Related papers: Revisiting an equivalence between maximum parsimon…
We establish a log-supermodularity property for probability distributions on binary patterns observed at the tips of a tree that are generated under any 2--state Markov process. We illustrate the applicability of this result in…
Concept of exponential family is generalized by simple and general exponential form. Simple and general potential are introduced. Maximum Entropy and Maximum Likelihood tasks are defined. ML task on the simple exponential form and ME task…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…
In 'no common mechanism' (NCM) models of character evolution, each character can evolve on a phylogenetic tree under a partially or totally separate process (e.g. with its own branch lengths). In such cases, the usual conditions that…
Labelled Markov chains (LMCs) are widely used in probabilistic verification, speech recognition, computational biology, and many other fields. Checking two LMCs for equivalence is a classical problem subject to extensive studies, while the…
Accurate reconstruction of phylogenies remains a key challenge in evolutionary biology. Most biologically plausible formulations of the problem are formally NP-hard, with no known efficient solution. The standard in practice are fast…
Using techniques from Poisson approximation, we prove explicit error bounds on the number of permutations that avoid any pattern. Most generally, we bound the total variation distance between the joint distribution of pattern occurrences…
We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…
One reason why classical phylogenetic reconstruction methods fail to correctly infer the underlying topology is because they assume oversimplified models. In this paper we propose a topology reconstruction method consistent with the most…
We prove polynomial upper and lower bounds on the expected size of the maximum agreement subtree of two random binary phylogenetic trees under both the uniform distribution and Yule-Harding distribution. This positively answers a question…
Maximum likelihood estimation is a fundamental computational problem in statistics. In this note, we give a bound for the maximum likelihood degree of algebraic statistical models for discrete data. As usual, such models are identified with…
Phylogenetic comparative methods (PCMs) are widely used to study trait evolution. However, many evolutionary histories involve reticulate evolutionary scenarios, such as hybridization, that violate core assumptions of these methods. In this…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…
Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…
Parametric inference for spatial max-stable processes is difficult since the related likelihoods are unavailable. A composite likelihood approach based on the bivariate distribution of block maxima has been recently proposed in the…
Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree…
We consolidate two widely believed conjectures about tautologies -- no optimal proof system exists, and most require superpolynomial size proofs in any system -- into a $p$-isomorphism-invariant condition satisfied by all paddable…
Phylogenetic reconciliation seeks to explain host-symbiont co-evolution by mapping parasite trees onto host trees through events such as cospeciation, duplication, host switching, and loss. Finding an optimal reconciliation that ensures…