Related papers: Parameterized Algorithms for the Maximum Agreement…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. Here we explore the practical impact of kernelization (i.e. data reduction) on the NP-hard problem of computing the TBR distance between two unrooted binary…
We design a deterministic algorithm for the $(1+\epsilon)$-approximate maximum matching problem. Our primary result demonstrates that this problem can be solved in $O(\epsilon^{-6})$ semi-streaming passes, improving upon the…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
We develop a time-optimal $O(mn^2)$-time algorithm to construct the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the previous bound of $O(mn^3)$. Such graphs are used to better…
In an edge-colored graph, the cost incurred at a vertex on a path when two incident edges with different colors are traversed is called reload or changeover cost. The "Minimum Changeover Cost Arborescence" (MINCCA) problem consists in…
This paper presents two new deterministic algorithms for constructing consensus trees. Given an input of k phylogenetic trees with identical leaf label sets and n leaves each, the first algorithm constructs the majority rule (+) consensus…
A rigorous runtime analysis of evolutionary multi-objective optimization for the classical vertex cover problem in the context of parameterized complexity analysis has been presented by Kratsch and Neumann (2013). In this paper, we extend…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
Parameterized analysis provides powerful mechanisms for obtaining fine-grained insights into different types of algorithms. In this work, we combine this field with evolutionary algorithms and provide parameterized complexity analysis of…
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…
Computing bounded depth decompositions is a bottleneck in many applications of the treedepth parameter. The fastest known algorithm, which is due to Reidl, Rossmanith, S\'{a}nchez Villaamil, and Sikdar [ICALP 2014], runs in…
Given an undirected graph $G$, a collection $\{(s_1,t_1),..., (s_k,t_k)\}$ of pairs of vertices, and an integer $p$, the Edge Multicut problem ask if there is a set $S$ of at most $p$ edges such that the removal of $S$ disconnects every…
Parallel parameterized complexity theory studies how fixed-parameter tractable (fpt) problems can be solved in parallel. Previous theoretical work focused on parallel algorithms that are very fast in principle, but did not take into account…
Parameterized algorithms are a way to solve hard problems more efficiently, given that a specific parameter of the input is small. In this paper, we apply this idea to the field of answer set programming (ASP). To this end, we propose two…
In this paper we propose and study a new complexity model for approximation algorithms. The main motivation are practical problems over large data sets that need to be solved many times for different scenarios, e.g., many multicast trees…
A mixed dominating set is a collection of vertices and edges that dominates all vertices and edges of a graph. We study the complexity of exact and parameterized algorithms for \textsc{Mixed Dominating Set}, resolving some open questions.…
The maximum/minimum bisection problems are, given an edge-weighted graph, to find a bipartition of the vertex set into two sets whose sizes differ by at most one, such that the total weight of edges between the two sets is…
As the development of distributed systems progresses, more and more challenges arise and the need for developing optimized systems and for optimizing existing systems from multiple perspectives becomes more stringent. In this paper I…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…