Related papers: The Complexity of Rooted Phylogeny Problems
We introduce a logical foundation to reason on tree structures with constraints on the number of node occurrences. Related formalisms are limited to express occurrence constraints on particular tree regions, as for instance the children of…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
In the stable marriage and roommates problems, a set of agents is given, each of them having a strictly ordered preference list over some or all of the other agents. A matching is a set of disjoint pairs of mutually accepted agents. If any…
This paper studies the "explanation problem" for tree- and linearly-ordered array data, a problem motivated by database applications and recently solved for the one-dimensional tree-ordered case. In this paper, one is given a matrix A whose…
Stable Marriage is a fundamental problem to both computer science and economics. Four well-known NP-hard optimization versions of this problem are the Sex-Equal Stable Marriage (SESM), Balanced Stable Marriage (BSM), max-Stable Marriage…
The Chinese Remainder Theorem for the integers says that every system of congruence equations is solvable as long as the system satisfies an obvious necessary condition. This statement can be generalized in a natural way to arbitrary…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
Constraint Satisfaction Problems (CSP) constitute a convenient way to capture many combinatorial problems. The general CSP is known to be NP-complete, but its complexity depends on a template, usually a set of relations, upon which they are…
An algorithm for a constraint satisfaction problem is called robust if it outputs an assignment satisfying at least $(1-g(\varepsilon))$-fraction of the constraints given a $(1-\varepsilon)$-satisfiable instance, where $g(\varepsilon)…
A normal network is uniquely determined by the set of phylogenetic trees that it displays. Given a set $\mathcal{P}$ of rooted binary phylogenetic trees, this paper presents a polynomial-time algorithm that reconstructs the unique binary…
We give practical, efficient algorithms that automatically determine the asymptotic distributed round complexity of a given locally checkable graph problem in the $[\Theta(\log n), \Theta(n)]$ region, in two settings. We present one…
Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…
We consider the k-disjoint-clique problem. The input is an undirected graph G in which the nodes represent data items, and edges indicate a similarity between the corresponding items. The problem is to find within the graph k disjoint…
$H$-Packing is the problem of finding a maximum number of vertex-disjoint copies of $H$ in a given graph $G$. $H$-Partition is the special case of finding a set of vertex-disjoint copies that cover each vertex of $G$ exactly once. Our goal…
In the rectilinear Steiner arborescence problem the task is to build a shortest rectilinear Steiner tree connecting a given root and a set of terminals which are placed in the plane such that all root-terminal-paths are shortest paths. This…
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…
We define the generalized Golomb triangular recursion by g_{j,s,lambda}(n) = g_{j,s,lambda}(n - s - g_{j,s,lambda}(n-j)) + \lambda j. For particular choices of the initial conditions, we show that the solution of the recursion is a non-slow…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
We prove a complexity dichotomy for the resilience problem for unions of conjunctive digraph queries (i.e., for existential positive sentences over the signature $\{R\}$ of directed graphs). Specifically, for every union $\mu$ of…