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ORCIDSaliya Ekanayake
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Journal Articles
- 2022
[j7]Vibhatha Abeykoon
, Geoffrey C. Fox, Minje Kim, Saliya Ekanayake, Supun Kamburugamuve, Kannan Govindarajan, Pulasthi Wickramasinghe, Niranda Perera, Chathura Widanage, Ahmet Uyar, Gurhan Gunduz, Selahatin Akkas:
Stochastic gradient descent-based support vector machines training optimization on Big Data and HPC frameworks. Concurr. Comput. Pract. Exp. 34(8) (2022)- 2020
- [j6]Vanessa Cedeno-Mieles, Zhihao Hu, Yihui Ren, Xinwei Deng, Abhijin Adiga, Christopher L. Barrett, Noshir Contractor, Saliya Ekanayake, Joshua M. Epstein, Brian J. Goode, Gizem Korkmaz, Chris J. Kuhlman, Dustin Machi, Michael W. Macy, Madhav V. Marathe, Naren Ramakrishnan, S. S. Ravi, Parang Saraf, Nathan Self:
Networked experiments and modeling for producing collective identity in a group of human subjects using an iterative abduction framework. Soc. Netw. Anal. Min. 10(1): 11 (2020) - 2019
- [j5]Saliya Ekanayake, Jose Cadena, Udayanga Wickramasinghe, Anil Vullikanti:
MIDAS: Multilinear detection at scale. J. Parallel Distributed Comput. 132: 363-382 (2019) - 2018
- [j4]Supun Kamburugamuve, Pulasthi Wickramasinghe, Saliya Ekanayake, Geoffrey C. Fox:
Anatomy of machine learning algorithm implementations in MPI, Spark, and Flink. Int. J. High Perform. Comput. Appl. 32(1): 61-73 (2018) - 2014
- [j3]Larissa Stanberry, Roger Higdon, Winston Haynes, Natali Kolker, William Broomall, Saliya Ekanayake, Adam Hughes, Yang Ruan, Judy Qiu, Eugene Kolker, Geoffrey C. Fox:
Visualizing the Protein Sequence Universe. Concurr. Comput. Pract. Exp. 26(6): 1313-1325 (2014) - 2012
- [j2]Adam Hughes, Yang Ruan, Saliya Ekanayake, Seung-Hee Bae, Qunfeng Dong, Mina Rho, Judy Qiu, Geoffrey C. Fox:
Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets. BMC Bioinform. 13(S-2): S9 (2012) - 2010
- [j1]Judy Qiu, Jaliya Ekanayake, Thilina Gunarathne, Jong Youl Choi, Seung-Hee Bae, Hui Li, Bingjing Zhang, Tak-Lon Wu, Yang Ruan, Saliya Ekanayake, Adam Hughes, Geoffrey C. Fox:
Hybrid cloud and cluster computing paradigms for life science applications. BMC Bioinform. 11(S-12): S3 (2010)
Conference and Workshop Papers
- 2022
- [c19]Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi, Muaaz G. Awan, Georgios A. Pavlopoulos, Ariful Azad, Nikos Kyrpides, Leonid Oliker, Katherine A. Yelick, Aydin Buluç:
Extreme-Scale Many-against-Many Protein Similarity Search. SC 2022: 1:1-1:12 - 2020
- [c18]Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi, Georgios A. Pavlopoulos, Ariful Azad, Aydin Buluç:
Distributed many-to-many protein sequence alignment using sparse matrices. SC 2020: 75 - 2019
- [c17]Vanessa Cedeno-Mieles, Zhihao Hu, Xinwei Deng, Yihui Ren, Abhijin Adiga, Christopher L. Barrett, Saliya Ekanayake, Gizem Korkmaz, Chris J. Kuhlman, Dustin Machi, Madhav V. Marathe, S. S. Ravi, Brian J. Goode, Naren Ramakrishnan, Parang Saraf, Nathan Self, Noshir Contractor, Joshua M. Epstein, Michael W. Macy:
Mechanistic and data-driven agent-based models to explain human behavior in online networked group anagram games. ASONAM 2019: 357-364 - [c16]Parantapa Bhattacharya, Saliya Ekanayake, Chris J. Kuhlman, Christian Lebiere, Don Morrison, Samarth Swarup, Mandy L. Wilson, Mark G. Orr:
The Matrix: An Agent-Based Modeling Framework for Data Intensive Simulations. AAMAS 2019: 1635-1643 - [c15]Udayanga Wickramasinghe, Andrew Lumsdaine, Saliya Ekanayake, Martin Swany:
RDMA Managed Buffers: A Case for Accelerating Communication Bound Processes via Fine-Grained Events for Zero-Copy Message Passing. ISPDC 2019: 121-130 - [c14]Zhihao Hu, Dustin Machi, Madhav V. Marathe, S. S. Ravi, Yihui Ren, Vanessa Cedeno-Mieles, Saliya Ekanayake, Xinwei Deng, Brian J. Goode, Naren Ramakrishnan, Parang Saraf, Nathan Self, Abhijin Adiga, Gizem Korkmaz, Chris J. Kuhlman:
On the Modeling and Agent-Based Simulation of a Cooperative Group Anagram Game. WSC 2019: 169-180 - 2018
- [c13]Yihui Ren, Vanessa Cedeno-Mieles, Zhihao Hu, Xinwei Deng, Abhijin Adiga, Christopher L. Barrett, Saliya Ekanayake, Brian J. Goode, Gizem Korkmaz, Chris J. Kuhlman, Dustin Machi, Madhav V. Marathe, Naren Ramakrishnan, S. S. Ravi, Parang Saraf, Nathan Self, Noshir Contractor, Joshua M. Epstein, Michael W. Macy:
Generative Modeling of Human Behavior and Social Interactions Using Abductive Analysis. ASONAM 2018: 413-420 - [c12]Saliya Ekanayake, Jose Cadena, Udayanga Wickramasinghe, Anil Vullikanti:
MIDAS: Multilinear Detection at Scale. IPDPS 2018: 2-11 - [c11]Vanessa Cedeno-Mieles, Yihui Ren, Saliya Ekanayake, Brian J. Goode, Chris J. Kuhlman, Dustin Machi, Madhav V. Marathe, Henning S. Mortveit, Zhihao Hu, Xinwei Deng, Naren Ramakrishnan, Parang Saraf, Nathan Self, Noshir Contractor, Joshua M. Epstein, Michael W. Macy:
Pipelines and their Compositions for Modeling and Analysis of controlled Online Networked Social Science Experiments. WSC 2018: 774-785 - 2017
- [c10]Jose Cadena, Saliya Ekanayake, Anil Vullikanti:
Fast graph scan statistics optimization using algebraic fingerprints. IEEE BigData 2017: 905-910 - 2016
- [c9]Saliya Ekanayake, Supun Kamburugamuve, Pulasthi Wickramasinghe, Geoffrey C. Fox:
Java thread and process performance for parallel machine learning on multicore HPC clusters. IEEE BigData 2016: 347-354 - [c8]Supun Kamburugamuve, Pulasthi Wickramasinghe, Saliya Ekanayake, Chathuri Wimalasena, Milinda Pathirage, Geoffrey C. Fox:
TSmap3D: Browser visualization of high dimensional time series data. IEEE BigData 2016: 3583-3592 - [c7]Supun Kamburugamuve, Saliya Ekanayake, Milinda Pathirage, Geoffrey C. Fox:
Towards High Performance Processing of Streaming Data in Large Data Centers. IPDPS Workshops 2016: 1637-1644 - [c6]Saliya Ekanayake, Supun Kamburugamuve, Geoffrey C. Fox:
SPIDAL Java: high performance data analytics with Java and MPI on large multicore HPC clusters. SpringSim (HPS) 2016: 3 - 2015
- [c5]Geoffrey C. Fox, Judy Qiu, Shantenu Jha, Saliya Ekanayake, Supun Kamburugamuve:
Big Data, Simulations and HPC Convergence. WBDB 2015: 3-17 - 2014
- [c4]Yang Ruan, Geoffrey L. House, Saliya Ekanayake, Ursel Schutte, James D. Bever, Haixu Tang, Geoffrey C. Fox:
Integration of Clustering and Multidimensional Scaling to Determine Phylogenetic Trees as Spherical Phylograms Visualized in 3 Dimensions. CCGRID 2014: 720-729 - [c3]Geoffrey C. Fox, Shantenu Jha, Judy Qiu, Saliya Ekanayake, André Luckow:
Towards a Comprehensive Set of Big Data Benchmarks. High Performance Computing Workshop 2014: 47-66 - 2012
- [c2]Yang Ruan, Saliya Ekanayake, Mina Rho, Haixu Tang, Seung-Hee Bae, Judy Qiu, Geoffrey C. Fox:
DACIDR: deterministic annealed clustering with interpolative dimension reduction using a large collection of 16S rRNA sequences. BCB 2012: 329-336 - 2010
- [c1]Judy Qiu, Scott Beason, Seung-Hee Bae, Saliya Ekanayake, Geoffrey C. Fox:
Performance of Windows Multicore Systems on Threading and MPI. CCGRID 2010: 814-819
Informal and Other Publications
- 2023
- [i4]Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi, Muaaz G. Awan, Georgios A. Pavlopoulos, Ariful Azad, Nikos Kyrpides, Leonid Oliker, Katherine A. Yelick, Aydin Buluç:
Extreme-scale many-against-many protein similarity search. CoRR abs/2303.01845 (2023) - 2021
- [i3]B. D. M. De Zoysa, Y. A. M. M. A. Ali, M. D. I. Maduranga, Indika Perera, Saliya Ekanayake, Anil Vullikanti:
Parallel Algorithms for Densest Subgraph Discovery Using Shared Memory Model. CoRR abs/2103.00154 (2021) - 2020
- [i2]Katherine A. Yelick, Aydin Buluç, Muaaz G. Awan, Ariful Azad, Benjamin Brock, Rob Egan, Saliya Ekanayake, Marquita Ellis, Evangelos Georganas, Giulia Guidi, Steven A. Hofmeyr, Oguz Selvitopi, Cristina Teodoropol, Leonid Oliker:
The Parallelism Motifs of Genomic Data Analysis. CoRR abs/2001.06989 (2020) - [i1]Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi, Georgios A. Pavlopoulos, Ariful Azad, Aydin Buluç:
Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices. CoRR abs/2009.14467 (2020)
Coauthor Index
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