Maria Angelica Cueto

An implicitization challenge for binary factor analysis

We use tropical geometry to compute the multidegree and Newton polytope of the hypersurface of a statistical model with two hidden and four observed binary random variables, solving an open question stated by Drton, Sturmfels and Sullivant in (Drton et al., 2009, Ch. VI, Problem 7.7). The model is obtained from the undirected graphical model of the complete bipartite graph K2,4 by marginalizing two of the six binary random variables. We present algorithms for computing the Newton polytope of its defining equation by parallel walks along the polytope and its normal fan. In this way we compute vertices of the polytope. Finally, we also compute and certify its facets by studying tangent cones of the polytope at the symmetry classes of vertices. The Newton polytope has 17214912 vertices in 44938 symmetry classes and 70646 facets in 246 symmetry classes.

Polyhedral Geometry of Phylogenetic Rogue Taxa

It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this “rogue taxon” effect. In this paper we characterize the behavior of balanced minimum evolution (BME) phylogenetics on data sets of this type using tools from polyhedral geometry. First we show that for any distance matrix there exist distances to a “rogue taxon” such that the BME-optimal tree for the data set with the new taxon does not contain any nontrivial splits (bipartitions) of the optimal tree for the original data. Second, we prove a theorem which restricts the topology of BME-optimal trees for data sets of this type, thus showing that a rogue taxon cannot have an arbitrary effect on the optimal tree. Third, we computationally construct polyhedral cones that give complete answers for BME rogue taxon behavior when our original data fits a tree on four, five, and six taxa. We use these cones to derive sufficient conditions for rogue taxon behavior for four taxa, and to understand the frequency of the rogue taxon effect via simulation.

Cremona Linearizations of Some Classical Varieties

In this paper we present an effective method for linearizing rational varieties of codimension at least two under Cremona transformations, starting from a given parametrization. Using these linearizing Cremonas, we simplify the equations of secant and tangential varieties of some classical examples, including Veronese, Segre and Grassmann varieties. We end the paper by treating the special case of the Segre embedding of the n-fold product of projective spaces, where cumulant Cremonas, arising from algebraic statistics, appear as specific cases of our general construction.

How to Repair Tropicalizations of Plane Curves Using Modifications

ABSTRACT Tropical geometry is sensitive to embeddings of algebraic varieties inside toric varieties. The purpose of this article is to advertise tropical modifications as a tool to locally repair bad embeddings of plane curves, allowing the re-embedded tropical curve to better reflect the geometry of the input curve. Our approach is based on the close connection between analytic curves (in the sense of Berkovich) and tropical curves. We investigate the effect of these tropical modifications on the tropicalization map defined on the analytification of the given curve. Our study is motivated by the case of plane elliptic cubics, where good embeddings are characterized in terms of the j-invariant. Given a plane elliptic cubic whose tropicalization contains a cycle, we present an effective algorithm, based on non-Archimedean methods, to linearly re-embed the curve in dimension 4 so that its tropicalization reflects the j-invariant. We give an alternative elementary proof of this result by interpreting the initial terms of the A-discriminant of the defining equation as a local discriminant in the Newton subdivision.

Tropical geometry of genus two curves

Abstract We exploit three classical characterizations of smooth genus two curves to study their tropical and analytic counterparts. First, we provide a combinatorial rule to determine the dual graph of each algebraic curve and the metric structure on its minimal Berkovich skeleton. Our main tool is the description of genus two curves via hyperelliptic covers of the projective line with six branch points. Given the valuations of these six points and their differences, our algorithm provides an explicit harmonic 2-to-1 map to a metric tree on six leaves. Second, we use tropical modifications to produce a faithful tropicalization in dimension three starting from a planar hyperelliptic embedding. Finally, we consider the moduli space of abstract genus two tropical curves and translate the classical Igusa invariants characterizing isomorphism classes of genus two algebraic curves into the tropical realm. While these tropical Igusa functions do not yield coordinates in the tropical moduli space, we propose an alternative set of invariants that provides new length data.