Related papers: BioEM: GPU-accelerated computing of Bayesian infer…
The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class bio-molecular dynamics (MD) simulation…
In this paper, a fast and practical GPU-based implementation of Fuzzy C-Means(FCM) clustering algorithm for image segmentation is proposed. First, an extensive analysis is conducted to study the dependency among the image pixels in the…
Bayesian variable selection methods are powerful techniques for fitting and inferring on sparse high-dimensional linear regression models. However, many are computationally intensive or require restrictive prior distributions on model…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
In this paper, we demonstrate how GPU-accelerated BEM routines can be used in a simple black-box fashion to accelerate fast boundary element formulations based on Hierarchical Matrices (H-Matrices) with ACA (Adaptive Cross Approximation).…
The rapid growth in genomic pathogen data spurs the need for efficient inference techniques, such as Hamiltonian Monte Carlo (HMC) in a Bayesian framework, to estimate parameters of these phylogenetic models where the dimensions of the…
Quantitative MRI (qMRI) offers tissue-specific biomarkers that can be tracked over time or compared across populations; however, its adoption in clinical research is hindered by significant computational demands of parameter estimation.…
Motivation: Surface generation and visualization are some of the most important tasks in biomolecular modeling and computation. Eulerian solvent excluded surface (ESES) software provides analytical solvent excluded surface (SES) in the…
Almost all fields of science rely upon statistical inference to estimate unknown parameters in theoretical and computational models. While the performance of modern computer hardware continues to grow, the computational requirements for the…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
We introduce a framework for recovering an image from its rotationally and translationally invariant features based on autocorrelation analysis. This work is an instance of the multi-target detection statistical model, which is mainly used…
This comprehensive review discusses the development of scanning electron microscopy and the application of this technology in different fields such as biology, nanobiotechnology and biomedical science. Besides being a tool for high…
Cellular Electron Cryo-Tomography (CECT) is a powerful imaging technique for the 3D visualization of cellular structure and organization at submolecular resolution. It enables analyzing the native structures of macromolecular complexes and…
The so-called matrix-element method (MEM) has long been used successfully as a classification tool in particle physics searches. In the presence of invisible final state particles, the traditional MEM typically assigns probabilities to an…
The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale…
Constructing of molecular structural models from Cryo-Electron Microscopy (Cryo-EM) density volumes is the critical last step of structure determination by Cryo-EM technologies. Methods have evolved from manual construction by structural…
Bayesian meta-learning enables robust and fast adaptation to new tasks with uncertainty assessment. The key idea behind Bayesian meta-learning is empirical Bayes inference of hierarchical model. In this work, we extend this framework to…
The recent improvements in cryo-electron microscopy (cryo-EM) in the past few years are now allowing to observe molecular complexes at atomic resolution. As a consequence, numerous structures derived from cryo-EM are now available in the…
Decision making often uses complex computer codes run at the exa-scale (10e18 flops). Such computer codes or models are often run in a hierarchy of different levels of fidelity ranging from the basic to the very sophisticated. The top…
The increasing availability of GPUs for scientific computing has prompted interest in accelerating quantum chemical calculations through their use. The complexity of integral kernels for high angular momentum basis functions however often…