Algebraic Unimodular Counting

We study algebraic algorithms for expressing the number of non-negative integer solutions to a unimodular system of linear equations as a function of the right hand side. Our methods include Todd classes of toric varieties via Gr\"obner bases, and rational generating functions as in Barvinok's algorithm. We report polyhedral and computational results for two special cases: counting contingency tables and Kostant's partition function.Comment: 21 page

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.Comment: 24 pages, 2 figure

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 "Lectures on Algebraic Statistics" (Problem 7.7). The model is obtained from the undirected graphical model of the complete bipartite graph $K_{2,4}$ 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 vertices. The Newton polytope has 17214912 vertices in 44938 symmetry classes and 70646 facets in 246 symmetry classes.Comment: 25 pages, 5 figures, presented at Mega 09 (Barcelona, Spain

Computing toric degenerations of flag varieties

We compute toric degenerations arising from the tropicalization of the full flag varieties $\mathcal{F}\ell_4$ and $\mathcal{F}\ell_5$ embedded in a product of Grassmannians. For $\mathcal{F}\ell_4$ and $\mathcal{F}\ell_5$ we compare toric degenerations arising from string polytopes and the FFLV polytope with those obtained from the tropicalization of the flag varieties. We also present a general procedure to find toric degenerations in the cases where the initial ideal arising from a cone of the tropicalization of a variety is not prime.Comment: 35 pages, 6 figure

Rational hypergeometric functions

Multivariate hypergeometric functions associated with toric varieties were introduced by Gel\u27fand, Kapranov and Zelevinsky. Singularities of such functions are discriminants, that is, divisors projectively dual to torus orbit closures. We show that most of these potential denominators never appear in rational hypergeometric functions. We conjecture that the denominator of any rational hypergeometric function is a product of resultants, that is, a product of special discriminants arising from Cayley configurations. This conjecture is proved for toric hypersurfaces and for toric varieties of dimension at most three. Toric residues are applied to show that every toric resultant appears in the denominator of some rational hypergeometric function

Bilinear identities on Schur symmetric functions

A series of bilinear identities on the Schur symmetric functions is obtained with the use of Pluecker relations.Comment: Accepted to Journal of Nonlinear Mathematical Physics. A reference to a connected result is adde

Effective Invariant Theory of Permutation Groups using Representation Theory

Using the theory of representations of the symmetric group, we propose an algorithm to compute the invariant ring of a permutation group. Our approach have the goal to reduce the amount of linear algebra computations and exploit a thinner combinatorial description of the invariant ring.Comment: Draft version, the corrected full version is available at http://www.springer.com