Manifold Optimization Over the Set of Doubly Stochastic Matrices: A Second-Order Geometry

Convex optimization is a well-established research area with applications in almost all fields. Over the decades, multiple approaches have been proposed to solve convex programs. The development of interior-point methods allowed solving a more general set of convex programs known as semi-definite programs and second-order cone programs. However, it has been established that these methods are excessively slow for high dimensions, i.e., they suffer from the curse of dimensionality. On the other hand, optimization algorithms on manifold have shown great ability in finding solutions to nonconvex problems in reasonable time. This paper is interested in solving a subset of convex optimization using a different approach. The main idea behind Riemannian optimization is to view the constrained optimization problem as an unconstrained one over a restricted search space. The paper introduces three manifolds to solve convex programs under particular box constraints. The manifolds, called the doubly stochastic, symmetric and the definite multinomial manifolds, generalize the simplex also known as the multinomial manifold. The proposed manifolds and algorithms are well-adapted to solving convex programs in which the variable of interest is a multidimensional probability distribution function. Theoretical analysis and simulation results testify the efficiency of the proposed method over state of the art methods. In particular, they reveal that the proposed framework outperforms conventional generic and specialized solvers, especially in high dimensions

Decomposition of Trees and Paths via Correlation

We study the problem of decomposing (clustering) a tree with respect to costs attributed to pairs of nodes, so as to minimize the sum of costs for those pairs of nodes that are in the same component (cluster). For the general case and for the special case of the tree being a star, we show that the problem is NP-hard. For the special case of the tree being a path, this problem is known to be polynomial time solvable. We characterize several classes of facets of the combinatorial polytope associated with a formulation of this clustering problem in terms of lifted multicuts. In particular, our results yield a complete totally dual integral (TDI) description of the lifted multicut polytope for paths, which establishes a connection to the combinatorial properties of alternative formulations such as set partitioning.Comment: v2 is a complete revisio

Numerical algebraic geometry for model selection and its application to the life sciences

Researchers working with mathematical models are often confronted by the related problems of parameter estimation, model validation, and model selection. These are all optimization problems, well-known to be challenging due to non-linearity, non-convexity and multiple local optima. Furthermore, the challenges are compounded when only partial data is available. Here, we consider polynomial models (e.g., mass-action chemical reaction networks at steady state) and describe a framework for their analysis based on optimization using numerical algebraic geometry. Specifically, we use probability-one polynomial homotopy continuation methods to compute all critical points of the objective function, then filter to recover the global optima. Our approach exploits the geometric structures relating models and data, and we demonstrate its utility on examples from cell signaling, synthetic biology, and epidemiology.Comment: References added, additional clarification