The evolutionary history of species may be described by a phylogenetic tree whose topology captures ancestral relationships among the species, and whose branch lengths denote evolution times. For a fixed topology and an assumed probabilistic model of nucleotide substitution, we show that the likelihood of a given tree is a d.c. (difference of convex) function … Read more
Medical Physics — January 2006 — Volume 33, Issue 1, pp. 225-234. CitationMedical Physics — January 2006 — Volume 33, Issue 1, pp. 225-234.
We propose minimum volume ellipsoids (MVE) clustering as an alternate clustering technique to k-means clustering for Gaussian data points and explore its value and practicality. MVE clustering allocates data points into clusters that minimizes the total volumes of each cluster’s covering ellipsoids. Motivations for this approach include its scale-invariance, its ability to handle asymmetric and … Read more
This paper is concerned with the application of semidefinite programming to the satisfiability problem, and in particular with using semidefinite liftings to efficiently obtain proofs of unsatisfiability. We focus on the Tseitin satisfiability instances which are known to be hard for many proof systems. We present an explicit semidefinite programming problem with dimension linear in … Read more
In this paper, we propose a new methodology for handling optimization problems with uncertain data. With the usual Robust Optimization paradigm, one looks for the decisions ensuring a required performance for all realizations of the data from a given bounded uncertainty set, whereas with the proposed approach, we require also a controlled deterioration in performance … Read more
We present a new method for regularization of ill-conditioned problems, such as those that arise in image restoration or mathematical processing of medical data. The method extends the traditional {\em trust-region subproblem}, \TRS, approach that makes use of the {\em L-curve} maximum curvature criterion, a strategy recently proposed to find a good regularization parameter. We … Read more
We develop and apply a novel framework which is designed to extract information in the form of a positive definite kernel matrix from possibly crude, noisy, incomplete, inconsistent dissimilarity information between pairs of objects, obtainable in a variety of contexts. Any positive definite kernel defines a consistent set of distances, and the fitted kernel provides … Read more
One of the fundamental clustering problems is to assign $n$ points into $k$ clusters based on the minimal sum-of-squares(MSSC), which is known to be NP-hard. In this paper, by using matrix arguments, we first model MSSC as a so-called 0-1 semidefinite programming (SDP). We show that our 0-1 SDP model provides an unified framework for … Read more
The facility layout problem is concerned with the arrangement of a given number of rectangular facilities so as to minimize the total cost associated with the (known or projected) interactions between them. We consider the one-dimensional space allocation problem (ODSAP), also known as the single-row facility layout problem, which consists in finding an optimal linear … Read more
I have been working for quite awhile with the treatment of experimental results in chemical thermodynamics. I have tried to organize my archives and make them available for others. There are several experimental datasets in computer readable format and I hope that they can be used as useful benchmarks for data fitting and nonlinear optimization. … Read more