Related papers: On recognizing graphs representing Persistent Perf…
Fast exact algorithms are known for Hamiltonian paths in undirected and directed bipartite graphs through elegant though involved algorithms that are quite different from each other. We devise algorithms that are simple and similar to each…
Temporal graphs are introduced to model systems where the relationships among the entities of the system evolve over time. In this paper, we consider the temporal graphs where the edge set changes with time and all the changes are known a…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
In a directed graph, a kernel is a subset of vertices that is both stable and absorbing. Not all digraphs have a kernel, but a theorem due to Boros and Gurvich guarantees the existence of a kernel in every clique-acyclic orientation of a…
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…
In this paper, we present a new exact algorithm for counting perfect matchings, which relies on neither inclusion-exclusion principle nor tree-decompositions. For any bipartite graph of $2n$ nodes and $\Delta n$ edges such that $\Delta \geq…
The independence gap of a graph was introduced by Ekim et al. (2018) as a measure of how far a graph is from being well-covered. It is defined as the difference between the maximum and minimum size of a maximal independent set. We…
Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees,…
The idea of enumeration algorithms with polynomial delay is to polynomially bound the running time between any two subsequent solutions output by the enumeration algorithm. While it is open for more than four decades if all minimal…
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…
Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the literals are rooted triples, is there a rooted binary…
Perfect phylogeny consisting of determining the compatibility of a set of characters is known to be NP-complete. We propose in this article a conjecture on the necessary and sufficient conditions of compatibility: Given a set $\mathcal{C}$…
We prove a complete dichotomy theorem for the parameterized sparse $t$-uniform hypergraphic degree sequence problem, $\mathrm{sparse}\text{-}t\text{-}\mathrm{uni}\text{-}\mathrm{HDS}_{\alpha',\alpha}$. For any fixed $t \ge 3$, given…
The maximum clique problem is a well known NP-Hard problem with applications in data mining, network analysis, information retrieval and many other areas related to the World Wide Web. There exist several algorithms for the problem with…
The transversal hypergraph problem is the task of enumerating the minimal hitting sets of a hypergraph. It is a long-standing open question whether this can be done in output-polynomial time. For hypergraphs whose solutions have bounded…
Series-parallel (SP) graphs are binary edge-labeled graphs with a designated source and target vertex, built using serial and parallel composition. A set of graphs is recognizable if membership depends only on its image under a homomorphism…
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabilities on the reticulation edges) describing the evolution of…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Function graphs are graphs representable by intersections of continuous real-valued functions on the interval [0,1] and are known to be exactly the complements of comparability graphs. As such they are recognizable in polynomial time.…
We investigate how efficiently a well-studied family of domination-type problems can be solved on bounded-treewidth graphs. For sets $\sigma,\rho$ of non-negative integers, a $(\sigma,\rho)$-set of a graph $G$ is a set $S$ of vertices such…