform. Comput. Appl. 37(6): 683-705 (2023) - [j49]Robert D. Olson, Rida Assaf, Thomas S. Brettin, Neal Conrad, Clark Cucinell, James J. Davis, Donald M. Dempsey, Allan Dickerman, Emily M. Dietrich, Ronald W. Kenyon, Mehmet Kuscuoglu, Elliot J. Lefkowitz, Jian Lu, Dustin Machi, Catherine Macken, Chunhong Mao, Anna Maria Niewiadomska, Marcus Nguyen, Gary J. Olsen, Jamie C. Overbeek, Bruce D. Parrello, Victoria Parrello, Jacob s Porter, Gordon D. Pusch, Maulik Shukla, Indresh Singh, Lucy Stewart, Gene Tan, Chris Thomas, Margo VanOeffelen, Veronika Vonstein, Zachary S. Wallace, Andrew S. Warren, Alice R. Wattam, Fangfang Xia, Hyun Seung Yoo, Yun Zhang, Christian M. Zmasek, Richard H. Scheuermann, Rick L. Stevens:
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. Nucleic Acids Res. 51(D1): 678-689 (2023) - [c63]Nathaniel Hudson, J. Gregory Pauloski, Matt Baughman, Alok Kamatar, Mansi Sakarvadia, Logan T. Ward, Ryan Chard, André Bauer, Maksim Levental, Wenyi Wang, Will Engler, Owen Price Skelly, Ben Blaiszik, Rick Stevens, Kyle Chard, Ian T. Foster:
Trillion Parameter AI Serving Infrastructure for Scientific Discovery: A Survey and Vision. BDCAT 2023: 15:1-15:10 - [c62]Justin M. Wozniak, Rajeev Jain, Andreas Wilke, Rylie Weaver, Alexander Partin, Thomas S. Brettin, Rick Stevens:
An Automation Framework for Comparison of Cancer Response Models Across Configurations. e-Science 2023: 1-10 - [c61]Wei Chen, Yihui Ren, Ai Kagawa, Matthew R. Carbone, Samuel Yen-Chi Chen, Xiaohui Qu, Shinjae Yoo, Austin Clyde, Arvind Ramanathan, Rick L. Stevens, Hubertus Van Dam, Deyu Lu:
Transferable Graph Neural Fingerprint Models for Quick Response to Future Bio-Threats. ICMLA 2023: 800-807 - [c60]Maurice Weber, Carlo Siebenschuh, Rory Butler, Anton Alexandrov, Valdemar Thanner, Georgios Tsolakis, Haris Jabbar, Ian T. Foster, Bo Li, Rick Stevens, Ce Zhang:
WordScape: a Pipeline to extract multilingual, visually rich Documents with Layout Annotations from Web Crawl Data. NeurIPS 2023 - [c59]Ashka Shah, Arvind Ramanathan, Valérie Hayot-Sasson, Rick Stevens:
Causal Discovery and Optimal Experimental Design for Genome-Scale Biological Network Recovery. PASC 2023: 1:1-1:11 - [c58]Oleksandr Narykov, Yitan Zhu, Thomas S. Brettin, Yvonne A. Evrard, Alexander Partin, Maulik Shukla, Priyanka Vasanthakumari, James H. Doroshow, Rick Stevens:
Entropy-Based Regularization on Deep Learning Models for Anti-Cancer Drug Response Prediction. SC Workshops 2023: 121-122 - [c57]Archit Vasan, Thomas S. Brettin, Rick Stevens, Arvind Ramanathan, Venkatram Vishwanath:
Scalable Lead Prediction with Transformers using HPC resources. SC Workshops 2023: 123 - [c56]Miao Tony He, Fangfang Xia, Rick L. Stevens:
Deep Fair Partition for Hyperspectral Image Classification. WHISPERS 2023: 1-12 - [i24]Ashka Shah, Arvind Ramanathan, Valérie Hayot-Sasson, Rick Stevens:
Causal Discovery and Optimal Experimental Design for Genome-Scale Biological Network Recovery. CoRR abs/2304.03210 (2023) - [i23]Wei Chen, Yihui Ren, Ai Kagawa, Matthew R. Carbone, Samuel Yen-Chi Chen, Xiaohui Qu, Shinjae Yoo, Austin Clyde, Arvind Ramanathan, Rick L. Stevens, Hubertus Johannes Jacobus Van Dam, Deyu Lu:
Transferable Graph Neural Fingerprint Models for Quick Response to Future Bio-Threats. CoRR abs/2308.01921 (2023) - [i22]Rafael Vescovi, Tobias Ginsburg, Kyle Hippe, Doga Ozgulbas, Casey Stone, Abraham Stroka, Rory Butler, Ben Blaiszik, Tom Brettin, Kyle Chard, Mark Hereld, Arvind Ramanathan, Rick Stevens, Aikaterini Vriza, Jie Xu, Qingteng Zhang, Ian T. Foster:
Towards a Modular Architecture for Science Factories. CoRR abs/2308.09793 (2023) - [i21]Xuefeng Liu, Takuma Yoneda, Rick L. Stevens, Matthew R. Walter, Yuxin Chen:
Blending Imitation and Reinforcement Learning for Robust Policy Improvement. CoRR abs/2310.01737 (2023) - [i20]Shuaiwen Leon Song, Bonnie Kruft, Minjia Zhang, Conglong Li, Shiyang Chen, Chengming Zhang, Masahiro Tanaka, Xiaoxia Wu, Jeff Rasley, Ammar Ahmad Awan, Connor Holmes, Martin Cai, Adam Ghanem, Zhongzhu Zhou, Yuxiong He, Pete Luferenko, Divya Kumar, Jonathan A. Weyn, Ruixiong Zhang, Sylwester Klocek, Volodymyr Vragov, Mohammed AlQuraishi, Gustaf Ahdritz, Christina Floristean, Cristina Negri, Rao Kotamarthi, Venkatram Vishwanath, Arvind Ramanathan, Sam Foreman, Kyle Hippe, Troy Arcomano, Romit Maulik, Maxim Zvyagin, Alexander Brace, Bin Zhang, Cindy Orozco Bohorquez, Austin Clyde, Bharat Kale, Danilo Perez-Rivera, Heng Ma, Carla M. Mann, Michael W. Irvin, J. Gregory Pauloski, Logan T. Ward, Valérie Hayot-Sasson, Murali Emani, Zhen Xie, Diangen Lin, Maulik Shukla, Ian T. Foster, James J. Davis, Michael E. Papka, Thomas S. Brettin, Prasanna Balaprakash, Gina Tourassi, John Gounley, Heidi A. Hanson, Thomas E. Potok, Massimiliano Lupo Pasini, Kate Evans, Dan Lu, Dalton D. Lunga, Junqi Yin, Sajal Dash, Feiyi Wang, Mallikarjun Shankar, Isaac Lyngaas, Xiao Wang, Guojing Cong, Pei Zhang, Ming Fan, Siyan Liu, Adolfy Hoisie, Shinjae Yoo, Yihui Ren, William Tang, Kyle Felker, Alexey Svyatkovskiy, Hang Liu, Ashwin M. Aji, Angela Dalton, Michael J. Schulte, Karl Schulz, Yuntian Deng, Weili Nie, Josh Romero, Christian Dallago, Arash Vahdat, Chaowei Xiao, Thomas Gibbs, Anima Anandkumar, Rick Stevens:
DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery through Sophisticated AI System Technologies. CoRR abs/2310.04610 (2023) - [i19]Maurice Weber, Carlo Siebenschuh, Rory Butler, Anton Alexandrov, Valdemar Thanner, Georgios Tsolakis, Haris Jabbar, Ian T. Foster, Bo Li, Rick Stevens, Ce Zhang:
WordScape: a Pipeline to extract multilingual, visually rich Documents with Layout Annotations from Web Crawl Data. CoRR abs/2312.10188 (2023) - 2022
- [j48]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) - [j47]Zachary S. Wallace, James J. Davis, Anna Maria Niewiadomska, Robert D. Olson, Maulik Shukla, Rick Stevens, Yun Zhang, Christian M. Zmasek, Richard H. Scheuermann:
Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation. Frontiers Bioinform. 2 (2022) - [j46]Anda Trifan, Defne Gorgun, Michael Salim, Zongyi Li, Alexander Brace, Maxim Zvyagin, Heng Ma, Austin Clyde, David Clark, David J. Hardy, Tom Burnley, Lei Huang, John D. McCalpin, Murali Emani, Hyenseung Yoo, Junqi Yin, Aristeidis Tsaris, Vishal Subbiah, Tanveer Raza, Jessica Liu, Noah Trebesch, Geoffrey Wells, Venkatesh Mysore, Tom Gibbs, James C. Phillips, S. Chakra Chennubhotla, Ian T. Foster, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, John E. Stone, Emad Tajkhorshid, Sarah A. Harris, Arvind Ramanathan:
Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action. Int. J. High Perform. Comput. Appl. 36(5-6): 603-623 (2022) - [j45]Austin Clyde, Stephanie Galanie, Daniel W. Kneller, Heng Ma, Yadu N. Babuji, Ben Blaiszik, Alexander Brace, Thomas S. Brettin, Kyle Chard, Ryan Chard, Leighton Coates, Ian T. Foster, Darin Hauner, Vilmos Kertesz, Neeraj Kumar, Hyungro Lee, Zhuozhao Li, André Merzky, Jurgen G. Schmidt, Li Tan, Mikhail Titov, Anda Trifan, Matteo Turilli, Hubertus Van Dam, Srinivas C. Chennubhotla, Shantenu Jha, Andrey Kovalevsky, Arvind Ramanathan, Martha S. Head, Rick Stevens:
High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. J. Chem. Inf. Model. 62(1): 116-128 (2022) - [c55]Yulun Wu, Nicholas Choma, Andrew Deru Chen, Mikaela Cashman, Érica Teixeira Prates, Verónica G. Melesse Vergara, Manesh Shah, Austin Clyde, Thomas S. Brettin, Wibe Albert de Jong, Neeraj Kumar, Martha S. Head, Rick L. Stevens, Peter Nugent, Daniel A. Jacobson, James B. Brown:
Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery. ICLR 2022 - [i18]Xuefeng Liu, Fangfang Xia, Rick L. Stevens, Yuxin Chen:
Cost-Effective Online Contextual Model Selection. CoRR abs/2207.06030 (2022) - [i17]Alexander Partin, Thomas S. Brettin, Yitan Zhu, Oleksandr Narykov, Austin Clyde, Jamie Overbeek, Rick L. Stevens:
Deep learning methods for drug response prediction in cancer: predominant and emerging trends. CoRR abs/2211.10442 (2022) - 2021
- [j44]Margo VanOeffelen, Marcus Nguyen, Derya Aytan-Aktug, Thomas S. Brettin, Emily M. Dietrich, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Robert Olson, Gordon D. Pusch, Maulik Shukla, Rick Stevens, Veronika Vonstein, Andrew S. Warren, Alice R. Wattam, Hyun Seung Yoo, James J. Davis:
A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes. Briefings Bioinform. 22(6) (2021) - [j43]Alexander Partin, Thomas S. Brettin, Yvonne A. Evrard, Yitan Zhu, Hyun Seung Yoo, Fangfang Xia, Songhao Jiang, Austin Clyde, Maulik Shukla, Michael Fonstein, James H. Doroshow, Rick L. Stevens:
Learning curves for drug response prediction in cancer cell lines. BMC Bioinform. 22(1): 252 (2021) - [j42]Murali Emani, Venkatram Vishwanath, Corey Adams, Michael E. Papka, Rick Stevens, Laura Florescu, Sumti Jairath, William Liu, Tejas Nama, Arvind Sujeeth, Volodymyr V. Kindratenko, Anne C. Elster:
Accelerating Scientific Applications With SambaNova Reconfigurable Dataflow Architecture. Comput. Sci. Eng. 23(2): 114-119 (2021) - [c54]Zixuan Zhao, Nathan Wycoff, Neil Getty, Rick Stevens, Fangfang Xia:
Neko: a Library for Exploring Neuromorphic Learning Rules. ICONS 2021: 9:1-9:5 - [c53]Aymen Al Saadi, Dario Alfè, Yadu N. Babuji, Agastya Bhati, Ben Blaiszik, Alexander Brace, Thomas S. Brettin, Kyle Chard, Ryan Chard, Austin Clyde, Peter V. Coveney, Ian T. Foster, Tom Gibbs, Shantenu Jha, Kristopher Keipert, Dieter Kranzlmüller, Thorsten Kurth, Hyungro Lee, Zhuozhao Li, Heng Ma, Gerald Mathias, André Merzky, Alexander Partin, Arvind Ramanathan, Ashka Shah, Abraham C. Stern, Rick Stevens, Li Tan, Mikhail Titov, Anda Trifan, Aristeidis Tsaris, Matteo Turilli, Huub J. J. Van Dam, Shunzhou Wan, David Wifling, Junqi Yin:
IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads. ICPP 2021: 40:1-40:12 - [c52]Hyungro Lee, André Merzky, Li Tan, Mikhail Titov, Matteo Turilli, Dario Alfè, Agastya Bhati, Alex Brace, Austin Clyde, Peter V. Coveney, Heng Ma, Arvind Ramanathan, Rick Stevens, Anda Trifan, Hubertus Van Dam, Shunzhou Wan, Sean R. Wilkinson, Shantenu Jha:
Scalable HPC & AI infrastructure for COVID-19 therapeutics. PASC 2021: 2:1-2:13 - [c51]Romain Égelé, Prasanna Balaprakash, Isabelle Guyon, Venkatram Vishwanath, Fangfang Xia, Rick Stevens, Zhengying Liu:
AgEBO-tabular: joint neural architecture and hyperparameter search with autotuned data-parallel training for tabular data. SC 2021: 30 - [i16]Agastya P. Bhati, Shunzhou Wan, Dario Alfè, Austin R. Clyde, Mathis Bode, Li Tan, Mikhail Titov, André Merzky, Matteo Turilli, Shantenu Jha, Roger R. Highfield, Walter Rocchia, Nicola Scafuri, Sauro Succi, Dieter Kranzlmüller, Gerald Mathias, David Wifling, Yann Donon, Alberto Di Meglio, Sofia Vallecorsa, Heng Ma, Anda Trifan, Arvind Ramanathan, Tom Brettin, Alexander Partin, Fangfang Xia, Xiaotan Duan, Rick Stevens, Peter V. Coveney:
Pandemic Drugs at Pandemic Speed: Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers. CoRR abs/2103.02843 (2021) - [i15]Austin Clyde, Arvind Ramanathan, Rick Stevens:
Scaffold Embeddings: Learning the Structure Spanned by Chemical Fragments, Scaffolds and Compounds. CoRR abs/2103.06867 (2021) - [i14]Zixuan Zhao, Nathan Wycoff, Neil Getty, Rick Stevens, Fangfang Xia:
Neko: a Library for Exploring Neuromorphic Learning Rules. CoRR abs/2105.00324 (2021) - [i13]Yulun Wu, Nicholas Choma, Andrew Deru Chen, Mikaela Cashman, Érica T. Prates, Manesh Shah, Verónica G. Melesse Vergara, Austin Clyde, Thomas S. Brettin, Wibe A. de Jong, Neeraj Kumar, Martha S. Head, Rick L. Stevens, Peter Nugent, Daniel A. Jacobson, James B. Brown:
Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery. CoRR abs/2106.02190 (2021) - [i12]Austin Clyde, Thomas S. Brettin, Alexander Partin, Hyun Seung Yoo, Yadu N. Babuji, Ben Blaiszik, André Merzky, Matteo Turilli, Shantenu Jha, Arvind Ramanathan, Rick Stevens:
Protein-Ligand Docking Surrogate Models: A SARS-CoV-2 Benchmark for Deep Learning Accelerated Virtual Screening. CoRR abs/2106.07036 (2021) - [i11]Luca Pion-Tonachini, Kristofer E. Bouchard, Héctor García Martín, Sean Peisert, W. Bradley Holtz, Anil Aswani, Dipankar Dwivedi, Haruko M. Wainwright, Ghanshyam Pilania, Benjamin Nachman, Babetta L. Marrone, Nicola Falco, Prabhat, Daniel B. Arnold, Alejandro Wolf-Yadlin, Sarah Powers, Sharlee Climer, Quinn Jackson, Ty Carlson, Michael Sohn, Petrus H. Zwart, Neeraj Kumar, Amy Justice, Claire J. Tomlin, Daniel A. Jacobson, Gos Micklem, Georgios V. Gkoutos, Peter J. Bickel, Jean-Baptiste Cazier, Juliane Müller, Bobbie-Jo Webb-Robertson, Rick Stevens, Mark Anderson, Kenneth Kreutz-Delgado, Michael W. Mahoney, James B. Brown:
Learning from learning machines: a new generation of AI technology to meet the needs of science. CoRR abs/2111.13786 (2021) - 2020
- [j41]James J. Davis, Alice R. Wattam, Ramy K. Aziz, Thomas S. Brettin, Ralph Butler, Rory Butler, Philippe Chlenski, Neal Conrad, Allan Dickerman, Emily M. Dietrich, Joseph L. Gabbard, Svetlana Gerdes, Andrew Guard, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Daniel E. Murphy-Olson, Marcus Nguyen, Eric K. Nordberg, Gary J. Olsen, Robert Olson, Jamie C. Overbeek, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, Maulik Shukla, Chris Thomas, Margo VanOeffelen, Veronika Vonstein, Andrew S. Warren, Fangfang Xia, Dawen Xie, Hyun Seung Yoo, Rick Stevens:
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res. 48(Database-Issue): D606-D612 (2020) - [c50]Rick Stevens:
Overview of HPC and AI Computing for COVID-19 in the US. PACT 2020: 1 - [c49]Justin M. Wozniak, Hyun Seung Yoo, Jamaludin Mohd-Yusof, Bogdan Nicolae, Nicholson T. Collier, Jonathan Ozik, Thomas S. Brettin, Rick Stevens:
High-bypass Learning: Automated Detection of Tumor Cells That Significantly Impact Drug Response. MLHPC/AI4S@SC 2020: 40-49 - [i10]Austin Clyde, Tom Brettin, Alexander Partin, Maulik Shaulik, Hyun Seung Yoo, Yvonne A. Evrard, Yitan Zhu, Fangfang Xia, Rick Stevens:
A Systematic Approach to Featurization for Cancer Drug Sensitivity Predictions with Deep Learning. CoRR abs/2005.00095 (2020) - [i9]Neil Getty, Thomas S. Brettin, Dong Jin, Rick Stevens, Fangfang Xia:
Deep Medical Image Analysis with Representation Learning and Neuromorphic Computing. CoRR abs/2005.05431 (2020) - [i8]Yitan Zhu, Thomas S. Brettin, Yvonne A. Evrard, Alexander Partin, Fangfang Xia, Maulik Shukla, Hyun Seung Yoo, James H. Doroshow, Rick Stevens:
Ensemble Transfer Learning for the Prediction of Anti-Cancer Drug Response. CoRR abs/2005.09572 (2020) - [i7]Austin Clyde, Xiaotian Duan, Rick Stevens:
Regression Enrichment Surfaces: a Simple Analysis Technique for Virtual Drug Screening Models. CoRR abs/2006.01171 (2020) - [i6]Yadu N. Babuji, Ben Blaiszik, Tom Brettin, Kyle Chard, Ryan Chard, Austin Clyde, Ian T. Foster, Zhi Hong, Shantenu Jha, Zhuozhao Li, Xuefeng Liu, Arvind Ramanathan, Yi Ren, Nicholaus Saint, Marcus Schwarting, Rick Stevens, Hubertus Van Dam, Rick Wagner:
Targeting SARS-CoV-2 with AI- and HPC-enabled Lead Generation: A First Data Release. CoRR abs/2006.02431 (2020) - [i5]Aymen Al Saadi, Dario Alfè, Yadu N. Babuji, Agastya Bhati, Ben Blaiszik, Thomas S. Brettin, Kyle Chard, Ryan Chard, Peter V. Coveney, Anda Trifan, Alex Brace, Austin Clyde, Ian T. Foster, Tom Gibbs, Shantenu Jha, Kristopher Keipert, Thorsten Kurth, Dieter Kranzlmüller, Hyungro Lee, Zhuozhao Li, Heng Ma, André Merzky, Gerald Mathias, Alexander Partin, Junqi Yin, Arvind Ramanathan, Ashka Shah, Abraham C. Stern, Rick Stevens, Li Tan, Mikhail Titov, Aristeidis Tsaris, Matteo Turilli, Huub J. J. Van Dam, Shunzhou Wan, David Wifling:
IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads. CoRR abs/2010.06574 (2020) - [i4]Hyungro Lee, André Merzky, Li Tan, Mikhail Titov, Matteo Turilli, Dario Alfè, Agastya Bhati, Alex Brace, Austin Clyde, Peter V. Coveney, Heng Ma, Arvind Ramanathan, Rick Stevens, Anda Trifan, Hubertus Van Dam, Shunzhou Wan, Sean R. Wilkinson, Shantenu Jha:
Scalable HPC and AI Infrastructure for COVID-19 Therapeutics. CoRR abs/2010.10517 (2020) - [i3]Alexander Partin, Thomas S. Brettin, Yvonne A. Evrard, Yitan Zhu, Hyun Seung Yoo, Fangfang Xia, Songhao Jiang, Austin Clyde, Maulik Shukla, Michael Fonstein, James H. Doroshow, Rick Stevens:
Learning Curves for Drug Response Prediction in Cancer Cell Lines. CoRR abs/2011.12466 (2020)
2010 – 2019
- 2019
- [j40]Dionysios A. Antonopoulos, Rida Assaf, Ramy Karam Aziz, Thomas S. Brettin, Christopher Bun, Neal Conrad, James J. Davis, Emily M. Dietrich, Terry Disz, Svetlana Gerdes, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Daniel E. Murphy-Olson, Eric K. Nordberg, Gary J. Olsen, Robert Olson, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, John Santerre, Maulik Shukla, Rick L. Stevens, Margo VanOeffelen, Veronika Vonstein, Andrew S. Warren, Alice R. Wattam, Fangfang Xia, Hyun Seung Yoo:
PATRIC as a unique resource for studying antimicrobial resistance. Briefings Bioinform. 20(4): 1094-1102 (2019) - [c48]Xingfu Wu, Valerie E. Taylor, Justin M. Wozniak, Rick Stevens, Thomas S. Brettin, Fangfang Xia:
Performance, Energy, and Scalability Analysis and Improvement of Parallel Cancer Deep Learning CANDLE Benchmarks. ICPP 2019: 78:1-78:11 - [c47]Prasanna Balaprakash, Romain Egele, Misha Salim, Stefan M. Wild, Venkatram Vishwanath, Fangfang Xia, Tom Brettin, Rick Stevens:
Scalable reinforcement-learning-based neural architecture search for cancer deep learning research. SC 2019: 37:1-37:33 - [i2]Prasanna Balaprakash, Romain Egele, Misha Salim, Stefan M. Wild, Venkatram Vishwanath, Fangfang Xia, Tom Brettin, Rick Stevens:
Scalable Reinforcement-Learning-Based Neural Architecture Search for Cancer Deep Learning Research. CoRR abs/1909.00311 (2019) - 2018
- [j39]Justin M. Wozniak, Rajeev Jain, Prasanna Balaprakash, Jonathan Ozik, Nicholson T. Collier, John Bauer, Fangfang Xia, Thomas S. Brettin, Rick Stevens, Jamaludin Mohd-Yusof, Cristina Garcia-Cardona, Brian Van Essen, Matthew Baughman:
CANDLE/Supervisor: a workflow framework for machine learning applied to cancer research. BMC Bioinform. 19-S(18): 59-69 (2018) - [j38]Fangfang Xia, Maulik Shukla, Thomas S. Brettin, Cristina Garcia-Cardona, Judith D. Cohn, Jonathan E. Allen, Sergei Maslov, Susan L. Holbeck, James H. Doroshow, Yvonne A. Evrard, Eric A. Stahlberg, Rick L. Stevens:
Predicting tumor cell line response to drug pairs with deep learning. BMC Bioinform. 19-S(18): 71-79 (2018) - [j37]Mark Asch, Terry Moore, Rosa M. Badia, Micah Beck, Peter H. Beckman, T. Bidot, François Bodin, Franck Cappello, Alok N. Choudhary, Bronis R. de Supinski, Ewa Deelman, Jack J. Dongarra, Anshu Dubey, Geoffrey C. Fox, H. Fu, Sergi Girona, William Gropp, Michael A. Heroux, Yutaka Ishikawa, Katarzyna Keahey, David E. Keyes, Bill Kramer, J.-F. Lavignon, Y. Lu, Satoshi Matsuoka, Bernd Mohr, Daniel A. Reed, S. Requena, Joel H. Saltz, Thomas C. Schulthess, Rick L. Stevens, D. Martin Swany, Alexander S. Szalay, William M. Tang, G. Varoquaux, Jean-Pierre Vilotte, Robert W. Wisniewski, Z. Xu, Igor Zacharov:
Big data and extreme-scale computing. Int. J. High Perform. Comput. Appl. 32(4): 435-479 (2018) - [c46]George F. Zaki, Justin M. Wozniak, Jonathan Ozik, Nicholson T. Collier, Thomas S. Brettin, Rick Stevens:
Portable and Reusable Deep Learning Infrastructure with Containers to Accelerate Cancer Studies. ESPM2@SC 2018: 54-61 - [i1]Edmon Begoli, Jim Brase, Bambi DeLaRosa, Penelope Jones, Dimitri Kusnezov, Jason Paragas, Rick Stevens, Frederick H. Streitz, Georgia D. Tourassi:
Precision Medicine as an Accelerator for Next Generation Cognitive Supercomputing. CoRR abs/1804.11002 (2018) - 2017
- [j36]Alice R. Wattam, James J. Davis, Rida Assaf, Sébastien Boisvert, Thomas S. Brettin, Christopher Bun, Neal Conrad, Emily M. Dietrich, Terry Disz, Joseph L. Gabbard, Svetlana Gerdes, Christopher S. Henry, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Eric K. Nordberg, Gary J. Olsen, Daniel E. Murphy-Olson, Robert Olson, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, Maulik Shukla, Veronika Vonstein, Andrew S. Warren, Fangfang Xia, Hyun Seung Yoo, Rick L. Stevens:
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 45(Database-Issue): D535-D542 (2017) - [c45]Rick Stevens:
Deep Learning in Cancer and Infectious Disease: Novel Driver Problems for Future HPC Architecture. HPDC 2017: 65 - 2014
- [j35]Ross A. Overbeek, Robert Olson, Gordon D. Pusch, Gary J. Olsen, James J. Davis, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Bruce D. Parrello, Maulik Shukla, Veronika Vonstein, Alice R. Wattam, Fangfang Xia, Rick Stevens:
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42(Database-Issue): 206-214 (2014) - [j34]Alice R. Wattam, David Abraham, Oral Dalay, Terry Disz, Timothy Driscoll, Joseph L. Gabbard, Joseph J. Gillespie, Roger Gough, Deborah Hix, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Eric K. Nordberg, Robert Olson, Ross A. Overbeek, Gordon D. Pusch, Maulik Shukla, Julie Schulman, Rick L. Stevens, Daniel E. Sullivan, Veronika Vonstein, Andrew S. Warren, Rebecca Will, Meredith J. C. Wilson, Hyun Seung Yoo, Chengdong Zhang, Yan Zhang, Bruno W. S. Sobral:
PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res. 42(Database-Issue): 581-591 (2014) - 2013
- [j33]Lorenzo L. Pesce, Hyong Chol Lee, Mark Hereld, Sid Visser, Rick L. Stevens, Albert Wildeman, Wim van Drongelen:
Large-Scale Modeling of Epileptic Seizures: Scaling Properties of Two Parallel Neuronal Network Simulation Algorithms. Comput. Math. Methods Medicine 2013: 182145:1-182145:10 (2013) - 2012
- [j32]Robert A. Edwards, Robert Olson, Terry Disz, Gordon D. Pusch, Veronika Vonstein, Rick Stevens, Ross A. Overbeek:
Real Time Metagenomics: Using k-mers to annotate metagenomes. Bioinform. 28(24): 3316-3317 (2012) - 2011
- [j31]Jack J. Dongarra, Peter H. Beckman, Terry Moore, Patrick Aerts, Giovanni Aloisio, Jean-Claude Andre, David Barkai, Jean-Yves Berthou, Taisuke Boku, Bertrand Braunschweig, Franck Cappello, Barbara M. Chapman, Xuebin Chi, Alok N. Choudhary, Sudip S. Dosanjh, Thom H. Dunning, Sandro Fiore, Al Geist, Bill Gropp, Robert J. Harrison, Mark Hereld, Michael A. Heroux, Adolfy Hoisie, Koh Hotta, Zhong Jin, Yutaka Ishikawa, Fred Johnson, Sanjay Kale, Richard Kenway, David E. Keyes, Bill Kramer, Jesús Labarta, Alain Lichnewsky, Thomas Lippert, Bob Lucas, Barney Maccabe, Satoshi Matsuoka, Paul Messina, Peter Michielse, Bernd Mohr, Matthias S. Müller, Wolfgang E. Nagel, Hiroshi Nakashima, Michael E. Papka, Daniel A. Reed, Mitsuhisa Sato, Edward Seidel, John Shalf, David Skinner, Marc Snir, Thomas L. Sterling, Rick Stevens, Frederick H. Streitz, Bob Sugar, Shinji Sumimoto, William M. Tang, John A. Taylor, Rajeev Thakur, Anne E. Trefethen, Mateo Valero, Aad J. van der Steen, Jeffrey S. Vetter, Peg Williams, Robert W. Wisniewski, Katherine A. Yelick:
The International Exascale Software Project roadmap. Int. J. High Perform. Comput. Appl. 25(1): 3-60 (2011) - [c44]Rick L. Stevens:
HPCS 2011 keynotes: Tuesday keynote I: High-performance computing and biology: The quest for a predictive biological theory. HPCS 2011 - 2010
- [j30]Terry Disz, Sajia Akhter, Daniel Cuevas, Robert Olson, Ross A. Overbeek, Veronika Vonstein, Rick Stevens, Robert A. Edwards:
Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinform. 11: 319 (2010) - [j29]Jennifer Dwyer, Hyong Lee, Amber Martell, Rick L. Stevens, Mark Hereld, Wim van Drongelen:
Oscillation in a network model of neocortex. Neurocomputing 73(7-9): 1051-1056 (2010) - [c43]José P. Faria, Miguel Rocha, Rick L. Stevens, Christopher S. Henry:
Analysis of the Effect of Reversibility Constraints on the Predictions of Genome-Scale Metabolic Models. IWPACBB 2010: 209-215
2000 – 2009
- 2009
- [j28]Jack J. Dongarra, Peter H. Beckman, Patrick Aerts, Franck Cappello, Thomas Lippert, Satoshi Matsuoka, Paul Messina, Terry Moore, Rick Stevens, Anne E. Trefethen, Mateo Valero:
The International Exascale Software Project: a Call To Cooperative Action By the Global High-Performance Community. Int. J. High Perform. Comput. Appl. 23(4): 309-322 (2009) - [j27]Florent E. Angly, Dana Willner, Alejandra Prieto-Davó, Robert A. Edwards, Robert Schmieder, Rebecca Vega-Thurber, Dionysios A. Antonopoulos, Katie Barott, Matthew T. Cottrell, Christelle Desnues, Elizabeth A. Dinsdale, Mike Furlan, Matthew Haynes, Matthew R. Henn, Yongfei Hu, David L. Kirchman, Tracey McDole, John D. McPherson, Folker Meyer, R. Michael Miller, Egbert Mundt, Robert K. Naviaux, Beltran Rodriguez-Mueller, Rick Stevens, Linda Wegley, Lixin Zhang, Baoli Zhu, Forest Rohwer:
The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes. PLoS Comput. Biol. 5(12) (2009) - [c42]Xinghua Shi, Rick L. Stevens:
A Bayesian Approach to High-Throughput Biological Model Generation. BICoB 2009: 376-387 - [c41]Fangfang Xia, Rick Stevens:
Inferring a Species Tree from Gene Trees in the Presence of HGT. BIOCOMP 2009: 840-847 - [c40]Wim van Drongelen, Hyong Lee, Amber Martell, Jennifer Dwyer, Rick Stevens, Mark Hereld:
Oscillation in a network model of neocortex. ESANN 2009 - 2008
- [j26]Folker Meyer, Daniel Paarmann, Mark D'Souza, Robert Olson, Elizabeth M. Glass, Michael Kubal, Tobias Paczian, Alexis A. Rodriguez, Rick Stevens, Andreas Wilke, Jared Wilkening, Robert A. Edwards:
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinform. 9 (2008) - [c39]Xinghua Shi, Rick Stevens:
SWARM: a scientific workflow for supporting bayesian approaches to improve metabolic models. CLADE 2008: 25-34 - [c38]Jonathan C. Silverstein, Colin Walsh, Fred Dech, Eric C. Olson, Michael E. Papka, Nigel M. Parsad, Rick Stevens:
Multi-Parallel Open Technology to Enable Collaborative Volume Visualization: How to Create Global Immersive Virtual Anatomy Classrooms. MMVR 2008: 463-468 - 2007
- [j25]Leslie Klis McNeil, Claudia Reich, Ramy K. Aziz, Daniela Bartels, Matthew Cohoon, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Kaitlyn Hwang, Michael Kubal, Gohar Rem Margaryan, Folker Meyer, William Mihalo, Gary J. Olsen, Robert Olson, Andrei Osterman, Daniel Paarmann, Tobias Paczian, Bruce D. Parrello, Gordon D. Pusch, Dmitry A. Rodionov, Xinghua Shi, Olga Vassieva, Veronika Vonstein, Olga Zagnitko, Fangfang Xia, Jenifer Zinner, Ross A. Overbeek, Rick Stevens:
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 35(Database-Issue): 347-353 (2007) - [c37]Guang R. Gao, Thomas L. Sterling, Rick Stevens, Mark Hereld, Weirong Zhu:
ParalleX: A Study of A New Parallel Computation Model. IPDPS 2007: 1-6 - [c36]Jonathan C. Silverstein, Colin Walsh, Fred Dech, Eric C. Olson, Michael E. Papka, Nigel M. Parsad, Rick L. Stevens:
Immersive Virtual Anatomy Course using a Cluster of Volume Visualization Machines and Passive Stereo. MMVR 2007: 439-444 - 2006
- [c35]Charlie Catlett, William E. Allcock, Phil Andrews, Ruth A. Aydt, Ray Bair, Natasha Balac, Bryan Banister, Trish Barker, Mark Bartelt, Peter H. Beckman, Francine Berman, Gary R. Bertoline, Alan Blatecky, Jay Boisseau, Jim Bottum, Sharon Brunett, Julian J. Bunn, Michelle Butler, David Carver, John Cobb, Tim Cockerill, Peter Couvares, Maytal Dahan, Diana Diehl, Thom H. Dunning, Ian T. Foster, Kelly P. Gaither, Dennis Gannon, Sebastien Goasguen, Michael Grobe, David L. Hart, Matt Heinzel, Chris Hempel, Wendy Huntoon, Joseph A. Insley, Christopher T. Jordan, Ivan R. Judson, Anke Kamrath, Nicholas T. Karonis, Carl Kesselman, Patricia A. Kovatch, Lex Lane, Scott A. Lathrop, Michael J. Levine, David Lifka, Lee Liming, Miron Livny, Rich Loft, Doru Marcusiu, Jim Marsteller, Stuart Martin, D. Scott McCaulay, John McGee, Laura McGinnis, Michael A. McRobbie, Paul Messina, Reagan W. Moore, Richard Lee Moore, John-Paul Navarro, Jeff Nichols, Michael E. Papka, Rob Pennington, Greg Pike, Jim Pool, Raghurama Reddy, Daniel A. Reed, Tony Rimovsky, Eric Roberts, Ralph Roskies, Sergiu Sanielevici, J. Ray Scott, Anurag Shankar, Mark Sheddon, Mike Showerman, Derek Simmel, Abe Singer, Dane Skow, Shava Smallen, Warren Smith, Carol X. Song, Rick L. Stevens, Craig A. Stewart, Robert B. Stock, Nathan Stone, John Towns, Tomislav Urban, Mike Vildibill, Edward Walker, Von Welch, Nancy Wilkins-Diehr, Roy Williams, Linda Winkler, Lan Zhao, Ann Zimmerman:
TeraGrid: Analysis of Organization, System Architecture, and Middleware Enabling New Types of Applications. High Performance Computing Workshop 2006: 225-249 - [c34]Han Gao, Michael E. Papka, Rick L. Stevens:
Extending Multicast Communications by Hybrid Overlay Network. ICC 2006: 820-828 - [c33]