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The \emph{Tree Augmentation Problem (TAP)} is given a tree $T=(V,E_T)$ and additional set of {\em links} $E$ on $V\times V$, find $F \subseteq E$ such that $T \cup F$ is $2$-edge-connected, and $|F|$ is minimum. The problem is APX-hard…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
We consider the tree consensus problem, an important problem in bioinformatics. Given a rooted tree $t$ and another tree $T$, one would like to incorporate compatible information from $T$ to $t$. This problem is a subproblem in the tree…
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…
The Matching Augmentation Problem (MAP) has recently received significant attention as an important step towards better approximation algorithms for finding cheap $2$-edge connected subgraphs. This has culminated in a…
We consider the well-studied problem of finding a spanning tree with minimum average distance between vertex pairs (called a MAD tree). This is a classic network design problem which is known to be NP-hard. While approximation algorithms…
Constrained forest problems form a class of graph problems where specific connectivity requirements for certain cuts within the graph must be satisfied by selecting the minimum-cost set of edges. The prize-collecting version of these…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
The automaton constrained tree knapsack problem is a variant of the knapsack problem in which the items are associated with the vertices of the tree, and we can select a subset of items that is accepted by a top-down tree automaton. If the…
We identify a sufficient condition, treewidth-pliability, that gives a polynomial-time algorithm for an arbitrarily good approximation of the optimal value in a large class of Max-2-CSPs parameterised by the class of allowed constraint…
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…
We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that…
We present a new approximation algorithm for the treewidth problem which finds an upper bound on the treewidth and constructs a corresponding tree decomposition as well. Our algorithm is a faster variation of Reed's classical algorithm. For…
The Mutliagent Path Finding (MAPF) problem consists of identifying the trajectories that a set of agents should follow inside a given network in order to reach their desired destinations as soon as possible, but without colliding with each…
Constructing a Depth First Search (DFS) tree is a fundamental graph problem, whose parallel complexity is still not settled. Reif showed parallel intractability of lex-first DFS. In contrast, randomized parallel algorithms (and more…
When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may…
The basic goal of survivable network design is to build cheap networks that guarantee the connectivity of certain pairs of nodes despite the failure of a few edges or nodes. A celebrated result by Jain [Combinatorica'01] provides a…
We develop and analyze methods for computing provably optimal {\em maximum a posteriori} (MAP) configurations for a subclass of Markov random fields defined on graphs with cycles. By decomposing the original distribution into a convex…
Solving (mixed) integer linear programs, (M)ILPs for short, is a fundamental optimization task. While hard in general, recent years have brought about vast progress for solving structurally restricted, (non-mixed) ILPs: $n$-fold, tree-fold,…