19 citations · 57 across the 11 of their papers we have counts for
14 papers
StFT: Spatio-temporal Fourier Transformer for Long-term Dynamics Prediction
Da Long, Shandian Zhe, Samuel Williams +2
Simulating the long-term dynamics of multi-scale and multi-physics systems poses a significant challenge in understanding complex phenomena across science and engineering. The comp…
FTL: Transfer Learning Nonlinear Plasma Dynamic Transitions in Low Dimensional Embeddings via Deep Neural Networks
Zhe Bai, Xishuo Wei, William Tang +3
Deep learning algorithms provide a new paradigm to study high-dimensional dynamical behaviors, such as those in fusion plasma systems. Development of novel model reduction methods,…
Evaluating the Potential of Disaggregated Memory Systems for HPC applications
Nan Ding, Pieter Maris, Hai Ah Nam +8
Disaggregated memory is a promising approach that addresses the limitations of traditional memory architectures by enabling memory to be decoupled from compute nodes and shared acr…
Extreme-scale many-against-many protein similarity search
Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi +7
Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncoverin…
Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly
Giulia Guidi, Gabriel Raulet, Daniel Rokhsar +3
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomi…
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…
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…
Extreme Scale De Novo Metagenome Assembly
Evangelos Georganas, Rob Egan, Steven Hofmeyr +6
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation o…
Communication-Avoiding Optimization Methods for Distributed Massive-Scale Sparse Inverse Covariance Estimation
Penporn Koanantakool, Alnur Ali, Ariful Azad +5
Across a variety of scientific disciplines, sparse inverse covariance estimation is a popular tool for capturing the underlying dependency relationships in multivariate data. Unfor…
Extreme-Scale De Novo Genome Assembly
Evangelos Georganas, Steven Hofmeyr, Rob Egan +4
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern…
LiRa: A New Likelihood-Based Similarity Score for Collaborative Filtering
Veronika Strnadova-Neeley, Aydin Buluc, John R. Gilbert +2
Recommender system data presents unique challenges to the data mining, machine learning, and algorithms communities. The high missing data rate, in combination with the large scale…
Modern Gyrokinetic Particle-In-Cell Simulation of Fusion Plasmas on Top Supercomputers
Bei Wang, Stephane Ethier, William Tang +4
The Gyrokinetic Toroidal Code at Princeton (GTC-P) is a highly scalable and portable particle-in-cell (PIC) code. It solves the 5D Vlasov-Poisson equation featuring efficient utili…