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05/08/2023
CPMA: An Efficient Batch-Parallel Compressed Set Without Pointers
This paper introduces the batch-parallel Compressed Packed Memory Array ...
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04/17/2023
Space Efficient Sequence Alignment for SRAM-Based Computing: X-Drop on the Graphcore IPU
Dedicated accelerator hardware has become essential for processing AI-ba...
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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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01/29/2023
Fast Exact Leverage Score Sampling from Khatri-Rao Products with Applications to Tensor Decomposition
We present a data structure to randomly sample rows from the Khatri-Rao ...
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10/11/2022
Distributed-Memory Randomized Algorithms for Sparse Tensor CP Decomposition
Low-rank Candecomp / PARAFAC (CP) Decomposition is a powerful tool for t...
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09/07/2022
Large Scale Enrichment and Statistical Cyber Characterization of Network Traffic
Modern network sensors continuously produce enormous quantities of raw d...
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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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03/25/2022
GraphBLAS on the Edge: Anonymized High Performance Streaming of Network Traffic
Long range detection is a cornerstone of defense in many operating domai...
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03/19/2022
Temporal Correlation of Internet Observatories and Outposts
The Internet has become a critical component of modern civilization requ...
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03/15/2022
Distributed-Memory Sparse Kernels for Machine Learning
Sampled Dense Times Dense Matrix Multiplication (SDDMM) and Sparse Times...
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12/19/2021
Parallel Algorithms for Adding a Collection of Sparse Matrices
We develop a family of parallel algorithms for the SpKAdd operation that...
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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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11/18/2021
Parallel Algorithms for Masked Sparse Matrix-Matrix Products
Computing the product of two sparse matrices (SpGEMM) is a fundamental o...
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08/15/2021
Spatial Temporal Analysis of 40,000,000,000,000 Internet Darkspace Packets
The Internet has never been more important to our society, and understan...
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06/28/2021
Combinatorial BLAS 2.0: Scaling combinatorial algorithms on distributed-memory systems
Combinatorial algorithms such as those that arise in graph analysis, mod...
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04/19/2021
Randomized Algorithms for Scientific Computing (RASC)
Randomized algorithms have propelled advances in artificial intelligence...
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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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10/16/2020
Communication-Avoiding and Memory-Constrained Sparse Matrix-Matrix Multiplication at Extreme Scale
Sparse matrix-matrix multiplication (SpGEMM) is a widely used kernel in ...
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09/30/2020
Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices
Identifying similar protein sequences is a core step in many computation...
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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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02/24/2020
Optimizing High Performance Markov Clustering for Pre-Exascale Architectures
HipMCL is a high-performance distributed memory implementation of the po...
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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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10/14/2019
A High-Throughput Solver for Marginalized Graph Kernels on GPU
We present the design of a solver for the efficient and high-throughput ...
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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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08/04/2019
GraphBLAST: A High-Performance Linear Algebra-based Graph Framework on the GPU
High-performance implementations of graph algorithms are challenging to ...
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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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04/10/2018
Implementing Push-Pull Efficiently in GraphBLAS
We factor Beamer's push-pull, also known as direction-optimized breadth-...
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04/05/2018
High-performance sparse matrix-matrix products on Intel KNL and multicore architectures
Sparse matrix-matrix multiplication (SpGEMM) is a computational primitiv...
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03/22/2018
Design Principles for Sparse Matrix Multiplication on the GPU
We implement two novel algorithms for sparse-matrix dense-matrix multipl...
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01/30/2018
A distributed-memory approximation algorithm for maximum weight perfect bipartite matching
We design and implement an efficient parallel approximation algorithm fo...
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12/12/2017
Integrated Model, Batch and Domain Parallelism in Training Neural Networks
We propose a new integrated method of exploiting model, batch and domain...
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12/12/2017
Integrated Model and Data Parallelism in Training Neural Networks
We propose a new integrated method of exploiting both model and data par...
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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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10/26/2016
The Reverse Cuthill-McKee Algorithm in Distributed-Memory
Ordering vertices of a graph is key to minimize fill-in and data structu...
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06/18/2016