Related papers: A Faster Construction of Greedy Consensus Trees
Trees are fundamental data structure for many areas of computer science and system engineering. In this report, we show how to ensure eventual consistency of optimistically replicated trees. In optimistic replication, the different replicas…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
Trees are useful entities allowing to model data structures and hierarchical relationships in networked decision systems ubiquitously. An ordered tree is a rooted tree where the order of the subtrees (children) of a node is significant. In…
Consider a collection of weighted subsets of a ground set N. Given a query subset Q of N, how fast can one (1) find the weighted sum over all subsets of Q, and (2) sample a subset of Q proportionally to the weights? We present a tree-based…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
Polytrees are a subclass of Bayesian networks that seek to capture the conditional dependencies between a set of $n$ variables as a directed forest and are motivated by their more efficient inference and improved interpretability. Since the…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
Decision trees are popular Classification and Regression tools and, when small-sized, easy to interpret. Traditionally, a greedy approach has been used to build the trees, yielding a very fast training process; however, controlling sparsity…
Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…
Decision trees and their ensembles are very popular models of supervised machine learning. In this paper we merge the ideas underlying decision trees, their ensembles and FCA by proposing a new supervised machine learning model which can be…
We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
We give an algorithm that, given an $n$-vertex graph $G$ and an integer $k$, in time $2^{O(k)} n$ either outputs a tree decomposition of $G$ of width at most $2k + 1$ or determines that the treewidth of $G$ is larger than $k$. This is the…
A $k$-decision tree $t$ (or $k$-tree) is a recursive partition of a matrix (2D-signal) into $k\geq 1$ block matrices (axis-parallel rectangles, leaves) where each rectangle is assigned a real label. Its regression or classification loss to…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Supertree construction is the process by which a set of phylogenetic trees, each on a subset of the overall set X of species, is combined into a tree on the full set S. The traditional use of supertree methods is the assembly of a large…