Related papers: Convergence of maximum likelihood supertree recons…
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…
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
Maximum likelihood estimators are used extensively to estimate unknown parameters of stochastic trait evolution models on phylogenetic trees. Although the MLE has been proven to converge to the true value in the independent-sample case, we…
Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide…
Consensus maximization is widely used for robust fitting in computer vision. However, solving it exactly, i.e., finding the globally optimal solution, is intractable. A* tree search, which has been shown to be fixed-parameter tractable, is…
Optimal transport provides a metric which quantifies the dissimilarity between probability measures. For measures supported in discrete metric spaces, finding the optimal transport distance has cubic time complexity in the size of the…
The relationship between two important problems in tree pattern matching, the largest common subtree and the smallest common supertree problems, is established by means of simple constructions, which allow one to obtain a largest common…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
Inference is typically intractable in high-treewidth undirected graphical models, making maximum likelihood learning a challenge. One way to overcome this is to restrict parameters to a tractable set, most typically the set of…
The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…
Ancestral maximum likelihood (AML) is a method that simultaneously reconstructs a phylogenetic tree and ancestral sequences from extant data (sequences at the leaves). The tree and ancestral sequences maximize the probability of observing…
A consensus tree is a phylogenetic tree that synthesizes a given collection of phylogenetic trees, all of which share the same leaf labels but may have different topologies, typically obtained through bootstrapping. Our research focuses on…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
Maximum-likelihood methods are applied to the problem of absorption tomography. The reconstruction is done with the help of an iterative algorithm. We show how the statistics of the illuminating beam can be incorporated into the…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
Temporal sequences of terrains arise in various application areas. To analyze them efficiently, one generally needs a suitable abstraction of the data as well as a method to compare and match them over time. In this paper we consider merge…
Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…
Tree trace reconstruction aims to learn the binary node labels of a tree, given independent samples of the tree passed through an appropriately defined deletion channel. In recent work, Davies, R\'acz, and Rashtchian used combinatorial…
We investigated testing the likelihood of a phylogenetic tree by comparison to its subtree pruning and regrafting (SPR) neighbors, with or without re-optimizing branch lengths. This is inspired by aspects of Bayesian significance tests, and…