Mahler Measuring the Genetic Code of Amoebae

The computation of amoebas has been a challenging open problem for the last dozen years. The most natural approach, namely to compute an amoeba via its boundary, has not been practical so far since only a superset of the boundary, the contour, is understood in theory and computable in practice. We define and characterize the extended boundary of an amoeba, which is sensitive to some degenerations that the topological boundary does not detect. Our description of the extended...

This paper is a report based on the results obtained during a three months internship at the University of Pittsburgh by the first author and under the mentorship of the second author. The notion of an amoeba of a subvariety in a torus $(\mathbb{C}^*)^n$ has been extended to subvarieties of the general linear group $GL_n(\mathbb{C})$ by the second author and Manon. In this paper, we show some basic properties of these matrix amoebas, e.g. any such amoeba is closed and the con...

We provide a unified framework of Mahler measure, dessins d'enfants, and gauge theory. With certain physically motivated Newton polynomials from reflexive polygons, the Mahler measure and the dessin are in one-to-one correspondence. From the Mahler measure, one can construct a Hauptmodul for a congruence subgroup of the modular group, which contains the subgroup associated to the dessin. In brane tilings and quiver gauge theories, the modular Mahler flow gives a natural resol...

Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry. Although they are important data structures, they face the significant challenge that sets of trees form a non-Euclidean phylogenetic tree space, which means that standard computational and statistical methods cannot be directly applied. In t...

The amoebas associated to algebraic varieties are certain concave regions in the Euclidean space whose shape reminds biological amoebas. This term was formally introduced to Mathematics in 1994 by Gelfand, Kapranov and Zelevinski. Some traces of amoebas were appearing from time to time, even before the formal introduction, as auxiliary tools in several problems. After 1994 amoebas have been seen and studied in several areas of mathematics, from algebraic geometry and topology...

The paper deals with amoebas of $k$-dimensional algebraic varieties in the algebraic complex torus of dimension $n\geq 2k$. First, we show that the area of complex algebraic curve amoebas is finite. Moreover, we give an estimate of this area in the rational curve case in terms of the degree of the rational parametrization coordinates. We also show that the volume of the amoeba of $k$-dimensional algebraic variety in $(\mathbb{C}^*)^{n}$, with $n\geq 2k$, is finite.

Given any complex Laurent polynomial $f$, $\mathrm{Amoeba}(f)$ is the image of its complex zero set under the coordinate-wise log absolute value map. We give an efficiently constructible polyhedral approximation, $\mathrm{ArchtTrop}(f)$, of $\mathrm{Amoeba}(f)$, and derive explicit upper and lower bounds, solely as a function of the number of monomial terms of $f$, for the Hausdorff distance between these two sets. We also show that deciding whether a given point lies in $\ma...

Principal component analysis is a widely-used method for the dimensionality reduction of a given data set in a high-dimensional Euclidean space. Here we define and analyze two analogues of principal component analysis in the setting of tropical geometry. In one approach, we study the Stiefel tropical linear space of fixed dimension closest to the data points in the tropical projective torus; in the other approach, we consider the tropical polytope with a fixed number of verti...

Let $V$ be a complex algebraic hypersurface defined by a polynomial $f$ with Newton polytope $\Delta$. It is well known that the spine of its amoeba has a structure of a tropical hypersurface. We prove in this paper that there exists a complex tropical hypersurface $V_{\infty, f}$ such that its coamoeba is homeomorphic to the closure in the real torus of the coamoeba of $V$. Moreover, the coamoeba of $V_{\infty, f}$ contains an arrangement of $(n-1)$-torus depending only on t...

In this paper we study the connection between dimers and Harnack curves discovered in math-ph/0311005. We prove that every Harnack curve arises as a spectral curve of some dimer model. We also prove that the space of Harnack curve of given degree is homeomorphic to a closed octant and that the areas of the amoeba holes and the distances between the amoeba tentacles give these global coordinates. We characterize Harnack curves of genus zero as spectral curves of isoradial dime...