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03/03/2023
Extreme-scale many-against-many protein similarity search
Similarity search is one of the most fundamental computations that are r...
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12/18/2022
High-Performance Filters For GPUs
Filters approximately store a set of items while trading off accuracy fo...
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07/10/2022
Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly
De novo genome assembly, i.e., rebuilding the sequence of an unknown gen...
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11/30/2021
Atos: A Task-Parallel GPU Dynamic Scheduling Framework for Dynamic Irregular Computations
We present Atos, a task-parallel GPU dynamic scheduling framework that i...
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11/02/2020
10 Years Later: Cloud Computing is Closing the Performance Gap
Can cloud computing infrastructures provide HPC-competitive performance ...
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10/30/2020
PersGNN: Applying Topological Data Analysis and Geometric Deep Learning to Structure-Based Protein Function Prediction
Understanding protein structure-function relationships is a key challeng...
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10/20/2020
Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly
One of the most computationally intensive tasks in computational biology...
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07/31/2020
Opportunities and Challenges for Next Generation Computing
Computing has dramatically changed nearly every aspect of our lives, fro...
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05/07/2020
Reducing Communication in Graph Neural Network Training
Graph Neural Networks (GNNs) are powerful and flexible neural networks t...
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02/12/2020
LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment
Pairwise sequence alignment is one of the most computationally intensive...
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01/27/2020
diBELLA: Distributed Long Read to Long Read Alignment
We present a parallel algorithm and scalable implementation for genome a...
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01/20/2020
The Parallelism Motifs of Genomic Data Analysis
Genomic data sets are growing dramatically as the cost of sequencing con...
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10/04/2019
RDMA vs. RPC for Implementing Distributed Data Structures
Distributed data structures are key to implementing scalable application...
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10/30/2018
BCL: A Cross-Platform Distributed Container Library
One-sided communication is a useful paradigm for irregular parallel appl...
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09/19/2018
Extreme Scale De Novo Metagenome Assembly
Metagenome assembly is the process of transforming a set of short, overl...
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10/30/2017
Communication-Avoiding Optimization Methods for Massive-Scale Graphical Model Structure Learning
Undirected graphical models compactly represent the structure of large, ...
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07/29/2016
An Asynchronous Task-based Fan-Both Sparse Cholesky Solver
Systems of linear equations arise at the heart of many scientific and en...
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04/06/2016
