{"id":7,"date":"2023-09-29T19:22:52","date_gmt":"2023-09-29T19:22:52","guid":{"rendered":"https:\/\/www.isi.edu\/poeple-jwalters\/?page_id=7"},"modified":"2025-06-13T17:44:31","modified_gmt":"2025-06-13T17:44:31","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.isi.edu\/people-jwalters\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n\n\t\n
\n\n

2025<\/h2>\n \n
\n

\n \n FedPaI: Achieving Extreme Sparsity in Federated Learning via Pruning at Initialization <\/a>\n <\/h3>\n\n
\n Haonan Wang, Zeli Liu, Kajimusugura Hoshino, Tuo Zhang, John Paul Walters, Stephen Crago <\/div>\n \n
\n arXiv preprint arXiv:2504.00308<\/i>, 2025\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n

2017<\/h2>\n \n
\n

\n \n Load balancing for minimizing deadline misses and total runtime for connected car systems in fog computing <\/a>\n <\/h3>\n\n
\n Yu-An Chen, John Paul Walters, Stephen P Crago <\/div>\n \n
\n 2017 IEEE International Symposium on Parallel and Distributed Processing \u2026<\/i>, 2017\n\n <\/div>\n\n <\/div>\n\n

2014<\/h2>\n \n
\n

\n \n GPU passthrough performance: A comparison of KVM, Xen, VMWare ESXi, and LXC for CUDA and OpenCL applications <\/a>\n <\/h3>\n\n
\n John Paul Walters, Andrew J Younge, Dong In Kang, Ke Thia Yao, Mikyung Kang, Stephen P Crago, Geoffrey C Fox <\/div>\n \n
\n 2014 IEEE 7th international conference on cloud computing, 636-643<\/i>, 2014\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n

2010<\/h2>\n \n
\n

\n \n Database Searching with Profile-Hidden Markov Models on Reconfigurable and Many-Core Architectures <\/a>\n <\/h3>\n\n
\n John Paul Walters, Vipin Chaudhary, Bertil Schmidt <\/div>\n \n
\n Bioinformatics: high performance parallel computer architectures 2, 203<\/i>, 2010\n\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Computation Checkpointing and Migration <\/a>\n <\/h3>\n\n
\n Vipin Chaudhary, John Paul N Walters, Hai Jiang <\/div>\n \n
\n Nova Science Publishers, Inc.<\/i>, 2010\n\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Applying graphics processor units to Monte Carlo dose calculation in radiation therapy <\/a>\n <\/h3>\n\n
\n M Bakhtiari, H Malhotra, MD Jones, V Chaudhary, JP Walters, D Nazareth <\/div>\n \n
\n Journal of Medical Physics 35 (2), 120-122<\/i>, 2010\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n

2009<\/h2>\n \n
\n

\n \n Improving MPI-HMMER's scalability with parallel I\/O <\/a>\n <\/h3>\n\n
\n John Paul Walters, Rohan Darole, Vipin Chaudhary <\/div>\n \n
\n Parallel & Distributed Processing. IPDPS 2009. IEEE International \u2026<\/i>, 2009\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Evaluating the use of GPUs in liver image segmentation and HMMER database searches <\/a>\n <\/h3>\n\n
\n John Paul Walters, Vidyananth Balu, Suryaprakash Kompalli, Vipin Chaudhary <\/div>\n \n
\n 2009 Ieee International Symposium on Parallel & Distributed Processing, 1-12<\/i>, 2009\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n A fault-tolerant strategy for virtualized HPC clusters <\/a>\n <\/h3>\n\n
\n John Paul Walters, Vipin Chaudhary <\/div>\n \n
\n The Journal of Supercomputing 50, 209-239<\/i>, 2009\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n

2008<\/h2>\n \n
\n

\n \n Replication-based fault tolerance for MPI applications <\/a>\n <\/h3>\n\n
\n John Paul Walters, Vipin Chaudhary <\/div>\n \n
\n IEEE Transactions on Parallel and Distributed Systems 20 (7), 997-1010<\/i>, 2008\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n A comparison of virtualization technologies for HPC <\/a>\n <\/h3>\n\n
\n John Paul Walters, Vipin Chaudhary, Minsuk Cha, Salvatore Guercio, Steve Gallo <\/div>\n \n
\n 22nd International Conference on Advanced Information Networking and \u2026<\/i>, 2008\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Evaluating the use of GPUs in liver image segmentation and HMMR database searches <\/a>\n <\/h3>\n\n
\n Vipin Chaudhary, Suryaprakash Kompalli, John Paul Walters, Vidyananth Balu <\/div>\n \n
\n 2008\n\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Improving MPI-HMMER's Scalability with Parallel I\/O <\/a>\n <\/h3>\n\n
\n Vipin Chaudhary, John Paul Walters, Rohan Darole <\/div>\n \n
\n 2008\n\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Accelerating molecular dynamics simulations with gpus <\/a>\n <\/h3>\n\n
\n John Paul Walters, Vidyananth Balu, Vipin Chaudhary, David Kofke, Andrew Schultz <\/div>\n \n
\n ISCA PDCCS, 44-49<\/i>, 2008\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Optimized Cluster\u2010Enabled HMMER Searches <\/a>\n <\/h3>\n\n
\n John Paul Walters, Joseph Landman, Vipin Chaudhary <\/div>\n \n
\n Grid computing for bioinformatics and computational biology, 51-70<\/i>, 2008\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Enabling interactive jobs in virtualized data centers <\/a>\n <\/h3>\n\n
\n John Paul Walters, Bhagyashree Bantwal, Vipin Chaudhary <\/div>\n \n
\n Cloud Computing and Its Applications<\/i>, 2008\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n

2007<\/h2>\n \n
\n

\n \n MPI-HMMER-Boost: Distributed fpga acceleration <\/a>\n <\/h3>\n\n
\n John Paul Walters, Xiandong Meng, Vipin Chaudhary, Tim Oliver, Leow Yuan Yeow, Bertil Schmidt, Darran Nathan, Joseph Landman <\/div>\n \n
\n The Journal of VLSI Signal Processing 48 (3), 223-238<\/i>, 2007\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Failure Prediction and Scalable Checkpointing for Reliable Large-Scale Grid Computing <\/a>\n <\/h3>\n\n
\n Brent Rood, John Paul Walters, Vipin Chaudhary, Michael J Lewis <\/div>\n \n
\n IEEE HPDC\u201907<\/i>, 2007\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Wireless sensor network security: A survey <\/a>\n <\/h3>\n\n
\n John Paul Walters, Zhengqiang Liang, Weisong Shi, Vipin Chaudhary <\/div>\n \n
\n Security in distributed, grid, mobile, and pervasive computing, 367<\/i>, 2007\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n A comprehensive user-level checkpointing strategy for MPI applications <\/a>\n <\/h3>\n\n
\n J Walters, Vipin Chaudhary <\/div>\n \n
\n Technical report, TR 2007-1<\/i>, 2007\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Wireless sensor network security: A survey, in book chapter of security <\/a>\n <\/h3>\n\n
\n John Paul Walters, Zhengqiang Liang, Weisong Shi, Vipin Chaudhary <\/div>\n \n
\n in Distributed, Grid, and Pervasive Computing, Yang Xiao (Eds, 0-849<\/i>, 2007\n\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Comprehensive User-level Checkpointing Strategy for MPI Applications <\/a>\n <\/h3>\n\n
\n Vipin Chaudhary, John Paul Walters <\/div>\n \n
\n 2007\n\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Fault-tolerant techniques for high performance computing and a bioinformatics application <\/a>\n <\/h3>\n\n
\n John Paul N Walters <\/div>\n \n
\n ProQuest<\/i>, 2007\n\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n A scalable asynchronous replication-based strategy for fault tolerant MPI applications <\/a>\n <\/h3>\n\n
\n John Walters, Vipin Chaudhary <\/div>\n \n
\n High Performance Computing, HiPC 2007, 257-268<\/i>, 2007\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n

2006<\/h2>\n \n
\n

\n \n An adaptive heterogeneous software DSM <\/a>\n <\/h3>\n\n
\n John Paul Walters, Hai Jiang, Vipin Chaudhary <\/div>\n \n
\n 2006 International Conference on Parallel Processing Workshops (ICPPW'06), 8 \u2026<\/i>, 2006\n\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Accelerating HMMer searches on Opteron processors with minimally invasive recoding <\/a>\n <\/h3>\n\n
\n Joseph Landman, Joydeep Ray, John Paul Walters <\/div>\n \n
\n 20th International Conference on Advanced Information Networking and \u2026<\/i>, 2006\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Accelerating the HMMER sequence analysis suite using conventional processors <\/a>\n <\/h3>\n\n
\n John Paul Walters, Bashar Qudah, Vipin Chaudhary <\/div>\n \n
\n 20th International Conference on Advanced Information Networking and \u2026<\/i>, 2006\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Data Conversion for Heterogeneous Migration\/Checkpointing <\/a>\n <\/h3>\n\n
\n Hai Jiang, Vipin Chaudhary, John Paul Walters <\/div>\n \n
\n High-performance computing: paradigm and infrastructure 44, 241<\/i>, 2006\n\n <\/div>\n\n <\/div>\n\n \n
\n

\n \n Application-level checkpointing techniques for parallel programs <\/a>\n <\/h3>\n\n
\n John Walters, Vipin Chaudhary <\/div>\n \n
\n Distributed Computing and Internet Technology, 221-234<\/i>, 2006\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n

2003<\/h2>\n \n
\n

\n \n Data conversion for process\/thread migration and checkpointing <\/a>\n <\/h3>\n\n
\n Hai Jiang, Vipin Chaudhary, John Paul Walters <\/div>\n \n
\n 2003 International Conference on Parallel Processing. Proceedings \u2026<\/i>, 2003\n\n
\n View Paper<\/a>\n <\/div>\n <\/div>\n\n <\/div>\n\n \n <\/div>\n\n \n\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":421,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"news_source":"","news_author":"","external_news_link":"","footnotes":""},"class_list":["post-7","page","type-page","status-publish","hentry"],"yoast_head":"\nPublications - John Paul Walters<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.isi.edu\/people-jwalters\/publications\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Publications - John Paul Walters\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.isi.edu\/people-jwalters\/publications\/\" \/>\n<meta property=\"og:site_name\" content=\"John Paul Walters\" \/>\n<meta property=\"article:modified_time\" content=\"2025-06-13T17:44:31+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/www.isi.edu\\\/people-jwalters\\\/publications\\\/\",\"url\":\"https:\\\/\\\/www.isi.edu\\\/people-jwalters\\\/publications\\\/\",\"name\":\"Publications - 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