Related papers: Compressing molecular dynamics trajectories: break…
We present a compact data structure to represent both the duration and length of homogeneous segments of trajectories from moving objects in a way that, as a data warehouse, it allows us to efficiently answer cumulative queries. The…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
We describe quantum circuits with only $\widetilde{\cal O}(N)$ Toffoli complexity that block encode the spectra of quantum chemistry Hamiltonians in a basis of $N$ arbitrary (e.g., molecular) orbitals. With ${\cal O}(\lambda / \epsilon)$…
This paper considers a risk-constrained motion planning problem and aims to find the solution combining the concepts of iterative model predictive control (MPC) and data-driven distributionally robust (DR) risk-constrained optimization. In…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
To efficiently deploy robotic systems in society, mobile robots must move autonomously and safely through complex environments. Nonlinear model predictive control (MPC) methods provide a natural way to find a dynamically feasible trajectory…
Many optimally scaling quantum simulation algorithms employ controlled time evolution of the Hamiltonian, which is typically the major bottleneck for their efficient implementation. This work establishes a compression protocol for encoding…
Molecular docking (MD) is a crucial task in drug design, which predicts the position, orientation, and conformation of the ligand when bound to a target protein. It can be interpreted as a combinatorial optimization problem, where quantum…
Standard Model Predictive Control (MPC) or trajectory optimization approaches perform only a local search to solve a complex non-convex optimization problem. As a result, they cannot capture the multi-modal characteristic of human driving.…
Accurate determination of particle track reconstruction parameters will be a major challenge for the High Luminosity Large Hadron Collider (HL-LHC) experiments. The expected increase in the number of simultaneous collisions at the HL-LHC…
Neural compression has brought tremendous progress in designing lossy compressors with good rate-distortion (RD) performance at low complexity. Thus far, neural compression design involves transforming the source to a latent vector, which…
Branching processes are a class of continuous-time Markov chains (CTMCs) with ubiquitous applications. A general difficulty in statistical inference under partially observed CTMC models arises in computing transition probabilities when the…
We present a systematic study of quantum system compression for the evolution of generic many-body problems. The necessary numerical simulations of such systems are seriously hindered by the exponential growth of the Hilbert space dimension…
The automatic reconstruction of three-dimensional particle tracks from Active Target Time Projection Chambers data can be a challenging task, especially in the presence of noise. In this article, we propose a non-parametric algorithm that…
Hamiltonian Monte Carlo (HMC) is the mainstay of applied Bayesian inference for differentiable models. However, HMC still struggles to sample from hierarchical models that induce densities with multiscale geometry: a large step size is…
Protein folding processes are a vital aspect of molecular biology that is hard to simulate with conventional computers. Quantum algorithms have been proven superior for certain problems and may help tackle this complex life science…
Many problems of practical interest rely on Continuous-time Markov chains~(CTMCs) defined over combinatorial state spaces, rendering the computation of transition probabilities, and hence probabilistic inference, difficult or impossible…
Hamiltonian Monte Carlo (HMC) is an efficient method of simulating smooth distributions and has motivated the widely used No-U-turn Sampler (NUTS) and software Stan. We build on NUTS and the technique of "unbiased sampling" to design HMC…
Machine learning (ML) is rapidly transforming the way molecular dynamics simulations are performed and analyzed, from materials modeling to studies of protein folding and function. ML algorithms are often employed to learn low-dimensional…
In this paper, we propose a hierarchical random compression method (HRCM) for kernel matrices in fast kernel summations. The HRCM combines the hierarchical framework of the H-matrix and a randomized sampling technique of the column and row…