Related papers: BioEM: GPU-accelerated computing of Bayesian infer…
Evolution can be broadly described in terms of mutations of the genotype and the subsequent selection of the phenotype. The full enumeration of a given genotype-phenotype (GP) map is therefore a powerful technique in examining evolutionary…
The cryo-electron microscope (cryo-EM) is increasingly popular these years. It helps to uncover the biological structures and functions of macromolecules. In this paper, we address image denoising problem in cryo-EM. Denoising the cryo-EM…
General Matrix Multiplication (GEMM) is a critical operation underpinning a wide range of applications in high-performance computing (HPC) and artificial intelligence (AI). The emergence of hardware optimized for low-precision arithmetic…
Bayesian inference for exponential family random graph models (ERGMs) is a doubly-intractable problem because of the intractability of both the likelihood and posterior normalizing factor. Auxiliary variable based Markov Chain Monte Carlo…
To accurately reproduce measurements from the real world, simulators need to have an adequate model of the physical system and require the parameters of the model be identified. We address the latter problem of estimating parameters through…
Programmable self-assembly has recently enabled the creation of complex structures through precise control of the interparticle interactions and the particle geometries. Targeting ever more structurally complex, dynamic, and functional…
The Expectation-Maximization (EM) algorithm is a fundamental tool in unsupervised machine learning. It is often used as an efficient way to solve Maximum Likelihood (ML) estimation problems, especially for models with latent variables. It…
Super-resolution imaging techniques have largely improved our capabilities to visualize nanometric structures in biological systems. Their application further enables one to potentially quantitate relevant parameters to determine the…
Energy-based models (EBMs) provide a powerful and flexible way of learning a joint probability distribution over data by constructing an energy surface. This energy surface enables insight extraction and conditional sampling. We apply EBMs…
Enhancing seismic fragility and risk assessment of nuclear power plants relies on accurate prediction of reactor building responses to seismic hazards, which can be further improved through dynamic analysis of high-fidelity finite element…
The number of noisy images required for molecular reconstruction in single-particle cryo-electron microscopy (cryo-EM) is governed by the autocorrelations of the observed, randomly-oriented, noisy projection images. In this work, we…
We show that de-focused single particle images recorded using a cryo-electron microscope (cryoEM) system may be processed like a Fresnel zone in-line hologram to obtain physically meaningful quantitative phase maps associated with…
This paper asks whether integrating multimodal EEG and fMRI data offers a better characterisation of functional brain architectures than either modality alone. This evaluation rests upon a dynamic causal model that generates both EEG and…
We present a GPU-accelerated cosmological simulation code, PhotoNs-GPU, based on algorithm of Particle Mesh Fast Multipole Method (PM-FMM), and focus on the GPU utilization and optimization. A proper interpolated method for truncated…
Quantitative high-resolution transmission electron microscopy (HRTEM) provides an indispensable means to understand the structure-property relationships of a material in atomic dimensions. Successful quantification requires reliable…
Cryo-EM reconstruction algorithms seek to determine a molecule's 3D density map from a series of noisy, unlabeled 2D projection images captured with an electron microscope. Although reconstruction algorithms typically model the 3D volume as…
The graphics processing unit (GPU) has emerged as a powerful and cost effective processor for general performance computing. GPUs are capable of an order of magnitude more floating-point operations per second as compared to modern central…
Controlling the properties of organic/inorganic materials requires detailed knowledge of their molecular adsorption geometries. This is often unattainable, even with current state-of-the-art tools. Visualizing the structure of complex…
Finite mixture models have been widely used for the modelling and analysis of data from heterogeneous populations. Maximum likelihood estimation of the parameters is typically carried out via the Expectation-Maximization (EM) algorithm. The…
The human neuromuscular system consisting of skeletal muscles and neural circuits is a complex system that is not yet fully understood. Surface electromyography (EMG) can be used to study muscle behavior from the outside. Computer…