Related papers: Best Match Graphs with Binary Trees
A rainbow matching in an edge-colored graph is a matching whose edges have distinct colors. We address the complexity issue of the following problem, \mrbm: Given an edge-colored graph $G$, how large is the largest rainbow matching in $G$?…
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…
Intersection graphs are well-studied in the area of graph algorithms. Some intersection graph classes are known to have algorithms enumerating all unlabeled graphs by reverse search. Since these algorithms output graphs one by one and the…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
This paper establishes a bridge between linear logic and mainstream graph theory, building on previous work by Retor\'e (2003). We show that the problem of correctness for MLL+Mix proof nets is equivalent to the problem of uniqueness of a…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
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…
Integrating multi-omics data, such as DNA methylation, mRNA expression, and microRNA (miRNA) expression, offers a comprehensive view of the biological mechanisms underlying disease. However, the high dimensionality of multi-omics data, the…
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…
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…
We propose the fully explainable Decision Tree Graph Neural Network (DT+GNN) architecture. In contrast to existing black-box GNNs and post-hoc explanation methods, the reasoning of DT+GNN can be inspected at every step. To achieve this, we…
A graph $G$ is {\em matching-decyclable} if it has a matching $M$ such that $G-M$ is acyclic. Deciding whether $G$ is matching-decyclable is an NP-complete problem even if $G$ is 2-connected, planar, and subcubic. In this work we present…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
Many combinatorial optimization problems can be phrased in the language of constraint satisfaction problems. We introduce a graph neural network architecture for solving such optimization problems. The architecture is generic; it works for…
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 $X$…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
We study the robustness verification problem for tree-based models, including decision trees, random forests (RFs) and gradient boosted decision trees (GBDTs). Formal robustness verification of decision tree ensembles involves finding the…
Perfect Matching-Cut is the problem of deciding whether a graph has a perfect matching that contains an edge-cut. We show that this problem is NP-complete for planar graphs with maximum degree four, for planar graphs with girth five, for…
The Graph Burning Problem (GBP) is a combinatorial optimization problem that has gained relevance as a tool for quantifying a graph's vulnerability to contagion. Although it is based on a very simple propagation model, its decision version…
We consider the problem of graph matching, or learning vertex correspondence, between two correlated stochastic block models (SBMs). The graph matching problem arises in various fields, including computer vision, natural language processing…