Related papers: Unique perfect phylogeny is NP-hard
This paper investigates the computational complexity of deciding whether the vertices of a graph can be partitioned into a disjoint union of cliques and a triangle-free subgraph. This problem is known to be $\NP$-complete on arbitrary…
We study the complexity of symmetric assembly puzzles: given a collection of simple polygons, can we translate, rotate, and possibly flip them so that their interior-disjoint union is line symmetric? On the negative side, we show that the…
Perfect phylogenies are fundamental in the study of evolutionary trees because they capture the situation when each evolutionary trait emerges only once in history; if such events are believed to be rare, then by Occam's Razor such…
We consider the following generalization of binary search in sorted arrays to tree domains. In each step of the search, an algorithm is querying a vertex $q$, and as a reply, it receives an answer, which either states that $q$ is the…
Tree representations of (sets of) symmetric binary relations, or equivalently edge-colored undirected graphs, are of central interest, e.g.\ in phylogenomics. In this context symbolic ultrametrics play a crucial role. Symbolic ultrametrics…
We show that some natural problems that are XNLP-hard (which implies W[t]-hardness for all t) when parameterized by pathwidth or treewidth, become FPT when parameterized by stable gonality, a novel graph parameter based on optimal maps from…
Given a bipartite graph $G=(U\cup V,E)$, a left-perfect many-to-one matching is a subset $M \subseteq E$ such that each vertex in $U$ is incident with exactly one edge in $M$. If $U$ is partitioned into some groups, the matching is called…
The fitting problem for conjunctive queries (CQs) is the problem to construct a CQ that fits a given set of labeled data examples. When a fitting CQ exists, it is in general not unique. This leads us to proposing natural refinements of the…
Computing a minimum-area planar straight-line drawing of a graph is known to be NP-hard for planar graphs, even when restricted to outerplanar graphs. However, the complexity question is open for trees. Only a few hardness results are known…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
We study a family of graph modification problems called the F-Vertex Splitting problem. Given a graph G, the task is to determine whether G can be transformed into a graph G-prime belonging to a graph class F through a sequence of at most k…
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
A spanning subgraph $F$ of a graph $G$ is called {\em perfect} if $F$ is a forest, the degree $d_F(x)$ of each vertex $x$ in $F$ is odd, and each tree of $F$ is an induced subgraph of $G$. Alex Scott (Graphs \& Combin., 2001) proved that…
Consider a set of labels $L$ and a set of trees ${\mathcal T} = \{{\mathcal T}^{(1), {\mathcal T}^{(2), ..., {\mathcal T}^{(k) \$ where each tree ${\mathcal T}^{(i)$ is distinctly leaf-labeled by some subset of $L$. One fundamental problem…
A common task in phylogenetics is to find an evolutionary tree representing proximity relationships between species. This motivates the notion of leaf powers: a graph G = (V, E) is a leaf power if there exist a tree T on leafset V and a…
We study the problem of connecting the parts of a multipartite graph using a minimum number of edges under a matching constraint. We introduce interconnection trees, defined as matchings whose projections onto the quotient graph form a…
A multilabeled tree (or MUL-tree) is a rooted tree in which every leaf is labelled by an element from some set, but in which more than one leaf may be labelled by the same element of that set. In phylogenetics, such trees are used in…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
Hypertree decompositions, as well as the more powerful generalized hypertree decompositions (GHDs), and the yet more general fractional hypertree decompositions (FHD) are hypergraph decomposition methods successfully used for answering…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…