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We describe birational representations of discrete groups generated by involutions, having their origin in the theory of exactly solvable vertex-models in lattice statistical mechanics. These involutions correspond respectively to two kinds…
Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…
A phylogenetic tree is a tree with a fixed set of leaves that has no vertices of degree two. In this paper, we axiomatically define four other discrete structures on the set of leaves. We prove that each of these structures is an equivalent…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
Using a probabilistic interpretation of the Burau representation of the braid group offered by Vaughan Jones, we generalize the Burau representation to a representation of the semigroup of string links. This representation is determined by…
We introduce a tree structure for the iterates of symmetric bimodal maps and identify a subset which we prove to be isomorphic to the family of unimodal maps. This subset is used as a second factor for a $\ast $-product that we define in…
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…
We show that if a strictly positive joint probability distribution for a set of binary random variables factors according to a tree, then vertex separation represents all and only the independence relations enclosed in the distribution. The…
Frequent pattern mining is a relevant method to analyse structured data, like sequences, trees or graphs. It consists in identifying characteristic substructures of a dataset. This paper deals with a new type of patterns for tree data:…
We develop a probabilistic approach to the celebrated Jacobian conjecture, which states that any Keller map (i.e. any polynomial mapping $F\colon \mathbb{C}^n \to \mathbb{C}^n$ whose Jacobian determinant is a nonzero constant) has a…
The transition matrix of a Markov chain $(X_k,k\geq 0)$ on a finite or infinite rooted tree is said to be almost upper-directed if, given $X_k$, the node $X_{k+1}$ is either a descendant of $X_k$ or the parent of $X_k$. It is said to be…
This paper defines a linear representation for nonlinear maps $F:\mathbb{F}^n\rightarrow\mathbb{F}^n$ where $\mathbb{F}$ is a finite field, in terms of matrices over $\mathbb{F}$. This linear representation of the map $F$ associates a…
Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
Discovering the latent structure from many observed variables is an important yet challenging learning task. Existing approaches for discovering latent structures often require the unknown number of hidden states as an input. In this paper,…
Phylogenetic varieties related to equivariant substitution models have been studied largely in the last years. One of the main objectives has been finding a set of generators of the ideal of these varieties, but this has not yet been…
The paper concerns the tree invariants of string links, introduced by Kravchenko and Polyak and closely related to the classical Milnor linking numbers also known as $\bar{\mu}$--invariants. We prove that, analogously as for…
In this paper we apply new geometric and combinatorial methods to the study of phylogenetic mixtures. The focus of the geometric approach is to describe the geometry of phylogenetic mixture distributions for the two state random cluster…
Dynamic regression trees are an attractive option for automatic regression and classification with complicated response surfaces in on-line application settings. We create a sequential tree model whose state changes in time with the…
Decompositions of networks are useful not only for structural exploration. They also have implications and use in analysis and computational solution of processes (such as the Ising model, percolation, SIR model) running on a given network.…