Related papers: A New Simulated Annealing Algorithm for the Multip…
We propose a new algorithm to the problem of polygonal curve approximation based on a multiresolution approach. This algorithm is suboptimal but still maintains some optimality between successive levels of resolution using dynamic…
Sampling equilibrium ensembles of dense polymer mixtures is a paradigmatically hard problem in computational physics, even in lattice-based models. Here, we develop a formalism based on interacting binary tensors that allows for tackling…
The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata…
In this paper, we develop a parameterized proximal point algorithm (P-PPA) for solving a class of separable convex programming problems subject to linear and convex constraints. The proposed algorithm is provable to be globally convergent…
Mixed packing and covering problems are problems that can be formulated as linear programs using only non-negative coefficients. Examples include multicommodity network flow, the Held-Karp lower bound on TSP, fractional relaxations of set…
We introduce a novel method for non-convex optimization, called Swarm-based Simulated Annealing (SSA), which is at the interface between the swarm-based gradient-descent (SBGD) [J. Lu et. al., ArXiv:2211.17157; E.Tadmor and A. Zenginoglu,…
We present a computer simulation of entangled polymer solutions at equilibrium. The chains repel each other via a soft Gaussian potential, appropriate for semi-dilute solutions at the scale of a correlation blob. The key innovation to…
We consider the problem of solving mixed random linear equations with $k$ components. This is the noiseless setting of mixed linear regression. The goal is to estimate multiple linear models from mixed samples in the case where the labels…
Rapid development of modern sequencing platforms enabled an unprecedented growth of protein families databases. The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence alignment…
We have developed a general Bayesian algorithm for determining the coordinates of points in a three-dimensional space. The algorithm takes as input a set of probabilistic constraints on the coordinates of the points, and an a priori…
The main objective of this paper is to solve the optimization problem that is associated with the classification of DNA samples in PCR plates for Sanger sequencing. To achieve this goal, we design an integer linear programming model. Given…
Approximate Bayes Computations (ABC) are used for parameter inference when the likelihood function of the model is expensive to evaluate but relatively cheap to sample from. In particle ABC, an ensemble of particles in the product space of…
Adaptive simulated annealing (ASA) is a global optimization algorithm based on an associated proof that the parameter space can be sampled much more efficiently than by using other previous simulated annealing algorithms. The author's ASA…
The Alternating Minimization Algorithm (AMA) has been proposed by Tseng to solve convex programming problems with two-block separable linear constraints and objectives, whereby (at least) one of the components of the latter is assumed to be…
For a graph $G$, let $Z(G,\lambda)$ be the partition function of the monomer-dimer system defined by $\sum_k m_k(G)\lambda^k$, where $m_k(G)$ is the number of matchings of size $k$ in $G$. We consider graphs of bounded degree and develop a…
Multivariate time series alignment is critical for ensuring coherent analysis across variables, but missing values and timestamp inconsistencies make this task highly challenging. Existing approaches often rely on prior imputation, which…
We develop a new randomized iterative algorithm---stochastic dual ascent (SDA)---for finding the projection of a given vector onto the solution space of a linear system. The method is dual in nature: with the dual being a non-strongly…
We propose a new method for solving binary optimization problems under inequality constraints using a quantum annealer. To deal with inequality constraints, we often use slack variables, as in previous approaches. When we use slack…
In the last decades, many efforts have focused on analyzing typical-case hardness in optimization and inference problems. Some recent work has pointed out that polynomial algorithms exist, running with a time that grows more than linearly…
We introduce a new algorithm to solve a regularized spatial-spectral image estimation problem. Our approach is based on the linearized alternating directions method of multipliers (LADMM), which is a variation of the popular ADMM algorithm.…