Related papers: Least resolved trees for two-colored best match gr…
In the Properly Colored Spanning Tree problem, we are given an edge-colored undirected graph and the goal is to find a spanning tree in which any two adjacent edges have distinct colors. Since finding such a tree is NP-hard in general,…
Color-constrained subgraph problems are those where we are given an edge-colored (directed or undirected) graph and the task is to find a specific type of subgraph, like a spanning tree, an arborescence, a single-source shortest path tree,…
A local algorithm is a distributed algorithm that completes after a constant number of synchronous communication rounds. We present local approximation algorithms for the minimum dominating set problem and the maximum matching problem in…
We introduce and investigate the approximability of the maximum binary tree problem (MBT) in directed and undirected graphs. The goal in MBT is to find a maximum-sized binary tree in a given graph. MBT is a natural variant of the…
For a set of red and blue points in the plane, a minimum bichromatic spanning tree (MinBST) is a shortest spanning tree of the points such that every edge has a red and a blue endpoint. A MinBST can be computed in $O(n\log n)$ time where…
Several implicit methods to infer Horizontal Gene Transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the…
An optimal algorithm is presented about Conflict-Free Coloring for connected subgraphs of tree of rings. Suppose the number of the rings in the tree is |T| and the maximum length of rings is |R|. A presented algorithm in [1] for a Tree of…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
An edge-colored graph is said to be balanced if it has an equal number of edges of each color. Given a graph $G$ whose edges are colored using two colors and a positive integer $k$, the objective in the Edge Balanced Connected Subgraph…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
Subgraph matching is a fundamental building block for graph-based applications and is challenging due to its high-order combinatorial nature. Existing studies usually tackle it by combinatorial optimization or learning-based methods.…
Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always…
In 1996, Bodlaender showed the celebrated result that an optimal tree decomposition of a graph of bounded treewidth can be found in linear time. The algorithm is based on an algorithm of Bodlaender and Kloks that computes an optimal tree…
We consider three variants of the problem of finding a maximum weight restricted $2$-matching in a subcubic graph $G$. (A $2$-matching is any subset of the edges such that each vertex is incident to at most two of its edges.) Depending on…
The best-performing models in ML are not interpretable. If we can explain why they outperform, we may be able to replicate these mechanisms and obtain both interpretability and performance. One example are decision trees and their…
We introduce a graph partitioning problem motivated by computational topology and propose two algorithms that produce approximate solutions. Specifically, given a weighted, undirected graph $G$ and a positive integer $k$, we desire to find…
In the Properly Colored Spanning Tree problem, we are given an edge-colored undirected graph and the goal is to find a properly colored spanning tree, i.e., a spanning tree in which any two adjacent edges have distinct colors. The problem…
Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…
Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…