Related papers: An efficient algorithm to compute the minimum free…
This paper considers a natural fault-tolerant shortest paths problem: for some constant integer $f$, given a directed weighted graph with no negative cycles and two fixed vertices $s$ and $t$, compute (either explicitly or implicitly) for…
We provide new algorithms and conditional hardness for the problem of estimating effective resistances in $n$-node $m$-edge undirected, expander graphs. We provide an $\widetilde{O}(m\epsilon^{-1})$-time algorithm that produces with high…
The Random-Facet algorithm of Kalai and of Matousek, Sharir and Welzl is an elegant randomized algorithm for solving linear programs and more general LP-type problems. Its expected subexponential time of $2^{\tilde{O}(\sqrt{m})}$, where $m$…
Spectral submanifolds (SSMs) have emerged as accurate and predictive model reduction tools for dynamical systems defined either by equations or data sets. While finite-elements (FE) models belong to the equation-based class of problems,…
In this paper, we study the combinatorial set of RNA secondary structures of length $n$ with $m$ base-pairs. For a compact representation, we encode an RNA secondary structure by the corresponding Motzkin word. For this combinatorial set,…
We study dynamic $(1-\epsilon)$-approximate rounding of fractional matchings -- a key ingredient in numerous breakthroughs in the dynamic graph algorithms literature. Our first contribution is a surprisingly simple deterministic rounding…
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…
We consider the fundamental algorithmic problem of finding a cycle of minimum weight in a weighted graph. In particular, we show that the minimum weight cycle problem in an undirected n-node graph with edge weights in {1,...,M} or in a…
The large sparse linear systems arising from the finite element or finite difference discretization of elliptic PDEs can be solved directly via, e.g., nested dissection or multifrontal methods. Such techniques reorder the nodes in the grid…
In this paper, we propose two time-splitting finite element methods to solve the semiclassical nonlinear Schr\"odinger equation (NLSE) with random potentials. We then introduce the multiscale finite element method (MsFEM) to reduce the…
Algorithms for dynamically maintaining minimum spanning trees (MSTs) have received much attention in both the parallel and sequential settings. While previous work has given optimal algorithms for dense graphs, all existing parallel…
We consider a spectrum of geometric optimization problems motivated by contexts such as satellite communication and astrophysics. In the problem Minimum Scan Cover with Angular Costs, we are given a graph $G$ that is embedded in Euclidean…
A new algorithm for efficient and fully time-reversible integration of first-principles molecular dynamics based on orbital-free density functional theory (OFDFT) is presented. The algorithm adapts to this nontrivial case the recently…
We consider cost constrained versions of the minimum spanning tree problem and the assignment problem. We assume edge weights are independent copies of a continuous random variable $Z$ that satisfies $F(x)=\Pr(Z\leq x)\approx x^\alpha$ as…
We propose a simple iterative algorithm to construct the optimal multi-configuration approximation of an $N$-fermion wave function. That is, $M\geq N $ single-particle orbitals are sought iteratively so that the projection of the given wave…
Many ncRNAs function through RNA-RNA interactions. Fast and reliable RNA structure prediction with consideration of RNA-RNA interaction is useful. Some existing tools are less accurate due to omitting the competing of intermolecular and…
Neural ordinary differential equations (neural ODEs) have emerged as a novel network architecture that bridges dynamical systems and deep learning. However, the gradient obtained with the continuous adjoint method in the vanilla neural ODE…
In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…
Deriving governing equations in Electromagnetic (EM) environment based on first principles can be quite tough when there are some unknown sources of noise and other uncertainties in the system. For nonlinear multiple-physics electromagnetic…
The random feature method (RFM), a mesh-free machine learning-based framework, has emerged as a promising alternative for solving PDEs on complex domains. However, for large three-dimensional nonlinear problems, attaining high accuracy…