Related papers: Hadamard Phylogenetic Methods and the n-taxon proc…
We survey results on the description of stochastically evolving genealogies of populations and marked genealogies of multitype populations or spatial populations via tree-valued Markov processes on (marked) ultrametric measure spaces. In…
The paper deals with a certain class of random evolutions. We develop a construction that yields an invariant measure for a continuous-time Markov process with random transitions. The approach is based on a particular way of constructing…
This is a presentation of recent work on quantum permutation groups, complex Hadamard matrices, and the connections between them. A long list of problems is included. We include as well some conjectural statements, about matrix models.
Model structure and complexity selection remains a challenging problem in system identification, especially for parametric non-linear models. Many Evolutionary Algorithm (EA) based methods have been proposed in the literature for estimating…
The paper introduces the Hidden Tree Markov Network (HTN), a neuro-probabilistic hybrid fusing the representation power of generative models for trees with the incremental and discriminative learning capabilities of neural networks. We put…
We consider a multi-type Moran model (in continuous time) with selection and type-dependent mutation. This paper is concerned with the evolution of genealogical information forward in time. For this purpose we define and analytically…
A method based on mapping a symbolic sequence into a set of patterns (strings resulting from the sequence parsing) is proposed as a tool for the reconstruction of ancestral sequences. The set union of patterns comprises all the patterns…
We consider a population with non-overlapping generations, whose size goes to infinity. It is described by a discrete genealogy which may be time non-homogeneous and we pay special attention to branching trees in varying environments. A…
In this paper, we study a family of lattice walks which are related to the Hadamard conjecture. There is a bijection between paths of these walks which originate and terminate at the origin and equivalence classes of partial Hadamard…
Hadamard matrices are square $n\times n$ matrices whose entries are ones and minus ones and whose rows are orthogonal to each other with respect to the standard scalar product in $\Bbb R^n$. Each Hadamard matrix can be transformed to a…
This paper describes the conversion of a Hidden Markov Model into a finite state transducer that closely approximates the behavior of the stochastic model. In some cases the transducer is equivalent to the HMM. This conversion is especially…
While convolution and self-attention mechanisms have dominated architectural design in deep learning, this survey examines a fundamental yet understudied primitive: the Hadamard product. Despite its widespread implementation across various…
We study various classes of random processes defined on the regular tree $T_d$ that are invariant under the automorphism group of $T_d$. Most important ones are factor of i.i.d. processes (randomized local algorithms), branching Markov…
Markov chains are a common framework for individual-based state and time discrete models in ecology and evolution. Their use, however, is largely limited to systems with a low number of states, since the transition matrices involved pose…
Stochastic models of evolution (Markov random fields on trivalent trees) generally assume that different characters (different runs of the stochastic process) are independent and identically distributed. In this paper we take the first…
We study a density-dependent Markov jump process describing a population where each individual is characterized by a type, and reproduces at rates depending both on its type and on the population type distribution. We are interested in the…
A calculational framework is proposed for phylogenetics, using nonlocal quantum field theories in hypercubic geometry. Quadratic terms in the Hamiltonian give the underlying Markov dynamics, while higher degree terms represent branching…
Posttranslational modification of proteins is key in transmission of signals in cells. Many signaling pathways contain several layers of modification cycles that mediate and change the signal through the pathway. Here, we study a simple…
We derive an invertible transform linking two widely used measures of species diversity: phylogenetic diversity and the expected proportions of segregating (non-constant) sites. We assume a bi-allelic, symmetric, finite site model of…
We present an investigation of stochastic evolution in which a family of evolution equations in $L^1$ are driven by continuous-time Markov processes. These are examples of so-called piecewise deterministic Markov processes (PDMP's) on the…