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We propose a framework based on Quadratic Unconstrained Binary Optimization (QUBO) for generating plausible ligand binding poses within protein pockets, enabling efficient structure-based virtual screening. The method discretizes the…
We propose a localized divide and conquer algorithm for inverse factorization $S^{-1} = ZZ^*$ of Hermitian positive definite matrices $S$ with localized structure, e.g. exponential decay with respect to some given distance function on the…
The partition problem is a well-known basic NP-complete problem. We mainly consider the optimization version of it in this paper. The problem has been investigated from various perspectives for a long time and can be solved efficiently in…
The design of large-scale colloidal quantum dots (QDs) assemblies and the investigation of their interaction with their close environment are of great interest for improving QD-based optoelectronic devices' performances. Understanding the…
Calculating interactions or correlations between pairs of particles is typically the most time-consuming task in particle simulation or correlation analysis. Straightforward implementations using a double loop over particle pairs have…
In parallel solution of partial differential equations, a complex stencil update formula that accesses multiple layers of neighboring grid points sometimes must be decomposed into atomic stages, ones that access only immediately neighboring…
We propose a set of constraints on the ground-state wavefunctions of fracton phases, which provide a possible generalization of the string-net equations used to characterize topological orders in two spatial dimensions. Our constraint…
Motivated by applications in wireless communications, this paper develops semidefinite programming (SDP) relaxation techniques for some mixed binary quadratically constrained quadratic programs (MBQCQP) and analyzes their approximation…
We introduce numerical optimization of multi-site support functions in the linear-scaling DFT code CONQUEST. Multi-site support functions, which are linear combinations of pseudo-atomic orbitals on a target atom and those neighbours within…
We propose a novel application of coded computing to the problem of the nearest neighbor estimation using MatDot Codes [Fahim. et.al. 2017], that are known to be optimal for matrix multiplication in terms of recovery threshold under storage…
A balanced partition is a clustering of a graph into a given number of equal-sized parts. For instance, the Bisection problem asks to remove at most k edges in order to partition the vertices into two equal-sized parts. We prove that…
Subspace codes are collections of subspaces of a projective space such that any two subspaces satisfy a pairwise minimum distance criterion. Recent results have shown that it is possible to construct optimal $(5,3)$ subspace codes from…
Mixed discrete-continuous optimization is central to engineering design, where discrete choices interact with continuous fields. These problems are difficult due to high-dimensional, complex search spaces. To tackle them, Quantum Annealing…
In this paper, we demonstrate that in many NP-complete variants of the stable matching problem, such as the Stable Hypergraph Matching problem, the Stable Multicommodity Flow problem, and the College Admission problem with common quotas, a…
The problem of reconstructing a sequence of independent and identically distributed symbols from a set of equal size, consecutive, fragments, as well as a dependent reference sequence, is considered. First, in the regime in which the…
This paper develops new semidefinite programming (SDP) relaxation techniques for two classes of mixed binary quadratically constrained quadratic programs (MBQCQP) and analyzes their approximation performance. The first class of problem…
Determining the binding pose of a ligand to a protein, known as molecular docking, is a fundamental task in drug discovery. Generative approaches promise faster, improved, and more diverse pose sampling than physics-based methods, but are…
The technique of semidefinite programming (SDP) relaxation can be used to obtain a nontrivial bound on the optimal value of a nonconvex quadratically constrained quadratic program (QCQP). We explore concave quadratic inequalities that hold…
We introduce an exact reformulation of a broad class of neighborhood filters, among which the bilateral filters, in terms of two functional rearrangements: the decreasing and the relative rearrangements. Independently of the image spatial…
In the classical context, it is well known that, sometimes, if the search does not find its target, it is better to start the process anew again, known as resetting. The quantum counterpart of resetting also indicates speeding up the…