Performance of Windows Multicore Systems on Threading and MPI. - Judy Qiu; Scott Beason; Seung-Hee Bae; Saliya Ekanayake; Geoffrey C. Fox (CCGRID, 2010)

Hybrid cloud and cluster computing paradigms for life science applications. - 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 (BMC Bioinform., 2010)

DACIDR: deterministic annealed clustering with interpolative dimension reduction using a large collection of 16S rRNA sequences. - Yang Ruan; Saliya Ekanayake; Mina Rho; Haixu Tang; Seung-Hee Bae; Judy Qiu; Geoffrey C. Fox (BCB, 2012)

Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets. - Adam Hughes; Yang Ruan; Saliya Ekanayake; Seung-Hee Bae; Qunfeng Dong; Mina Rho; Judy Qiu; Geoffrey C. Fox (BMC Bioinform., 2012)

Integration of Clustering and Multidimensional Scaling to Determine Phylogenetic Trees as Spherical Phylograms Visualized in 3 Dimensions. - Yang Ruan; Geoffrey L. House; Saliya Ekanayake; Ursel Schutte; James D. Bever; Haixu Tang; Geoffrey C. Fox (CCGRID, 2014)

Towards a Comprehensive Set of Big Data Benchmarks. - Geoffrey C. Fox; Shantenu Jha; Judy Qiu; Saliya Ekanayake; André Luckow (High Performance Computing Workshop, 2014)

Visualizing the Protein Sequence Universe. - Larissa Stanberry; Roger Higdon; Winston Haynes; Natali Kolker; William Broomall; Saliya Ekanayake; Adam Hughes; Yang Ruan; Judy Qiu; Eugene Kolker; Geoffrey C. Fox (Concurr. Comput. Pract. Exp., 2014)

Big Data, Simulations and HPC Convergence. - Geoffrey C. Fox; Judy Qiu; Shantenu Jha; Saliya Ekanayake; Supun Kamburugamuve (WBDB, 2015)

Java thread and process performance for parallel machine learning on multicore HPC clusters. - Saliya Ekanayake; Supun Kamburugamuve; Pulasthi Wickramasinghe; Geoffrey C. Fox (IEEE BigData, 2016)

TSmap3D: Browser visualization of high dimensional time series data. - Supun Kamburugamuve; Pulasthi Wickramasinghe; Saliya Ekanayake; Chathuri Wimalasena; Milinda Pathirage; Geoffrey C. Fox (IEEE BigData, 2016)

Towards High Performance Processing of Streaming Data in Large Data Centers. - Supun Kamburugamuve; Saliya Ekanayake; Milinda Pathirage; Geoffrey C. Fox (IPDPS Workshops, 2016)

SPIDAL Java: high performance data analytics with Java and MPI on large multicore HPC clusters. - Saliya Ekanayake; Supun Kamburugamuve; Geoffrey C. Fox (SpringSim (HPS), 2016)

Fast graph scan statistics optimization using algebraic fingerprints. - Jose Cadena; Saliya Ekanayake; Anil Vullikanti (IEEE BigData, 2017)

Generative Modeling of Human Behavior and Social Interactions Using Abductive Analysis. - Yihui Ren 001; 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; et al. (ASONAM, 2018)

Pipelines and their Compositions for Modeling and Analysis of controlled Online Networked Social Science Experiments. - Vanessa Cedeno-Mieles; Yihui Ren 001; Saliya Ekanayake; Brian J. Goode; Chris J. Kuhlman; Dustin Machi; Madhav V. Marathe; Henning S. Mortveit; Zhihao Hu; Xinwei Deng; Naren Ramakrishnan; Parang Saraf; et al. (WSC, 2018)

Anatomy of machine learning algorithm implementations in MPI, Spark, and Flink. - Supun Kamburugamuve; Pulasthi Wickramasinghe; Saliya Ekanayake; Geoffrey C. Fox (Int. J. High Perform. Comput. Appl., 2018)

Mechanistic and data-driven agent-based models to explain human behavior in online networked group anagram games. - Vanessa Cedeno-Mieles; Zhihao Hu; Xinwei Deng; Yihui Ren 001; Abhijin Adiga; Christopher L. Barrett; Saliya Ekanayake; Gizem Korkmaz; Chris J. Kuhlman; Dustin Machi; Madhav V. Marathe; S. S. Ravi; et al. (ASONAM, 2019)

The Matrix: An Agent-Based Modeling Framework for Data Intensive Simulations. - Parantapa Bhattacharya; Saliya Ekanayake; Chris J. Kuhlman; Christian Lebiere; Don Morrison; Samarth Swarup; Mandy L. Wilson; Mark G. Orr (AAMAS, 2019)

RDMA Managed Buffers: A Case for Accelerating Communication Bound Processes via Fine-Grained Events for Zero-Copy Message Passing. - Udayanga Wickramasinghe; Andrew Lumsdaine; Saliya Ekanayake; Martin Swany (ISPDC, 2019)

On the Modeling and Agent-Based Simulation of a Cooperative Group Anagram Game. - Zhihao Hu; Dustin Machi; Madhav V. Marathe; S. S. Ravi; Yihui Ren 001; Vanessa Cedeno-Mieles; Saliya Ekanayake; Xinwei Deng; Brian J. Goode; Naren Ramakrishnan; Parang Saraf; Nathan Self; et al. (WSC, 2019)

MIDAS: Multilinear detection at scale. - Saliya Ekanayake; Jose Cadena; Udayanga Wickramasinghe; Anil Vullikanti (J. Parallel Distributed Comput., 2019)

Distributed many-to-many protein sequence alignment using sparse matrices. - Oguz Selvitopi; Saliya Ekanayake; Giulia Guidi; Georgios A. Pavlopoulos; Ariful Azad; Aydin Buluç (SC, 2020)

The Parallelism Motifs of Genomic Data Analysis. - 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; et al. (CoRR, 2020)

Networked experiments and modeling for producing collective identity in a group of human subjects using an iterative abduction framework. - Vanessa Cedeno-Mieles; Zhihao Hu; Yihui Ren 001; Xinwei Deng; Abhijin Adiga; Christopher L. Barrett; Noshir Contractor; Saliya Ekanayake; Joshua M. Epstein; Brian J. Goode; Gizem Korkmaz; Chris J. Kuhlman; et al. (Soc. Netw. Anal. Min., 2020)

Parallel Algorithms for Densest Subgraph Discovery Using Shared Memory Model. - B. D. M. De Zoysa; Y. A. M. M. A. Ali; M. D. I. Maduranga; Indika Perera; Saliya Ekanayake; Anil Vullikanti (CoRR, 2021)

Extreme-Scale Many-against-Many Protein Similarity Search. - Oguz Selvitopi; Saliya Ekanayake; Giulia Guidi; Muaaz G. Awan; Georgios A. Pavlopoulos; Ariful Azad; Nikos Kyrpides; Leonid Oliker; Katherine A. Yelick; Aydin Buluç (SC, 2022)

Stochastic gradient descent-based support vector machines training optimization on Big Data and HPC frameworks. - 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 (Concurr. Comput. Pract. Exp., 2022)