27 citations · 150 across the 20 of their papers we have counts for
9 papers · 1 filter
10 Years Later: Cloud Computing is Closing the Performance Gap
Giulia Guidi, Marquita Ellis, Aydin Buluc +2
Can cloud computing infrastructures provide HPC-competitive performance for scientific applications broadly? Despite prolific related literature, this question remains open. Answer…
PersGNN: Applying Topological Data Analysis and Geometric Deep Learning to Structure-Based Protein Function Prediction
Nicolas Swenson, Aditi S. Krishnapriyan, Aydin Buluc +2
Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While…
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…
Opportunities and Challenges for Next Generation Computing
Gregory D. Hager, Mark D. Hill, Katherine Yelick
Computing has dramatically changed nearly every aspect of our lives, from business and agriculture to communication and entertainment. As a nation, we rely on computing in the desi…
Reducing Communication in Graph Neural Network Training
Alok Tripathy, Katherine Yelick, Aydin Buluc
Graph Neural Networks (GNNs) are powerful and flexible neural networks that use the naturally sparse connectivity information of the data. GNNs represent this connectivity as spars…
QFAST: Quantum Synthesis Using a Hierarchical Continuous Circuit Space
Ed Younis, Koushik Sen, Katherine Yelick +1
We present QFAST, a quantum synthesis tool designed to produce short circuits and to scale well in practice. Our contributions are: 1) a novel representation of circuits able to en…
LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment
Alberto Zeni, Giulia Guidi, Marquita Ellis +6
Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applic…
diBELLA: Distributed Long Read to Long Read Alignment
Marquita Ellis, Giulia Guidi, Aydın Buluç +2
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long r…
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…