The bottleneck degree of algebraic varieties

A bottleneck of a smooth algebraic variety $X \subset \mathbb{C}^n$ is a pair of distinct points $(x,y) \in X$ such that the Euclidean normal spaces at $x$ and $y$ contain the line spanned by $x$ and $y$. The narrowness of bottlenecks is a fundamental complexity measure in the algebraic geometry of data. In this paper we study the number of bottlenecks of affine and projective varieties, which we call the bottleneck degree. The bottleneck degree is a measure of the complexity of computing all bottlenecks of an algebraic variety, using for example numerical homotopy methods. We show that the bottleneck degree is a function of classical invariants such as Chern classes and polar classes. We give the formula explicitly in low dimension and provide an algorithm to compute it in the general case.Comment: Major revision. New introduction. Added some new illustrative lemmas and figures. Added pseudocode for the algorithm to compute bottleneck degree. Fixed some typo

On the Power of Manifold Samples in Exploring Configuration Spaces and the Dimensionality of Narrow Passages

We extend our study of Motion Planning via Manifold Samples (MMS), a general algorithmic framework that combines geometric methods for the exact and complete analysis of low-dimensional configuration spaces with sampling-based approaches that are appropriate for higher dimensions. The framework explores the configuration space by taking samples that are entire low-dimensional manifolds of the configuration space capturing its connectivity much better than isolated point samples. The contributions of this paper are as follows: (i) We present a recursive application of MMS in a six-dimensional configuration space, enabling the coordination of two polygonal robots translating and rotating amidst polygonal obstacles. In the adduced experiments for the more demanding test cases MMS clearly outperforms PRM, with over 20-fold speedup in a coordination-tight setting. (ii) A probabilistic completeness proof for the most prevalent case, namely MMS with samples that are affine subspaces. (iii) A closer examination of the test cases reveals that MMS has, in comparison to standard sampling-based algorithms, a significant advantage in scenarios containing high-dimensional narrow passages. This provokes a novel characterization of narrow passages which attempts to capture their dimensionality, an attribute that had been (to a large extent) unattended in previous definitions.Comment: 20 page

Global Identifiability of Differential Models

Many real-world processes and phenomena are modeled using systems of ordinary differential equations with parameters. Given such a system, we say that a parameter is globally identifiable if it can be uniquely recovered from input and output data. The main contribution of this paper is to provide theory, an algorithm, and software for deciding global identifiability. First, we rigorously derive an algebraic criterion for global identifiability (this is an analytic property), which yields a deterministic algorithm. Second, we improve the efficiency by randomizing the algorithm while guaranteeing the probability of correctness. With our new algorithm, we can tackle problems that could not be tackled before. A software based on the algorithm (called SIAN) is available at https://github.com/pogudingleb/SIAN

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