Complexity of Model Testing for Dynamical Systems with Toric Steady States

In this paper we investigate the complexity of model selection and model testing for dynamical systems with toric steady states. Such systems frequently arise in the study of chemical reaction networks. We do this by formulating these tasks as a constrained optimization problem in Euclidean space. This optimization problem is known as a Euclidean distance problem; the complexity of solving this problem is measured by an invariant called the Euclidean distance (ED) degree. We determine closed-form expressions for the ED degree of the steady states of several families of chemical reaction networks with toric steady states and arbitrarily many reactions. To illustrate the utility of this work we show how the ED degree can be used as a tool for estimating the computational cost of solving the model testing and model selection problems

Phylogenetic Algebraic Geometry

Phylogenetic algebraic geometry is concerned with certain complex projective algebraic varieties derived from finite trees. Real positive points on these varieties represent probabilistic models of evolution. For small trees, we recover classical geometric objects, such as toric and determinantal varieties and their secant varieties, but larger trees lead to new and largely unexplored territory. This paper gives a self-contained introduction to this subject and offers numerous open problems for algebraic geometers.Comment: 15 pages, 7 figure

A primal-dual formulation for certifiable computations in Schubert calculus

Formulating a Schubert problem as the solutions to a system of equations in either Pl\"ucker space or in the local coordinates of a Schubert cell typically involves more equations than variables. We present a novel primal-dual formulation of any Schubert problem on a Grassmannian or flag manifold as a system of bilinear equations with the same number of equations as variables. This formulation enables numerical computations in the Schubert calculus to be certified using algorithms based on Smale's \alpha-theory.Comment: 21 page

The ideal of the trifocal variety

Techniques from representation theory, symbolic computational algebra, and numerical algebraic geometry are used to find the minimal generators of the ideal of the trifocal variety. An effective test for determining whether a given tensor is a trifocal tensor is also given