Decomposing Tensors into Frames
A symmetric tensor of small rank decomposes into a configuration of only few vectors. We study the variety of tensors for which this configuration is a unit norm tight frame.
math.AG↗
arXiv subjects
Bernd Sturmfels
Publications and source records attributed to Bernd Sturmfels.
Generic Spectrahedral Shadows
Spectrahedral shadows are projections of linear sections of the cone of positive semidefinite matrices. We characterize the polynomials that vanish on the boundaries of these convex sets when both the section and the projection are generic.
math.OC↗
Fixed points of the EM algorithm and nonnegative rank boundaries
Mixtures of $r$ independent distributions for two discrete random variables can be represented by matrices of nonnegative rank $r$. Likelihood inference for the model of such joint distributions leads to problems in real algebraic geometry that are addressed here for the first time. We characterize the set of fixed points of the Expectation-Maximization algorithm, and we study the boundary of the space of matrices with nonnegative rank at most $3$. Both of these sets correspond to algebraic varieties with many irreducible components.
math.ST↗
Algebraic Systems Biology: A Case Study for the Wnt Pathway
Steady state analysis of dynamical systems for biological networks give rise to algebraic varieties in high-dimensional spaces whose study is of interest in their own right. We demonstrate this for the shuttle model of the Wnt signaling pathway. Here the variety is described by a polynomial system in 19 unknowns and 36 parameters. Current methods from computational algebraic geometry and combinatorics are applied to analyze this model.
q-bio.MN↗
Tropicalization of Del Pezzo Surfaces
We determine the tropicalizations of very affine surfaces over a valued field that are obtained from del Pezzo surfaces of degree 5, 4 and 3 by removing their (-1)-curves. On these tropical surfaces, the boundary divisors are represented by trees at infinity. These trees are glued together according to the Petersen, Clebsch and Schläfli graphs, respectively. There are 27 trees on each tropical cubic surface, attached to a bounded complex with up to 73 polygons. The maximal cones in the 4-dimensional moduli fan reveal two generic types of such surfaces.
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Cayley-Bacharach Formulas
The Cayley-Bacharach Theorem states that all cubic curves through eight given points in the plane also pass through a unique ninth point. We write that point as an explicit rational function in the other eight.
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The Euclidean distance degree of an algebraic variety
The nearest point map of a real algebraic variety with respect to Euclidean distance is an algebraic function. For instance, for varieties of low rank matrices, the Eckart-Young Theorem states that this map is given by the singular value decomposition. This article develops a theory of such nearest point maps from the perspective of computational algebraic geometry. The Euclidean distance degree of a variety is the number of critical points of the squared distance to a generic point outside the variety. Focusing on varieties seen in applications, we present numerous tools for exact computations.
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Moduli of Tropical Plane Curves
We study the moduli space of metric graphs that arise from tropical plane curves. There are far fewer such graphs than tropicalizations of classical plane curves. For fixed genus $g$, our moduli space is a stacky fan whose cones are indexed by regular unimodular triangulations of Newton polygons with $g$ interior lattice points. It has dimension $2g+1$ unless $g \leq 3$ or $g = 7$. We compute these spaces explicitly for $g \leq 5$.
math.CO↗
Quartic Spectrahedra
Quartic spectrahedra in 3-space form a semialgebraic set of dimension 24. This set is stratified by the location of its ten nodes. There are twenty maximal strata, identified recently by Degtyarev and Itenberg, via the global Torelli Theorem for real K3 surfaces. We here give a new proof that is self-contained and algorithmic. This involves extending Cayley's characterization of quartic symmetroids, by the property that the branch locus of the projection from a node consists of two cubic curves. This paper represents a first step towards the classification of all spectrahedra of a given degree and dimension.
math.OC↗
Certifying the Existence of Epipolar Matrices
Given a set of point correspondences in two images, the existence of a fundamental matrix is a necessary condition for the points to be the images of a 3-dimensional scene imaged with two pinhole cameras. If the camera calibration is known then one requires the existence of an essential matrix. We present an efficient algorithm, using exact linear algebra, for testing the existence of a fundamental matrix. The input is any number of point correspondences. For essential matrices, we characterize the solvability of the Demazure polynomials. In both scenarios, we determine which linear subspaces intersect a fixed set defined by non-linear polynomials. The conditions we derive are polynomials stated purely in terms of image coordinates. They represent a new class of two-view invariants, free of fundamental (resp.~essential)~matrices.
cs.CV↗
A Family of Quasisymmetry Models
We present a one-parameter family of models for square contingency tables that interpolates between the classical quasisymmetry model and its Pearsonian analogue. Algebraically, this corresponds to deformations of toric ideals associated with graphs. Our discussion of the statistical issues centers around maximum likelihood estimation.
math.ST↗
Rational Design of Antibiotic Treatment Plans
The development of reliable methods for restoring susceptibility after antibiotic resistance arises has proven elusive. A greater understanding of the relationship between antibiotic administration and the evolution of resistance is key to overcoming this challenge. Here we present a data-driven mathematical approach for developing antibiotic treatment plans that can reverse the evolution of antibiotic resistance determinants. We have generated adaptive landscapes for 16 genotypes of the TEM beta-lactamase that vary from the wild type genotype TEM-1 through all combinations of four amino acid substitutions. We determined the growth rate of each genotype when treated with each of 15 beta-lactam antibiotics. By using growth rates as a measure of fitness, we computed the probability of each amino acid substitution in each beta-lactam treatment using two different models named the Correlated Probability Model (CPM) and the Equal Probability Model (EPM). We then performed an exhaustive search through the 15 treatments for substitution paths leading from each of the 16 genotypes back to the wild type TEM-1. We identified those treatment paths that returned the highest probabilities of selecting for reversions of amino acid substitutions and returning TEM to the wild type state. For the CPM model, the optimized probabilities ranged between 0.6 and 1.0. For the EPM model, the optimized probabilities ranged between 0.38 and 1.0. For cyclical CPM treatment plans in which the starting and ending genotype was the wild type, the probabilities were between 0.62 and 0.7. Overall this study shows that there is promise for reversing the evolution of resistance through antibiotic treatment plans.
q-bio.PE↗
Hypersurfaces and their singularities in partial correlation testing
An asymptotic theory is developed for computing volumes of regions in the parameter space of a directed Gaussian graphical model that are obtained by bounding partial correlations. We study these volumes using the method of real log canonical thresholds from algebraic geometry. Our analysis involves the computation of the singular loci of correlation hypersurfaces. Statistical applications include the strong-faithfulness assumption for the PC-algorithm, and the quantification of confounder bias in causal inference. A detailed analysis is presented for trees, bow-ties, tripartite graphs, and complete graphs.
math.ST↗
Tropicalization of classical moduli spaces
The image of the complement of a hyperplane arrangement under a monomial map can be tropicalized combinatorially using matroid theory. We apply this to classical moduli spaces that are associated with complex reflection arrangements. Starting from modular curves, we visit the Segre cubic, the Igusa quartic, and moduli of marked del Pezzo surfaces of degrees 2 and 3. Our primary example is the Burkhardt quartic, whose tropicalization is a 3-dimensional fan in 39-dimensional space. This effectuates a synthesis of concrete and abstract approaches to tropical moduli of genus 2 curves.
math.AG↗
Likelihood Geometry
We study the critical points of monomial functions over an algebraic subset of the probability simplex. The number of critical points on the Zariski closure is a topological invariant of that embedded projective variety, known as its maximum likelihood degree. We present an introduction to this theory and its statistical motivations. Many favorite objects from combinatorial algebraic geometry are featured: toric varieties, A-discriminants, hyperplane arrangements, Grassmannians, and determinantal varieties. Several new results are included, especially on the likelihood correspondence and its bidegree. These notes were written for the second author's lectures at the CIME-CIRM summer course on Combinatorial Algebraic Geometry at Levico Terme in June 2013.
math.AG↗
The Universal Kummer Threefold
The universal Kummer threefold is a 9-dimensional variety that represents the total space of the 6-dimensional family of Kummer threefolds in 7-dimensional projective space. We compute defining polynomials for three versions of this family, over the Satake hypersurface, over the Göpel variety, and over the reflection representation of type E7. We develop classical themes such as theta functions and Coble's quartic hypersurface using current tools from combinatorics, geometry, and commutative algebra. Symbolic and numerical computations for genus 3 moduli spaces appear alongside toric and tropical methods.
math.AG↗
Tensors of Nonnegative Rank Two
A nonnegative tensor has nonnegative rank at most 2 if and only if it is supermodular and has flattening rank at most 2. We prove this result, then explore the semialgebraic geometry of the general Markov model on phylogenetic trees with binary states, and comment on possible extensions to tensors of higher rank.
math.AG↗
Maximum Likelihood for Matrices with Rank Constraints
Maximum likelihood estimation is a fundamental optimization problem in statistics. We study this problem on manifolds of matrices with bounded rank. These represent mixtures of distributions of two independent discrete random variables. We determine the maximum likelihood degree for a range of determinantal varieties, and we apply numerical algebraic geometry to compute all critical points of their likelihood functions. This led to the discovery of maximum likelihood duality between matrices of complementary ranks, a result proved subsequently by Draisma and Rodriguez.
math.AG↗