Related papers: Towards the fixed parameter tractability of constr…
Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…
We consider the problem of finding weights and biases for a two-layer fully connected neural network to fit a given set of data points as well as possible, also known as EmpiricalRiskMinimization. Our main result is that the associated…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
Motivated by alignment of correlated sparse random graphs, we introduce a hypothesis testing problem of deciding whether or not two random trees are correlated. We obtain sufficient conditions under which this testing is impossible or…
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…
Given two rooted, ordered, and labeled trees $P$ and $T$ the tree inclusion problem is to determine if $P$ can be obtained from $T$ by deleting nodes in $T$. This problem has recently been recognized as an important query primitive in XML…
It was recently shown that a large class of phylogenetic networks, the `labellable' networks, is in bijection with the set of `expanding' covers of finite sets. In this paper, we show how several prominent classes of phylogenetic networks…
A tree-based network on a set $X$ of $n$ leaves is said to be universal if any rooted binary phylogenetic tree on $X$ can be its base tree. Francis and Steel showed that there is a universal tree-based network on $X$ in the case of $n=3$,…
We present an exact algorithm that decides, for every fixed $r \geq 2$ in time $O(m) + 2^{O(k^2)}$ whether a given multiset of $m$ clauses of size $r$ admits a truth assignment that satisfies at least $((2^r-1)m+k)/2^r$ clauses. Thus…
One of Courcelle's celebrated results states that if C is a class of graphs of bounded tree-width, then model-checking for monadic second order logic (MSO_2) is fixed-parameter tractable (fpt) on C by linear time parameterized algorithms,…
We consider the decentralized binary hypothesis testing problem on trees of bounded degree and increasing depth. For a regular tree of depth t and branching factor k>=2, we assume that the leaves have access to independent and identically…
This paper presents the novel `uniqueness tree' algorithm, as one possible method for determining whether two finite, undirected graphs are isomorphic. We prove that the algorithm has polynomial time complexity in the worst case, and that…
This paper introduces a new combinatorial framework for modeling the growth of binary trees through a discrete evolution process that incorporates a growing rule and an extinction rule. Building upon the theory of increasingly labeled…
Rare events have played an increasing role in molecular phylogenetics as potentially homoplasy-poor characters.In this contribution we analyze the phylogenetic information content from a combinatorial point of view by consid-ering the…
We consider extremal problems related to decks and multidecks of rooted binary trees (a.k.a. rooted phylogenetic tree shapes). Here, the deck (resp. multideck) of a tree $T$ refers to the set (resp. multiset) of leaf induced binary subtrees…
Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…
For a given graph $G$, a depth-first search (DFS) tree $T$ of $G$ is an $r$-rooted spanning tree such that every edge of $G$ is either an edge of $T$ or is between a \textit{descendant} and an \textit{ancestor} in $T$. A graph $G$ together…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…