Saliya Ekanayake

Publication Activity (10 Years)

Years Active: 2010-2023
Publications (10 Years): 22

Top Topics

Multidimensional Scaling

Sequence Alignment

Top Venues

Concurr. Comput. Pract. Exp.

Publications

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 (2023)
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)
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)
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 (2021)
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)
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) (2020)
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 (2020)
Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi, Georgios A. Pavlopoulos, Ariful Azad, Aydin Buluç
Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices. CoRR (2020)
Saliya Ekanayake, Jose Cadena, Udayanga Wickramasinghe, Anil Vullikanti
MIDAS: Multilinear detection at scale. J. Parallel Distributed Comput. 132 (2019)
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)
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)
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)
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)
Saliya Ekanayake, Jose Cadena, Udayanga Wickramasinghe, Anil Vullikanti
MIDAS: Multilinear Detection at Scale. IPDPS (2018)
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)
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) (2018)
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)
Jose Cadena, Saliya Ekanayake, Anil Vullikanti
Fast graph scan statistics optimization using algebraic fingerprints. IEEE BigData (2017)
Supun Kamburugamuve, Saliya Ekanayake, Milinda Pathirage, Geoffrey C. Fox
Towards High Performance Processing of Streaming Data in Large Data Centers. IPDPS Workshops (2016)
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)
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)
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)
Geoffrey C. Fox, Judy Qiu, Shantenu Jha, Saliya Ekanayake, Supun Kamburugamuve
Big Data, Simulations and HPC Convergence. WBDB (2015)
Geoffrey C. Fox, Shantenu Jha, Judy Qiu, Saliya Ekanayake, André Luckow
Towards a Comprehensive Set of Big Data Benchmarks. High Performance Computing Workshop (2014)
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)
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) (2014)
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) (2012)
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)
Judy Qiu, Scott Beason, Seung-Hee Bae, Saliya Ekanayake, Geoffrey C. Fox
Performance of Windows Multicore Systems on Threading and MPI. CCGRID (2010)
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) (2010)