Mahler Measuring the Genetic Code of Amoebae

In this paper we try to look at the compactification of Teichmuller spaces from a tropical viewpoint. We describe a general construction for the compactification of algebraic varieties, using their amoebas, and we describe the boundary via tropical varieties. When we apply this construction to the Teichmuller spaces we see that they can be mapped in a real algebraic hypersurface in such a way that the cone over the boundary is a subpolyhedron of a tropical hypersurface. We wa...

When we apply comparative phylogenetic analyses to genome data, it is a well-known problem and challenge that some of given species (or taxa) often have missing genes. In such a case, we have to impute a missing part of a gene tree from a sample of gene trees. In this short paper we propose a novel method to infer a missing part of a phylogenetic tree using an analogue of a classical linear regression in the setting of tropical geometry. In our approach, we consider a tropica...

We study a statistical model of random plane partitions. The statistical model has interpretations as five-dimensional $\mathcal{N}=1$ supersymmetric SU(N) Yang-Mills on $\mathbb{R}^4\times S^1$ and as K\"ahler gravity on local SU(N) geometry. At the thermodynamic limit a typical plane partition called the limit shape dominates in the statistical model. The limit shape is linked with a hyperelliptic curve, which is a five-dimensional version of the SU(N) Seiberg-Witten curve....

In this paper we suggest that, under suitable conditions, supervised learning can provide the basis to formulate at the microscopic level quantitative questions on the phenotype structure of multicellular organisms. The problem of explaining the robustness of the phenotype structure is rephrased as a real geometrical problem on a fixed domain. We further suggest a generalization of path integrals that reduces the problem of deciding whether a given molecular network can gener...

Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of phylogenetic trees with a fixed set of labels on leaves is not Euclidean, we cannot simply apply tools in data science. In this paper we survey some new developments of machine learning models using tropical geometry to analyze a set of phylogene...

We consider the metric space of all toric K\"ahler metrics on a compact toric manifold; when "looking at it from infinity" (following Gromov), we obtain the tangent cone at infinity, which is parametrized by equivalence classes of complete geodesics. In the present paper, we study the associated limit for the family of metrics on the toric variety, its quantization, and degeneration of generic divisors. The limits of the corresponding K\"ahler polarizations become degenerat...

We review recent efforts to machine learn relations between knot invariants. Because these knot invariants have meaning in physics, we explore aspects of Chern-Simons theory and higher dimensional gauge theories. The goal of this work is to translate numerical experiments with Big Data to new analytic results.

We implement Genetic Algorithms for triangulations of four-dimensional reflexive polytopes which induce Calabi-Yau threefold hypersurfaces via Batryev's construction. We demonstrate that such algorithms efficiently optimize physical observables such as axion decay constants or axion-photon couplings in string theory compactifications. For our implementation, we choose a parameterization of triangulations that yields homotopy inequivalent Calabi-Yau threefolds by extending fin...

We introduce machine learning methodology to the study of lattice polytopes. With supervised learning techniques, we predict standard properties such as volume, dual volume, reflexivity, etc, with accuracies up to 100%. We focus on 2d polygons and 3d polytopes with Pl\"ucker coordinates as input, which out-perform the usual vertex representation.

The purpose of the present work is to provide a detailed asymptotic analysis of the $k\times\ell$ doubly periodic Aztec diamond dimer model of growing size for any $k$ and $\ell$ and under mild conditions on the edge weights. We explicitly describe the limit shape and the 'arctic' curves that separate different phases, as well as prove the convergence of local fluctuations to the appropriate translation-invariant Gibbs measures away from the arctic curves. We also obtain a ho...