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Reachability is the problem of deciding whether there is a path from one vertex to the other in the graph. Standard graph traversal algorithms such as DFS and BFS take linear time to decide reachability however their space complexity is…
Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special…
For the vast majority of local graph problems standard dynamic programming techniques give c^tw V^O(1) algorithms, where tw is the treewidth of the input graph. On the other hand, for problems with a global requirement (usually…
An NP-hard graph problem may be intractable for general graphs but it could be efficiently solvable using dynamic programming for graphs with bounded width (or depth or some other structural parameter). Dynamic programming is a well-known…
Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer.…
The notion of treewidth plays an important role in theoretical and practical studies of graph problems. It has been recognized that, especially in practical environments, when computing the treewidth of a graph it is invaluable to first…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
Given a simplicial complex with $n$ simplices, we consider the Connected Subsurface Recognition (c-SR) problem of finding a subcomplex that is homeomorphic to a given connected surface with a fixed boundary. We also study the related…
We propose polynomial-time algorithms that sparsify planar and bounded-genus graphs while preserving optimal or near-optimal solutions to Steiner problems. Our main contribution is a polynomial-time algorithm that, given an unweighted graph…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…
Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…
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…
In this paper we study the Spanning Tree Congestion problem, where we are given a graph $G=(V,E)$ and are asked to find a spanning tree $T$ of minimum maximum congestion. Here, the congestion of an edge $e\in T$ is the number of edges…
The strong thin tree conjecture states that every $k$-edge-connected graph $G$ contains an $O(1/k)$-thin spanning tree, meaning a spanning tree which contains at most an $O(1/k)$ fraction of the edges across each cut in $G$. This conjecture…
Motivated by applications in network epidemiology, we consider the problem of determining whether it is possible to delete at most $k$ edges from a given input graph (of small treewidth) so that the resulting graph avoids a set…
The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem…
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…
In the Vertex Planarization problem one asks to delete the minimum possible number of vertices from an input graph to obtain a planar graph. The parameterized complexity of this problem, parameterized by the solution size (the number of…
In this paper we propose a new wavelet transform applicable to functions defined on graphs, high dimensional data and networks. The proposed method generalizes the Haar-like transform proposed in [1], and it is defined via a hierarchical…
Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…