Related papers: A kernel for the maximum agreement forest problem …
This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
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…
Let $P$ and $S$ be two disjoint sets of $n$ and $m$ points in the plane, respectively. We consider the problem of computing a Steiner tree whose Steiner vertices belong to $S$, in which each point of $P$ is a leaf, and whose longest edge…
Many multiagent tasks -- such as reviewer assignment, coalition formation, or fair resource allocation -- require selecting a group of agents such that collaboration remains effective even in the worst case. The \emph{weighted max-min…
The number of trees T in the random forest (RF) algorithm for supervised learning has to be set by the user. It is controversial whether T should simply be set to the largest computationally manageable value or whether a smaller T may in…
A variant of the Erd\H{o}s-S\'os conjecture, posed by Havet, Reed, Stein and Wood, states that every graph with minimum degree at least $\lfloor 2k/3 \rfloor$ and maximum degree at least $k$ contains a copy of every tree with $k$ edges.…
For an arbitrary tree we investigate the problems of constructing a maximum matching which minimizes or maximizes the cardinality of a maximum matching of the graph obtained from original one by its removal and present corresponding…
Ancestral maximum likelihood (AML) is a method that simultaneously reconstructs a phylogenetic tree and ancestral sequences from extant data (sequences at the leaves). The tree and ancestral sequences maximize the probability of observing…
We prove an approximate max-multiflow min-multicut theorem for bounded treewidth graphs. In particular, we show the following: Given a treewidth-$r$ graph, there exists a (fractional) multicommodity flow of value $f$, and a multicut of…
Let $G$ be a graph on $n$ vertices. A linear forest is a graph consisting of vertex-disjoint paths and isolated vertices. A maximum linear forest of $G$ is a subgraph of $G$ with maximum number of edges, which is a linear forest. We denote…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
Three standard subtree transfer operations for binary trees, used in particular for phylogenetic trees, are: tree bisection and reconnection ($TBR$), subtree prune and regraft ($SPR$) and rooted subtree prune and regraft ($rSPR$). For a…
A decision tree recursively splits a feature space $\mathbb{R}^{d}$ and then assigns class labels based on the resulting partition. Decision trees have been part of the basic machine-learning toolkit for decades. A large body of work treats…
We investigate the computation of minimum-cost spanning trees satisfying prescribed vertex degree constraints: Given a graph $G$ and a constraint function $D$, we ask for a (minimum-cost) spanning tree $T$ such that for each vertex $v$, $T$…
We deepen the link between two classic areas of combinatorial optimization: augmentation and packing arborescences. We consider the following type of questions: What is the minimum number of arcs to be added to a digraph so that in the…
Random Forests (RF) and Extreme Gradient Boosting (XGBoost) are two of the most widely used and highly performing classification and regression models. They aggregate equally weighted CART trees, generated randomly in RF or sequentially in…
Linear arrangements of graphs are a well-known type of graph labeling and are found in many important computational problems, such as the Minimum Linear Arrangement Problem ($\texttt{minLA}$). A linear arrangement is usually defined as a…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
We present an axiomatic framework for analyzing the algorithmic properties of decision trees. This framework supports the classification of decision tree problems through structural and ancestral constraints within a rigorous mathematical…