56 citations · 79 across the 8 of their papers we have counts for
8 papers
Fast sequence to graph alignment using the graph wavefront algorithm
Haowen Zhang, Shiqi Wu, Srinivas Aluru +1
Motivation: A pan-genome graph represents a collection of genomes and encodes sequence variations between them. It is a powerful data structure for studying multiple similar genome…
The Complexity of Approximate Pattern Matching on De Bruijn Graphs
Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru
Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with edges that exa…
Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems
Vasimuddin Md, Sanchit Misra, Heng Li +1
Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data at ever faster rates and at very low cost. Large sequencing centers typically employ hundreds…
Cooperative neural networks (CoNN): Exploiting prior independence structure for improved classification
Harsh Shrivastava, Eugene Bart, Bob Price +3
We propose a new approach, called cooperative neural networks (CoNN), which uses a set of cooperatively trained neural networks to capture latent representations that exploit prior…
Parallelized Kendall's Tau Coefficient Computation via SIMD Vectorized Sorting On Many-Integrated-Core Processors
Yongchao Liu, Tony Pan, Oded Green +1
Pairwise association measure is an important operation in data analytics. Kendall's tau coefficient is one widely used correlation coefficient identifying non-linear relationships…
Parallel Pairwise Correlation Computation On Intel Xeon Phi Clusters
Yongchao Liu, Tony Pan, Srinivas Aluru
Co-expression network is a critical technique for the identification of inter-gene interactions, which usually relies on all-pairs correlation (or similar measure) computation betw…
LightScan: Faster Scan Primitive on CUDA Compatible Manycore Processors
Yongchao Liu, Srinivas Aluru
Scan (or prefix sum) is a fundamental and widely used primitive in parallel computing. In this paper, we present LightScan, a faster parallel scan primitive for CUDA-enabled GPUs,…
A Parallel Algorithm for Exact Bayesian Structure Discovery in Bayesian Networks
Yetian Chen, Jin Tian, Olga Nikolova +1
Exact Bayesian structure discovery in Bayesian networks requires exponential time and space. Using dynamic programming (DP), the fastest known sequential algorithm computes the exa…