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We present a novel algorithm for the minimum-depth elimination tree problem, which is equivalent to the optimal treedepth decomposition problem. Our algorithm makes use of two cheaply-computed lower bound functions to prune the search tree,…
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabilities on the reticulation edges) describing the evolution of…
We consider the classic problem of Network Reliability. A network is given together with a source vertex, one or more target vertices, and probabilities assigned to each of the edges. Each edge appears in the network with its associated…
We give an algorithm for finding the arboricity of a weighted, undirected graph, defined as the minimum number of spanning forests that cover all edges of the graph, in $\sqrt{n} m^{1+o(1)}$ time. This improves on the previous best bound of…
We consider the problem of detecting a planted clique of size $k$ in a random graph on $n$ vertices. When the size of the clique exceeds $\Theta(\sqrt{n})$, polynomial-time algorithms for detection proliferate. We study faster -- namely,…
Many problems are known to be solvable in subexponential parameterized time when the input graph is planar. The bidimensionality framework of Demaine, Fomin, Hajiaghay, and Thilikos [JACM'05] and the treewidth-pattern-covering approach by…
The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are…
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…
We consider the problem of learning the structure of undirected graphical models with bounded treewidth, within the maximum likelihood framework. This is an NP-hard problem and most approaches consider local search techniques. In this…
We study two fundamental decremental dynamic graph problems. In both problems, we need to maintain a vertex-weighted forest of size $n$ under edge deletions, weight updates, and a certain information-retrieval query. Both problems can be…
Calculation of the log-likelihood stands as the computational bottleneck for many statistical phylogenetic algorithms. Even worse is its gradient evaluation, often used to target regions of high probability. Order ${\cal…
We develop two different methods to achieve subexponential time parameterized algorithms for problems on sparse directed graphs. We exemplify our approaches with two well studied problems. For the first problem, {\sc $k$-Leaf…
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…
Hypertree decompositions provide a way to evaluate Conjunctive Queries (CQs) in polynomial time, where the exponent of this polynomial is determined by the width of the decomposition. In theory, the goal of efficient CQ evaluation therefore…
We study the low-degree hardness of broadcasting on trees. Broadcasting on trees has been extensively studied in statistical physics, in computational biology in relation to phylogenetic reconstruction and in statistics and computer science…
The Steiner tree problem aims to determine a minimum edge-weighted tree that spans a given set of terminal vertices from a given graph. In the past decade, a considerable number of algorithms have been developed to solve this…
Motivated by the increasing need to understand the algorithmic foundations of distributed large-scale graph computations, we study a number of fundamental graph problems in a message-passing model for distributed computing where $k \geq 2$…
Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…
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.…