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
We propose the DISCO algorithm for graph realization in $\real^d$, given sparse and noisy short-range inter-vertex distances as inputs. Our divide-and-conquer algorithm works as follows. When a group has a sufficiently small number of vertices, the basis step is to form a graph realization by solving a semidefinite program. The recursive step is to break … Read more
Given a power grid modeled by a network together with equations describing the power flows, power generation and consumption, and the laws of physics, the so-called N – k problem asks whether there exists a set of k or fewer arcs whose removal will cause the system to fail. We present theoretical results and computation … Read more
The integration to steady state of many initial value ODEs and PDEs using the forward Euler method can alternatively be considered as gradient descent for an associated minimization problem. Greedy algorithms such as steepest descent for determining the step size are as slow to reach steady state as is forward Euler integration with the best … Read more
We study the asymptotic behavior of almost-orbits of abstract evolution systems in Banach spaces with or without a Lipschitz assumption. In particular, we establish convergence, convergence in average and almost-convergence of almost-orbits both for the weak and the strong topologies based on the behavior of the orbits. We also analyze the set of almost-stationary points. … Read more
We provide a sharp generalization to the nonautonomous case of the well-known Ko\-ba\-yashi estimate for proximal iterates associated with maximal monotone operators. We then derive a bound for the distance between a continuous-in-time trajectory, namely the solution to the differential inclusion $\dot{x} + A(t)x\ni 0$, and the corresponding proximal iterations. We also establish continuity properties … Read more
We study general algorithmic frameworks for online learning tasks. These include binary classification, regression, multiclass problems and cost-sensitive multiclass classification. The theorems that we present give loss bounds on the behavior of our algorithms that depend on general conditions on the iterative step sizes. CitationInternational Journal of Pure and Applied Mathematics, Vol. 46 (2008), pp. … Read more
The basis pursuit problem seeks a minimum one-norm solution of an underdetermined least-squares problem. Basis pursuit denoise (BPDN) fits the least-squares problem only approximately, and a single parameter determines a curve that traces the optimal trade-off between the least-squares fit and the one-norm of the solution. We prove that this curve is convex and continuously … Read more
Parsimonious haplotype estimation from aligned Single Nucleotide Polymorphism (SNP) fragments consists of finding the minimum number of haplotypes necessary to explain a given set of genotypes. This problem is known to be NP-Hard. Here we describe a new integer linear-programming model to tackle this problem based on the concept of class representatives, already used for … Read more
Very hard optimization problems, i.e., problems with a large number of variables and local minima, have been effectively attacked with algorithms which mix local searches with heuristic procedures in order to widely explore the search space. A Population Based Approach based on a Monotonic Basin Hopping optimization algorithm has turned out to be very effective … Read more