Related papers: Many-core algorithms for high-dimensional gradient…
Calculation of the log-likelihood stands as the computational bottleneck for many statistical phylogenetic algorithms. Even worse is its gradient evaluation, often used to target regions of high probability. Order ${\cal…
Phylogenetic comparative methods correct for shared evolutionary history among a set of non-independent organisms by modeling sample traits as arising from a diffusion process along on the branches of a possibly unknown history. To…
In recent years, the Hamiltonian Monte Carlo (HMC) algorithm has been found to work more efficiently compared to other popular Markov Chain Monte Carlo (MCMC) methods (such as random walk Metropolis-Hastings) in generating samples from a…
Specialized function gradient computing hardware could greatly improve the performance of state-of-the-art optimization algorithms, e.g., based on gradient descent or conjugate gradient methods that are at the core of control, machine…
In this work, we consider the reformulation of hierarchical ($\mathcal{H}$) matrix algorithms for many-core processors with a model implementation on graphics processing units (GPUs). $\mathcal{H}$ matrices approximate specific dense…
Heterogeneity in the cell population of cancer tissues poses many challenges in cancer diagnosis and treatment. Studying the heterogeneity in cell populations from gene expression measurement data in the context of cancer research is a…
The widely-adopted practice is to train deep learning models with specialized hardware accelerators, e.g., GPUs or TPUs, due to their superior performance on linear algebra operations. However, this strategy does not employ effectively the…
Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC…
We propose a CPU-GPU heterogeneous computing method for solving time-evolution partial differential equation problems many times with guaranteed accuracy, in short time-to-solution and low energy-to-solution. On a single-GH200 node, the…
We advocate for a new paradigm of cosmological likelihood-based inference, leveraging recent developments in machine learning and its underlying technology, to accelerate Bayesian inference in high-dimensional settings. Specifically, we…
We present a versatile GPU-based parallel version of Logistic Regression (LR), aiming to address the increasing demand for faster algorithms in binary classification due to large data sets. Our implementation is a direct translation of the…
Training Large Language Models(LLMs) is one of the most compute-intensive tasks in high-performance computing. Predicting end-to-end training time for multi-billion parameter models distributed across hundreds of GPUs remains challenging…
Gene gain-loss-duplication models are commonly based on continuous-time birth-death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes.…
Eulerian nonlinear uncertainty propagation methods often suffer from finite domain limitations and computational inefficiencies. A recent approach to this class of algorithm, Grid-based Bayesian Estimation Exploiting Sparsity, addresses the…
Hamiltonian Monte Carlo is a widely used algorithm for sampling from posterior distributions of complex Bayesian models. It can efficiently explore high-dimensional parameter spaces guided by simulated Hamiltonian flows. However, the…
We present a deep neural network (DNN) accelerated Hamiltonian Monte Carlo (HMC) algorithm called DeepHMC for the inference of binary neutron star systems. The HMC is a non-random walk sampler that uses background gradient information to…
Inferring dependencies between complex biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The…
Traditional logic programming relies on symbolic computation on the CPU, which can limit performance for large-scale inference tasks. Recent advances in GPU hardware enable high-throughput matrix operations, motivating a shift toward…
In Bayesian phylogenetics, our goal is to estimate the posterior distribution over phylogenetic trees. Markov chain Monte Carlo methods are widely used to approximate the phylogenetic posterior distributions. For large-scale sequence data,…
Graph Convolutional Neural Network (GCNN) is a popular class of deep learning (DL) models in material science to predict material properties from the graph representation of molecular structures. Training an accurate and comprehensive GCNN…