Related papers: BioEM: GPU-accelerated computing of Bayesian infer…
We describe a Bayesian framework for an inverse problem arising from monitoring block caving operations via muon tomography. We work with a low dimensional surface-based representation of the geometry of the block cave, which dramatically…
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…
If classical algorithms have been successful in reproducing the estimation of expectation values of observables of some quantum circuits using off-the-shelf computing resources, matching the performance of the most advanced quantum devices…
We present a GPU-accelerated version of the real-space SPARC electronic structure code for performing Kohn-Sham density functional theory calculations within the local density and generalized gradient approximations. In particular, we…
Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep…
Computational microscopy, in which hardware and algorithms of an imaging system are jointly designed, shows promise for making imaging systems that cost less, perform more robustly, and collect new types of information. Often, the…
The CryoEM single particle imaging method has recently received broad attention in the field of structural biology for determining the structures of biological molecules. The structures can be resolved to near-atomic resolutions after…
Discrete optimization is a central problem in artificial intelligence. The optimization of the aggregated cost of a network of cost functions arises in a variety of problems including (W)CSP, DCOP, as well as optimization in stochastic…
We study Bayesian methods for large-scale linear inverse problems, focusing on the challenging task of hyperparameter estimation. Typical hierarchical Bayesian formulations that follow a Markov Chain Monte Carlo approach are possible for…
It has been widely accepted that Graphics Processing Units (GPU) is one of promising schemes for encryption acceleration, in particular, the support of complex mathematical calculations such as integer and logical operations makes the…
Cellular Electron Cryotomography (CryoET) offers the ability to look inside cells and observe macromolecules frozen in action. A primary challenge for this technique is identifying and extracting the molecular components within the crowded…
Principal component analysis (PCA) plays an important role in the analysis of cryo-EM images for various tasks such as classification, denoising, compression, and ab-initio modeling. We introduce a fast method for estimating a compressed…
Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients induced by differing concentrations of charged ions. A growing body of research suggests that…
It is time-consuming and error-prone to implement inference procedures for each new probabilistic model. Probabilistic programming addresses this problem by allowing a user to specify the model and having a compiler automatically generate…
Reconstruction of the tridimensional geometry of a visual scene using the binocular disparity information is an important issue in computer vision and mobile robotics, which can be formulated as a Bayesian inference problem. However,…
Nowadays, the amount of heterogeneous biomedical data is increasing more and more thanks to novel sensing techniques and high-throughput technologies. In reference to biomedical image analysis, the advances in image acquisition modalities…
Single-beam scanning electron microscopes (SEM) are widely used to acquire massive data sets for biomedical study, material analysis, and fabrication inspection. Datasets are typically acquired with uniform acquisition: applying the…
Computational spectral imaging is drawing increasing attention owing to the snapshot advantage, and amplitude, phase, and wavelength encoding systems are three types of representative implementations. Fairly comparing and understanding the…
We propose a multistage method for making inference at all levels of a Bayesian hierarchical model (BHM) using natural data partitions to increase efficiency by allowing computations to take place in parallel form using software that is…
The goal of cryo-electron microscopy (EM) is to reconstruct the 3-dimensional structure of a molecule from a collection of its 2-dimensional projected images. In this article, we show that the basic premise of cryo-EM --- patching together…