Related papers: Using data-reduction techniques to analyse biomole…

Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…

Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…

In this paper, we propose a method for semantic segmentation of pedestrian trajectories based on pedestrian behavior models, or agents. The agents model the dynamics of pedestrian movements in two-dimensional space using a linear dynamics…

Diffusions are a successful technique to sample from high-dimensional distributions. The target distribution can be either explicitly given or learnt from a collection of samples. They implement a diffusion process whose endpoint is a…

Multiple time scale stochastic dynamical systems are ubiquitous in science and engineering, and the reduction of such systems and their models to only their slow components is often essential for scientific computation and further analysis.…

Dynamically changing graphs are used in many applications of graph algorithms. The scope of these graphs are in graphics, communication networks and in VLSI designs where graphs are subjected to change, such as addition and deletion of…

Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their…

We introduce a data-driven approach to building reduced dynamical models through manifold learning; the reduced latent space is discovered using Diffusion Maps (a manifold learning technique) on time series data. A second round of Diffusion…

The classical method of determining the atomic structure of complex molecules by analyzing diffraction patterns is currently undergoing drastic developments. Modern techniques for producing extremely bright and coherent X-ray lasers allow a…

The movement of intracellular cargo transported by molecular motors is commonly marked by switches between directed motion and stationary pauses. The predominant measure for assessing movement is effective diffusivity, which predicts the…

The advent of compact, handheld devices has given us a pool of tracked movement data that could be used to infer trends and patterns that can be made to use. With this flooding of various trajectory data of animals, humans, vehicles, etc.,…

We have previously shown that Good-Turing statistics can be applied to molecular dynamics trajectories to estimate the probability of observing completely new (thus far unobserved) biomolecular structures, and showed that the method is…

We introduce a novel diffusion-based spectral algorithm to tackle regression analysis on high-dimensional data, particularly data embedded within lower-dimensional manifolds. Traditional spectral algorithms often fall short in such…

Many algorithms have been developed for enumerating various combinatorial objects in time exponentially less than the number of objects. Two common classes of algorithms are dynamic programming and the transfer matrix method. This paper…

Recent advancements in the ability to construct three-dimensional (3D) tissues and organoids from stem cells and biomaterials have not only opened abundant new research avenues in disease modeling and regenerative medicine but also have…

In this paper, a reduced-rank scheme with joint iterative optimization is presented for direction of arrival estimation. A rank-reduction matrix and an auxiliary reduced-rank parameter vector are jointly optimized to calculate the output…

Modeling data as being sampled from a union of independent subspaces has been widely applied to a number of real world applications. However, dimensionality reduction approaches that theoretically preserve this independence assumption have…

Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…

Thinning is the removal of contour pixels/points of connected components in an image to produce their skeleton with retained connectivity and structural properties. The output requirements of a thinning procedure often vary with…

Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…