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Nonnegative matrix factorizations are often encountered in data mining applications where they are used to explain datasets by a small number of parts. For many of these applications it is desirable that there exists a unique nonnegative matrix factorization up to trivial modifications given by scalings and permutations. This means that model parameters are uniquely identifiable from the data. Rigidity theory of bar and joint frameworks is a field that studies uniqueness of point configurations given some of the pairwise distances. The goal of this paper is to use ideas from rigidity theory to study uniqueness of nonnegative matrix factorizations in the case when nonnegative rank of a matrix is equal to its rank. We characterize infinitesimally rigid nonnegative factorizations, prove that a nonnegative factorization is infinitesimally rigid if and only if it is locally rigid and a certain matrix achieves its maximal possible Kruskal rank, and show that locally rigid nonnegative factorizations can be extended to globally rigid nonnegative factorizations. These results give so far the strongest necessary condition for the uniqueness of a nonnegative factorization. We also explore connections between rigidity of nonnegative factorizations and boundaries of the set of matrices of fixed nonnegative rank. Finally we extend these results from nonnegative factorizations to completely positive factorizations., Comment: 34 pages, 3 figures

Macaulay dual spaces provide a local description of an affine scheme and give rise to computational machinery that is compatible with the methods of numerical algebraic geometry. We introduce eliminating dual spaces, use them for computing dual spaces of quotient ideals, and develop an algorithm for detection of embedded points on an algebraic curve., Comment: 18 pages, 0 figures. arXiv admin note: substantial text overlap with arXiv:1405.7871

The Cayley-Menger variety is the Zariski closure of the set of vectors specifying the pairwise squared distances between $n$ points in $\mathbb{R}^d$. This variety is fundamental to algebraic approaches in rigidity theory. We study the tropicalization of the Cayley-Menger variety. In particular, when $d = 2$, we show that it is the Minkowski sum of the set of ultrametrics on $n$ leaves with itself, and we describe its polyhedral structure. We then give a new, tropical, proof of Laman's theorem.

We describe the typical homological properties of monomial ideals defined by random generating sets. We show that, under mild assumptions, random monomial ideals (RMI's) will almost always have resolutions of maximal length; that is, the projective dimension will almost always be $n$, where $n$ is the number of variables in the polynomial ring. We give a rigorous proof that Cohen-Macaulayness is a "rare" property. We characterize when an RMI is generic/strongly generic, and when it "is Scarf"---in other words, when the algebraic Scarf complex of $M\subset S=k[x_1,\ldots,x_n]$ gives a minimal free resolution of $S/M$. As a result we see that, outside of a very specific ratio of model parameters, RMI's are Scarf only when they are generic. We end with a discussion of the average magnitude of Betti numbers., Comment: Final version, to appear in Proceedings of the AMS

We consider a large class of monomial maps respecting an action of the infinite symmetric group, and prove that the toric ideals arising as their kernels are finitely generated up to symmetry. Our class includes many important examples where Noetherianity was recently proved or conjectured. In particular, our results imply Hillar-Sullivant's Independent Set Theorem and settle several finiteness conjectures due to Aschenbrenner, Martin del Campo, Hillar, and Sullivant. We introduce a matching monoid and show that its monoid ring is Noetherian up to symmetry. Our approach is then to factorize a more general equivariant monomial map into two parts going through this monoid. The kernels of both parts are finitely generated up to symmetry: recent work by Yamaguchi-Ogawa-Takemura on the (generalized) Birkhoff model provides an explicit degree bound for the kernel of the first part, while for the second part the finiteness follows from the Noetherianity of the matching monoid ring., Comment: 20 pages

In this paper we study group-based Markov models of evolution and their mixtures. In the algebreo-geometric setting, group-based phylogenetic tree models correspond to toric varieties, while their mixtures correspond to secant and join varieties. Determining properties of these secant and join varieties can aid both in model selection and establishing parameter identifiability. Here we explore the first natural geometric property of these varieties: their dimension. The expected projective dimension of the join variety of a set of varieties is one more than the sum of their dimensions. A join variety that realizes the expected dimension is nondefective. Nondefectiveness is not only interesting from a geometric point-of-view, but has been used to establish combinatorial identifiability for several classes of phylogenetic mixture models. In this paper, we focus on group-based models where the equivalence classes of identified parameters are orbits of a subgroup of the automorphism group of the group defining the model. In particular, we show that, for these group-based models, the variety corresponding to the mixture of $r$ trees with $n$ leaves is nondefective when $n \geq 2r+5$. We also give improved bounds for claw trees and give computational evidence that 2-tree and 3-tree mixtures are nondefective for small~$n$., Comment: 24 pages, 4 figures

We provide a closed formula for the degree of \(\mathop{\mathrm{SO}}\nolimits (n, \mathbb{C})\). In addition, we test symbolic and numerical techniques for computing the degree of \(\mathop{\mathrm{SO}}\nolimits (n, \mathbb{C})\). As an application of our results, we give a formula for the number of critical points of a low-rank semidefinite programming problem. Finally, we provide evidence for a conjecture regarding the real locus of \(\mathop{\mathrm{SO}}\nolimits (n, \mathbb{C})\).

We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for its dimension. Finally, we show how methods within the package can be used to compute a generating set for the join of any two ideals.

Let $R$ be the polynomial ring $K[x_{i,j}]$ where $1 \le i \le r$ and $j \in \mathbb{N}$, and let $I$ be an ideal of $R$ stable under the natural action of the infinite symmetric group $S_{\infty}$. Nagel--R\"omer recently defined a Hilbert series $H_I(s,t)$ of $I$ and proved that it is rational. We give a much shorter proof of this theorem using tools from the theory of formal languages and a simple algorithm that computes the series., Comment: 8 pages, no figures

An ideal of a local polynomial ring can be described by calculating a standard basis with respect to a local monomial ordering. However standard basis algorithms are not numerically stable. Instead we can describe the ideal numerically by finding the space of dual functionals that annihilate it, reducing the problem to one of linear algebra. There are several known algorithms for finding the truncated dual up to any specified degree, which is useful for describing zero-dimensional ideals. We present a stopping criterion for positive-dimensional cases based on homogenization that guarantees all generators of the initial monomial ideal are found. This has applications for calculating Hilbert functions., Comment: 19 pages, 4 figures