The main task of genetic regulatory networks is to construct a sparse probabilistic Boolean network (PBN) based on a given transition-probability matrix and a set of Boolean networks (BNs). In this paper, a Bregman alternating direction method of multipliers (BADMM) is proposed to solve the minimization problem raised in PBN. All the customized subproblem-solvers of … Read more
We consider a Procrustes matching problem for non-negative matrices that arose in random tomography. As an alternative to the Frobenius distance, we propose an alternative non-symmetric distance using generalized inverses. Among its advantages is that it leads to a relatively simple quadratic function that can be optimized with least-square methods on manifolds. Citation Accepted for … Read more
A split feasibility formulation for the inverse problem of intensity-modulated radiation therapy (IMRT) treatment planning with dose-volume constraints (DVCs) included in the planning algorithm is presented. It involves a new type of sparsity constraint that enables the inclusion of a percentage-violation constraint in the model problem and its handling by continuous (as opposed to integer) … Read more
The implicit convex feasibility problem attempts to find a point in the intersection of a finite family of convex sets, some of which are not explicitly determined but may vary. We develop simultaneous and sequential projection methods capable of handling such problems and demonstrate their applicability to image denoising in a specific medical imaging situation. … Read more
In radiation therapy planning, uncertainties in target volume definition yield a risk of underdosing the tumor. The classical way to prevent this in the context of external beam radiotherapy (EBRT) has been to expand the clinical target volume (CTV) with an isotropic margin to obtain the planning target volume (PTV). However, the EBRT-based PTV concept … Read more
This is a review paper on some of the physics, modeling, and iterative algorithms in proton computed tomography (pCT) image reconstruction. The primary challenge in pCT image reconstruction lies in the degraded spatial resolution resulting from multiple Coulomb scattering within the imaged object. Analytical models such as the most likely path (MLP) have been proposed … Read more
Medical treatment decisions involve complex tradeoffs between the risks and benefits of various treatment options. The diversity of treatment options that patients can choose over time and uncertainties in future health outcomes, result in a difficult sequential decision making problem. Markov decision processes (MDPs) are commonly used to study medical treatment decisions; however, optimal policies … Read more
We define two algorithms for propagating information in classification problems with pairwise relationships. The algorithms involve contraction maps and are related to non-linear diffusion and random walks on graphs. The approach is also related to message passing and mean field methods. The algorithms we describe are guaranteed to converge on graphs with arbitrary topology. Moreover … Read more
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