When a weighted graph is an instance of the Distance Geometry Problem (DGP), certain types of vertex orders (called discretization orders) allow the use of a very efficient, precise and robust discrete search algorithm (called Branch-and-Prune). Accordingly, finding such orders is critically important in order to solve DGPs in practice. We discuss three types of … Read more
This paper presents a novel application of operations research techniques to the analysis of HIV env gene sequences, aiming to identify key features that are possible vaccine targets. These targets are identified as being critical to the transmission of HIV by being present in early transmitted (founder) sequences and absent in later chronic sequences. Identifying … Read more
In this paper we consider bound constrained global optimization problems where first-order derivatives of the objective function can be neither computed nor approximated explicitly. For the solution of such problems the DIRECT Algorithm has been proposed which has strong convergence properties and a good ability to locate promising regions of the feasible domain. However, the … Read more
We study the maximum likelihood model in emission tomography and propose a new family of algorithms for its solution, called String-Averaging Expectation-Maximization (SAEM). In the String-Averaging algorithmic regime, the index set of all underlying equations is split into subsets, called “strings,” and the algorithm separately proceeds along each string, possibly in parallel. Then, the end-points … Read more
We apply the recently proposed superiorization methodology (SM) to the inverse planning problem in radiation therapy. The inverse planning problem is represented here as a constrained minimization problem of the total variation (TV) of the intensity vector over a large system of linear two-sided inequalities. The SM can be viewed conceptually as lying between feasibility-seeking … Read more
In this paper we address the problem of identifying the most likely infection pattern responsible for the spread of a disease in a network. In particular, we focus on the scenario where limited information (i.e. infection reports) is available during an ongoing outbreak. For this problem we propose a maximum likelihood model and present an … Read more
This paper investigates the population dynamics of a system of identically prepared B cells whose proliferation trajectories have been individually tracked using live-cell imaging techniques. The main goal is to investigate whether the system behavior can be determined using an optimality criterion. In order to achieve this goal we assume the existence of an intracellular … Read more
We are interested in optimizing the co-administration of two drugs for some acute myeloid leukemias (AML), and we are looking for in vitro protocols as a first step. This issue can be formulated as an optimal control problem. The dynamics of leukemic cell populations in culture is given by age-structured partial differential equations, which can … Read more
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid sites. This is mainly due to the difficulty in formulating a computationally tractable model since rate matrices can no longer be used. Here we … Read more
The projected subgradient method for constrained minimization repeatedly interlaces subgradient steps for the objective function with projections onto the feasible region, which is the intersection of closed and convex constraints sets, to regain feasibility. The latter poses a computational difficulty and, therefore, the projected subgradient method is applicable only when the feasible region is “simple … Read more