Related papers: Reconstruction on Trees and Low-Degree Polynomials
Message-passing algorithms based on the Belief Propagation (BP) equations constitute a well-known distributed computational scheme. It is exact on tree-like graphical models and has also proven to be effective in many problems defined on…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
We often encounter probability distributions given as unnormalized products of non-negative functions. The factorization structures are represented by hypergraphs called factor graphs. Such distributions appear in various fields, including…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
Consider a Markov chain $(\xi_v)_{v \in V} \in [k]^V$ on the infinite $b$-ary tree $T = (V,E)$ with irreducible edge transition matrix $M$, where $b \geq 2$, $k \geq 2$ and $[k] = \{1,...,k\}$. We denote by $L_n$ the level-$n$ vertices of…
This paper presents a gentle tutorial and a structured reformulation of Bock's 1971 Algol procedure for constructing minimum directed spanning trees. Our aim is to make the original algorithm readable and reproducible for modern readers,…
A method was developed for Bayesian inference of species phylogeny using the multi-species coalescent model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we…
In multivariate data analysis, it is often important to estimate a graph characterizing dependence among (p) variables. A popular strategy uses the non-zero entries in a (p\times p) covariance or precision matrix, typically requiring…
In this article, we construct explicit examples of pairs of non-isomorphic trees with the same restricted $U$-polynomial for every $k$; by this we mean that the polynomials agree on terms with degree at most $k+1$. The main tool for this…
We study probability distributions over free algebras of trees. Probability distributions can be seen as particular (formal power) tree series [Berstel et al 82, Esik et al 03], i.e. mappings from trees to a semiring K . A widely studied…
We consider the probability that a spanning tree chosen uniformly at random from a graph can be partitioned into a fixed number $k$ of trees of equal size by removing $k-1$ edges. In that case, the spanning tree is called {\em splittable}.…
Recently, researchers have demonstrated that loopy belief propagation - the use of Pearls polytree algorithm IN a Bayesian network WITH loops OF error- correcting codes.The most dramatic instance OF this IS the near Shannon - limit…
The evolution of aligned DNA sequence sites is generally modeled by a Markov process operating along the edges of a phylogenetic tree. It is well known that the probability distribution on the site patterns at the tips of the tree…
Variable-length Markov chains (VLMCs) are a flexible class of higher-order Markov models that admit a natural representation as context trees. Existing Bayesian methods for specifying prior distributions on tree structures rely on branching…
We present an algorithm that enumerates all the minimal triangulations of a graph in incremental polynomial time. Consequently, we get an algorithm for enumerating all the proper tree decompositions, in incremental polynomial time, where…
We study the inference of network archaeology in growing random geometric graphs. We consider the root finding problem for a random nearest neighbor tree in dimension $d \in \mathbb{N}$, generated by sequentially embedding vertices…
Characterization of joint probability distribution for large networks of random variables remains a challenging task in data science. Probabilistic graph approximation with simple topologies has practically been resorted to; typically the…
Causal Bayesian networks are widely used tools for summarising the dependencies between variables and elucidating their putative causal relationships. By restricting the search to trees, for example, learning the optimum from data is…
A major task of evolutionary biology is the reconstruction of phylogenetic trees from molecular data. The evolutionary model is given by a Markov chain on a tree. Given samples from the leaves of the Markov chain, the goal is to reconstruct…
Spanning tree problems with specialized constraints can be difficult to solve in real-world scenarios, often requiring intricate algorithmic design and exponential time. Recently, there has been growing interest in end-to-end deep neural…