Related papers: The genesis sequence, tree records and endofunctio…
We prove that every amenable one-ended Cayley graph has an invariant spanning tree of one end. More generally, for any 1-ended amenable unimodular random graph we construct a factor of iid percolation (jointly unimodular subgraph) that is…
We present here a new and universal approach for the study of random and/or trees, unifying in one framework many different models, including some novel ones not yet understood in the literature. An and/or tree is a Boolean expression…
The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant…
To a given gene tree topology $G$ and species tree topology $S$ with leaves labeled bijectively from a fixed set $X$, one can associate a set of ancestral configurations, each of which encodes a set of gene lineages that can be found at a…
An attempt to come closer to a resolution of the Collatz conjecture is presented. The central idea is the formation of a tree consisting of positive odd numbers with number 1 as root. Functions for generating the tree from the root are…
In this paper, we study merge trees induced by a discrete Morse function on a tree. Given a discrete Morse function, we provide a method to constructing an induced merge tree and define a new notion of equivalence of discrete Morse…
We study the generating function of rooted and unrooted hyperforests in a general complete hypergraph with n vertices by using a novel Grassmann representation of their generating functions. We show that this new approach encodes the known…
For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
Motivation: While the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well-known that numerous other coexisting processes (e.g. horizontal gene…
We are interested in random uniform minimal factorizations of the $n$-cycle which are factorizations of $(1~2\dots n)$ into a product of $n-1$ transpositions. Our main result is an explicit formula for the joint probability that 1 and 2…
In this work we introduce and study various generalizations of the notion of increasingly labelled trees, where the label of a child node is always larger than the label of its parent node, to multilabelled tree families, where the nodes in…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals -- each with many genes -- splitting into new populations or species. The coalescent…
This note presents an encoding and a decoding algorithms for a forest of (labelled) rooted uniform hypertrees and hypercycles in linear time, by using as few as $n - 2$ integers in the range $[1,n]$. It is a simple extension of the…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…
In this paper, we investigate the complexity of an infinite family of Cayley graphs $\mathcal{D}_{n}=Cay(\mathbb{D}_{n}, b^{\pm\beta_1},b^{\pm\beta_2},\ldots,b^{\pm\beta_s}, a b^{\gamma_1}, a b^{\gamma_2},\ldots, a b^{\gamma_t} )$ on the…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
Causal theory is now widely developed with many applications to medicine and public health. However within the discipline of reliability, although causation is a key concept in this field, there has been much less theoretical attention. In…
We explore a generating function trick which allows us to keep track of infinitely many statistics using finitely many variables, by recording their individual distributions rather than their joint distributions. Building on previous work…