We improve the best known lower bounds on the distance between two points of a Morse cluster in $\mathbb{R}^3$, with $\rho \in [4.967,15]$. Our method is a generalization of the one applied to the Lennard-Jones potential in~\cite{Schac}, and it also leads to improvements of lower bounds for the energy of a Morse cluster. Some of … Read more
To minimize or upper-bound the value of a function “robustly”, we might instead minimize or upper-bound the “epsilon-robust regularization”, defined as the map from a point to the maximum value of the function within an epsilon-radius. This regularization may be easy to compute: convex quadratics lead to semidefinite-representable regularizations, for example, and the spectral radius … Read more
We study the modeling of non-convex piecewise linear functions as Mixed Integer Programming (MIP) problems. We review several new and existing MIP formulations for continuous piecewise linear functions with special attention paid to multivariate non-separable functions. We compare these formulations with respect to their theoretical properties and their relative computational performance. In addition, we study … Read more
SESOP-TN is a method for very large scale unconstrained optimization of smooth functions. It combines ideas of Sequential Subspace Optimization (SESOP) [Narkiss-Zibulevsky-2005] with those of the Truncated Newton (TN) method . Replacing TN line search with subspace optimization, we allow Conjugate Gradient (CG) iterations to stay matched through consequent TN steps. This resolves the problem … Read more
Identifying critical nodes in a graph is important to understand the structural characteristics and the connectivity properties of the network. In this paper, we focus on detecting critical nodes, or nodes whose deletion results in the minimum pair-wise connectivity among the remaining nodes. This problem, known as the CRITICAL NODE PROBLEM has applications in several … Read more
This work addresses the computation of free-energy di fferences between protein conformations by using morphing (i.e., transformation) of a source conformation into a target conformation. To enhance the morph- ing procedure, we employ permutations of atoms; we transform atom n in the source conformation into atom \sigma(n) in the target conformation rather than directly transforming atom … Read more
PSwarm was developed originally for the global optimization of functions without derivatives and where the variables are within upper and lower bounds. The underlying algorithm used is a pattern search method, more specifically a coordinate search method, which guarantees convergence to stationary points from arbitrary starting points. In the (optional) search step of coordinate search, … Read more
This paper addresses derivative-free optimization problems where the variables lie implicitly in an unknown discrete closed set. The evaluation of the objective function follows a projection onto the discrete set, which is assumed dense rather than sparse. Such a mathematical setting is a rough representation of what is common in many real-life applications where, despite … Read more
We describe Pyomo, an open-source tool for modeling optimization applications in Python. Pyomo can be used to define abstract problems, create concrete problem instances, and solve these instances with standard solvers. Pyomo provides a capability that is commonly associated with algebraic modeling languages like AMPL and GAMS. Pyomo leverages the capabilities of the Coopr software, … Read more
In this paper, we develop a convexification tool that enables the construction of convex hulls for orthogonal disjunctive sets using convex extensions and disjunctive programming techniques. A distinguishing feature of our technique is that, unlike most applications of disjunctive programming, it does not require the introduction of new variables in the relaxation. We develop and … Read more