Related papers: H-Representation of the Kimura-3 Polytope

We apply the theory of markov random fields on trees to derive a phase transition in the number of samples needed in order to reconstruct phylogenies. We consider the Cavender-Farris-Neyman model of evolution on trees, where all the inner…

In this article we introduce a framization of the Hecke algebra of type B. For this framization we construct a faithful tensorial representation and two linear bases. We finally construct a Markov trace on these algebras and from this trace…

We consider the continuous-time presentation of the strand symmetric phylogenetic substitution model (in which rate parameters are unchanged under nucleotide permutations given by Watson-Crick base conjugation). Algebraic analysis of the…

This thesis splits into two major parts. The connection between the two parts is the notion of "categorification" which we shortly explain/recall in the introduction. In the first part of this thesis we extend Bar-Natan's cobordism based…

We introduce the tropical $F$-polynomial $f_M$ of a quiver representation $M$. We study its interplay with the general presentation for any finite-dimensional basic algebra. We give an interpretation of evaluating $f_M$ at a weight vector.…

We adapt methods from quiver representation theory and Hall algebra techniques to the counting of representations of virtually free groups over finite fields. This gives rise to the computation of the E-polynomials of…

Good representations for phylogenetic trees and networks are important for optimizing storage efficiency and implementation of scalable methods for the inference and analysis of evolutionary trees for genes, genomes and species. We…

We introduce a probabilistic representation of the derivative of the semigroup associated to a multidimensional killed diffusion process defined on the half-space. The semigroup derivative is expressed as a functional of a process that is…

Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…

Using brane quantization, we study the representation theory of the spherical double affine Hecke algebra of type $A_1$ in terms of the topological A-model on the moduli space of flat SL(2,C)-connections on a once-punctured torus. In…

We search for realistic supersymmetric standard-like models from SO(32) heterotic string theory on factorizable tori with multiple magnetic fluxes. Three chiral ganerations of quarks and leptons are derived from the adjoint and vector…

We provide a construction of examples of semistable degeneration via toric geometry. The applications include a higher dimensional generalization of classical degeneration of K3 surface into 4 rational components, an algebraic geometric…

We construct knot invariants categorifying the quantum knot variants for all representations of quantum groups. We show that these invariants coincide with previous invariants defined by Khovanov for sl_2 and sl_3 and by Mazorchuk-Stroppel…

We give an algorithm to explicitly compute the largest subtree, in the local Bruhat-Tits tree for PSL_2(k), whose vertices correspond to orders containing a given suborder H, in terms of a set of generators for H. The shape of this subtree…

We revisit the representation theory in type $A$used previously to establish that the dissimilarity vectors of phylogenetic trees are points on the tropical Grassmannian variety. We use a different version of this construction to show that…

Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…

We study the representation of a finite group acting on the cohomology of a non-degenerate, invariant hypersurface of a projective toric variety. We deduce an explicit description of the representation when the toric variety has at worst…

The solutions to a large class of semi-linear parabolic PDEs are given in terms of expectations of suitable functionals of a tree of branching particles. A sufficient, and in some cases necessary, condition is given for the integrability of…

Let $L$ be the function field of a projective space ${\mathbb P}^n_k$ over an algebraically closed field $k$ of characteristic zero, and $H$ be the group of projective transformations. An $H$-sheaf ${\mathcal V}$ on ${\mathbb P}^n_k$ is a…

We say that a space X admits a homology exponent if there exists an exponent for the torsion subgroup of the integral homology. Our main result states if an H-space of finite type admits a homology exponent, then either it is, up to…