Related papers: Parameterized Algorithms for the Maximum Agreement…
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…
The recently introduced graph parameter tree-cut width plays a similar role with respect to immersions as the graph parameter treewidth plays with respect to minors. In this paper, we provide the first algorithmic applications of tree-cut…
Fixed tree topologies are widely used in phylodynamic analyses to reduce computational burden, yet the consequences of this assumption remain insufficiently understood. Here, we systematically assess the impact of various fixed-topology…
In the longest plane spanning tree problem, we are given a finite planar point set $\mathcal{P}$, and our task is to find a plane (i.e., noncrossing) spanning tree for $\mathcal{P}$ with maximum total Euclidean edge length. Despite more…
Finding a minimum spanning tree (MST) for $n$ points in an arbitrary metric space is a fundamental primitive for hierarchical clustering and many other ML tasks, but this takes $\Omega(n^2)$ time to even approximate. We introduce a…
We present the first fixed-parameter tractable (FPT) algorithms for exact computation of generalized hypertree width (ghw) and fractional hypertree width (fhw). Our algorithms are parameterized by the target width, the rank, and the maximum…
We consider the NP-hard problem of finding a spanning tree with a maximum number of internal vertices. This problem is a generalization of the famous Hamiltonian Path problem. Our dynamic-programming algorithms for general and…
We present an efficient fixed-parameter algorithm for #SAT parameterized by the incidence treewidth, i.e., the treewidth of the bipartite graph whose vertices are the variables and clauses of the given CNF formula; a variable and a clause…
Let $G=(V,E)$ be a graph on $n$ vertices and $R$ be a set of pairs of vertices in $V$ called \emph{requests}. A \emph{multicut} is a subset $F$ of $E$ such that every request $xy$ of $R$ is cut by $F$, \i.e. every $xy$-path of $G$…
We propose a new methodology to develop heuristic algorithms using tree decompositions. Traditionally, such algorithms construct an optimal solution of the given problem instance through a dynamic programming approach. We modify this…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
Random forests are decision tree ensembles that can be used to solve a variety of machine learning problems. However, as the number of trees and their individual size can be large, their decision making process is often incomprehensible. In…
The graph isomorphism problem is theoretically interesting and also has many practical applications. The best known classical algorithms for graph isomorphism all run in time super-polynomial in the size of the graph in the worst case. An…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…
We study a natural generalization of the maximum weight many-to-one matching problem. We are given an undirected bipartite graph $G= (A \cup P, E)$ with weights on the edges in $E$, and with lower and upper quotas on the vertices in $P$. We…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
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…
In the Maximum-size Properly Colored Forest problem, we are given an edge-colored undirected graph and the goal is to find a properly colored forest with as many edges as possible. We study this problem within a broader framework by…