20 citations · 40 across the 9 of their papers we have counts for
10 papers
Evaluating the Potential of Disaggregated Memory Systems for HPC applications
Nan Ding, Pieter Maris, Hai Ah Nam +8
Disaggregated memory is a promising approach that addresses the limitations of traditional memory architectures by enabling memory to be decoupled from compute nodes and shared acr…
Extreme-scale many-against-many protein similarity search
Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi +7
Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncoverin…
Parallel Algorithms for Masked Sparse Matrix-Matrix Products
Srđan Milaković, Oguz Selvitopi, Israt Nisa +2
Computing the product of two sparse matrices (SpGEMM) is a fundamental operation in various combinatorial and graph algorithms as well as various bioinformatics and data analytics…
Combinatorial BLAS 2.0: Scaling combinatorial algorithms on distributed-memory systems
Ariful Azad, Oguz Selvitopi, Md Taufique Hussain +2
Combinatorial algorithms such as those that arise in graph analysis, modeling of discrete systems, bioinformatics, and chemistry, are often hard to parallelize. The Combinatorial B…
Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly
Giulia Guidi, Oguz Selvitopi, Marquita Ellis +3
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous…
Communication-Avoiding and Memory-Constrained Sparse Matrix-Matrix Multiplication at Extreme Scale
Md Taufique Hussain, Oguz Selvitopi, Aydin Buluç +1
Sparse matrix-matrix multiplication (SpGEMM) is a widely used kernel in various graph, scientific computing and machine learning algorithms. In this paper, we consider SpGEMMs perf…
Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices
Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi +3
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein gra…
Optimizing High Performance Markov Clustering for Pre-Exascale Architectures
Oguz Selvitopi, Md Taufique Hussain, Ariful Azad +1
HipMCL is a high-performance distributed memory implementation of the popular Markov Cluster Algorithm (MCL) and can cluster large-scale networks within hours using a few thousand…
The Parallelism Motifs of Genomic Data Analysis
Katherine Yelick, Aydin Buluc, Muaaz Awan +11
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and shar…
A High-Throughput Solver for Marginalized Graph Kernels on GPU
Yu-Hang Tang, Oguz Selvitopi, Doru Popovici +1
We present the design and optimization of a linear solver on General Purpose GPUs for the efficient and high-throughput evaluation of the marginalized graph kernel between pairs of…