7 papers
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…