Related papers: An efficient algorithm to compute the minimum free…
In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…
We give new quantum algorithms for evaluating composed functions whose inputs may be shared between bottom-level gates. Let $f$ be an $m$-bit Boolean function and consider an $n$-bit function $F$ obtained by applying $f$ to conjunctions of…
Solving unsteady partial differential equations (PDEs) using recurrent neural networks (RNNs) typically requires numerical derivatives between each block of the RNN to form the physics informed loss function. However, this introduces the…
We study dynamic $(1+\epsilon)$-approximation algorithms for the all-pairs shortest paths problem in unweighted undirected $n$-node $m$-edge graphs under edge deletions. The fastest algorithm for this problem is a randomized algorithm with…
Despite nearly two scores of research on RNA secondary structure and RNA-RNA interaction prediction, the accuracy of the state-of-the-art algorithms are still far from satisfactory. Researchers have proposed increasingly complex energy…
We propose an efficient algorithm for the evaluation of the potential and its gradient of gravitational/electrostatic $N$-body systems, which we call particle mesh multipole method (PMMM or PM$^3$). PMMM can be understood both as an…
Solving partial differential equations (PDEs) by numerical methods meet computational cost challenge for getting the accurate solution since fine grids and small time steps are required. Machine learning can accelerate this process, but…
Partitioning algorithms play a key role in many scientific and engineering disciplines. A partitioning algorithm divides a set into a number of disjoint subsets or partitions. Often, the quality of the resulted partitions is measured by the…
Dynamical low-rank approximation allows for solving large-scale matrix differential equations (MDEs) with significantly fewer degrees of freedom and has been applied to a growing number of applications. However, most existing techniques…
The Poisson-Nernst-Planck (PNP) equations are one of the most effective model for describing electrostatic interactions and diffusion processes in ion solution systems, and have been widely used in the numerical simulations of biological…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
This work proposes a hybrid modeling framework based on recurrent neural networks (RNNs) and the finite element (FE) method to approximate model discrepancies in time dependent, multi-fidelity problems, and use the trained hybrid models to…
We introduce the Free Energy Manifold (FEM), a score-trained conditional energy model specialized for inference in hybrid Bayesian networks with discrete and continuous variables. FEM represents each conditional factor as an energy…
Edge computing must be capable of executing computationally intensive algorithms, such as Deep Neural Networks (DNNs) while operating within a constrained computational resource budget. Such computations involve Matrix Vector…
Constructing the outer crust of the neutron stars requires the knowledge of the Binding Energy (BE) of the atomic nuclei. Although the BE of a lot of the nuclei is experimentally determined and can be obtained from the AME data table, for…
The joint optimization of the integer matrix $\mathbf{A}$ and the power scaling matrix $\mathbf{D}$ is central to achieving the capacity-approaching performance of Integer-Forcing (IF) precoding. This problem, however, is known to be…
Machine learning force fields (MLFFs) have emerged as a sophisticated tool for cost-efficient atomistic simulations approaching DFT accuracy, with recent message passing MLFFs able to cover the entire periodic table. We present an invariant…
In this paper, we investigate the sequence estimation problem of faster-than-Nyquist (FTN) signaling as a promising approach for increasing spectral efficiency (SE) in future communication systems. In doing so, we exploit the concept of…
In this work, we introduce a new algorithm for N-to-M checkpointing in finite element simulations. This new algorithm allows efficient saving/loading of functions representing physical quantities associated with the mesh representing the…
We consider a classical scheduling problem on $m$ identical machines. For an arbitrary constant $q>1$, the aim is to assign jobs to machines such that $\sum_{i=1}^m C_i^q$ is minimized, where $C_i$ is the total processing time of jobs…