Related papers: Average-Tree Phylogenetic Diversity Parameterized …
The notion of directed treewidth was introduced by Johnson, Robertson, Seymour and Thomas [Journal of Combinatorial Theory, Series B, Vol 82, 2001] as a first step towards an algorithmic metatheory for digraphs. They showed that some…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
We consider the problem of PAC-learning decision trees, i.e., learning a decision tree over the n-dimensional hypercube from independent random labeled examples. Despite significant effort, no polynomial-time algorithm is known for learning…
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest…
Recently there has been considerable interest in the problem of finding a phylogenetic network with a minimum number of reticulation vertices which displays a given set of phylogenetic trees, that is, a network with minimum hybrid number.…
Generalised hypertree width ($ghw$) is a hypergraph parameter that is central to the tractability of many prominent problems with natural hypergraph structure. Computing $ghw$ of a hypergraph is notoriously hard. The decision version of the…
In this paper, we present a Branch and Bound algorithm called QuickBB for computing the treewidth of an undirected graph. This algorithm performs a search in the space of perfect elimination ordering of vertices of the graph. The algorithm…
In this paper, we revisit the problem of sampling edges in an unknown graph $G = (V, E)$ from a distribution that is (pointwise) almost uniform over $E$. We consider the case where there is some a priori upper bound on the arboriciy of $G$.…
Phylogenetic networks are mathematical structures for modeling and visualization of reticulation processes in the study of evolution. Galled networks, reticulation visible networks, nearly-stable networks and stable-child networks are the…
We give an algorithm that takes as input an $n$-vertex graph $G$ and an integer $k$, runs in time $2^{O(k^2)} n^{O(1)}$, and outputs a tree decomposition of $G$ of width at most $k$, if such a decomposition exists. This resolves the…
Phylogenetic diversity indices are commonly used to rank the elements in a collection of species or populations for conservation purposes. The derivation of these indices is typically based on some quantitative description of the…
Vertex deletion and edge deletion problems play a central role in Parameterized Complexity. Examples include classical problems like Feedback Vertex Set, Odd Cycle Transversal, and Chordal Deletion. Interestingly, the study of edge…
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…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
A communication network can be modeled as a directed connected graph with edge weights that characterize performance metrics such as loss and delay. Network tomography aims to infer these edge weights from their pathwise versions measured…
The minimal number of rooted subtree prune and regraft (rSPR) operations needed to transform one phylogenetic tree into another one induces a metric on phylogenetic trees - the rSPR-distance. The rSPR-distance between two phylogenetic trees…
For an arbitrary, fixed graph (pattern graph), we study the algorithmic complexity of counting homomorphisms, subgraph isomorphisms, and induced subgraph isomorphisms from the pattern graph to $n$-vertex, $d$-degenerate graphs as input.…
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…