Related papers: Species Trees Forcing Parsimony to Fail
Decision trees are widely used for non-linear modeling, as they capture interactions between predictors while producing inherently interpretable models. Despite their popularity, performing inference on the non-linear fit remains largely…
Inferring a decision tree from a given dataset is one of the classic problems in machine learning. This problem consists of buildings, from a labelled dataset, a tree such that each node corresponds to a class and a path between the tree…
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…
For a graph property $\Pi$, Subgraph Complementation to $\Pi$ is the problem to find whether there is a subset $S$ of vertices of the input graph $G$ such that modifying $G$ by complementing the subgraph induced by $S$ results in a graph…
Minimum Bisection denotes the NP-hard problem to partition the vertex set of a graph into two sets of equal sizes while minimizing the width of the bisection, which is defined as the number of edges between these two sets. We first consider…
The $\text{NJ}_{st}$ method was proposed by Liu and Yu to infer a species tree topology from unrooted topological gene trees. While its statistical consistency under the multispecies coalescent model was established only for a 4-taxon tree,…
When we apply comparative phylogenetic analyses to genome data, it is a well-known problem and challenge that some of given species (or taxa) often have missing genes. In such a case, we have to impute a missing part of a gene tree from a…
We study the simple random walk on trees and give estimates on the mixing and relaxation time. Relying on a recent characterization by Basu, Hermon and Peres, we give geometric criteria, which are easy to verify and allow to determine…
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…
Treewidth is a graph parameter that plays a fundamental role in several structural and algorithmic results. We study the problem of decomposing a given graph $G$ into node-disjoint subgraphs, where each subgraph has sufficiently large…
Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…
The tree spanner problem for a graph $G$ is as follows: For a given integer $k$, is there a spanning tree $T$ of $G$ (called a tree $k$-spanner) such that the distance in $T$ between every pair of vertices is at most $k$ times their…
We construct long sequences of braids that are descending with respect to the standard order of braids (``Dehornoy order''), and we deduce that, contrary to all usual algebraic properties of braids, certain simple combinatorial statements…
Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands. It also remains unclear how complicated networks can be for consistent inference…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
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…
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the…
Given a tree $T$ on $n$ vertices, and $k, b, s_1, \ldots, s_b \in N$, the Tree Partitioning problem asks if at most $k$ edges can be removed from $T$ so that the resulting components can be grouped into $b$ groups such that the number of…
We construct generating trees with one, two, and three labels for some classes of permutations avoiding generalized patterns of length 3 and 4. These trees are built by adding at each level an entry to the right end of the permutation,…
Given a solution to a recursive distributional equation, a natural (and non-trivial) question is whether the corresponding recursive tree process is endogenous. That is, whether the random environment almost surely defines the tree process.…