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Artificial Neural Networks (ANN) comprise important symmetry properties, which can influence the performance of Monte Carlo methods in Neuroevolution. The problem of the symmetries is also known as the competing conventions problem or…
Reconstructing ancestral gene orders is an important step towards understanding genome evolution. The Small Parsimony Problem (SPP) has been extensively studied in this regard. The problem aims at finding the gene orders at internal nodes…
We investigate the symmetry of circular genome rearrangement models, discuss the implementation of a new representation-theoretic method of calculating evolutionary distances between circular genomes, and give the results of some initial…
Determining whether two STRIPS planning instances are isomorphic is the simplest form of comparison between planning instances. It is also a particular case of the problem concerned with finding an isomorphism between a planning instance…
We study the 2-edge-connected spanning subgraph (2-ECSS) problem: Given a graph $G$, compute a connected subgraph $H$ of $G$ with the minimum number of edges such that $H$ is spanning, i.e., $V(H) = V(G)$, and $H$ is 2-edge-connected, i.e.,…
We consider the following problem: from a given set of gene families trees on a set of genomes, find a first speciation, that splits these genomes into two subsets, that minimizes the number of gene duplications that happened before this…
The distance of a graph from being triangle-free is a fundamental graph parameter, counting the number of edges that need to be removed from a graph in order for it to become triangle-free. Its corresponding computational problem is the…
The domination problem is a well-studied problem in graph theory. In this paper, we study two natural variants: the hop domination problem and the $2$-step domination problem. Let $G$ be a graph with vertex set $V$ and edge set $E$. For a…
The invariance to permutations of the adjacency matrix, i.e., graph isomorphism, is an overarching requirement for Graph Neural Networks (GNNs). Conventionally, this prerequisite can be satisfied by the invariant operations over node…
The reconstruction problem for permutations on $n$ elements from their erroneous patterns which are distorted by transpositions is presented in this paper. It is shown that for any $n \geq 3$ an unknown permutation is uniquely…
Imagine that unlabelled tokens are placed on the edges of a graph, such that no two tokens are placed on incident edges. A token can jump to another edge if the edges having tokens remain independent. We study the problem of determining the…
We study the computational complexity of the map redistricting problem (gerrymandering). Mathematically, the electoral district designer (gerrymanderer) attempts to partition a weighted graph into $k$ connected components (districts) such…
A distributed computing system is a collection of processors that communicate either by reading and writing from a shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing…
A permutation graph can be defined as an intersection graph of segments whose endpoints lie on two parallel lines $l_1$ and $l_2$, one on each. A bipartite permutation graph is a permutation graph which is bipartite. In this paper we study…
We study the perfect matching reconfiguration problem: Given two perfect matchings of a graph, is there a sequence of flip operations that transforms one into the other? Here, a flip operation exchanges the edges in an alternating cycle of…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
We study the Maximum Bipartite Subgraph (MBS) problem, which is defined as follows. Given a set $S$ of $n$ geometric objects in the plane, we want to compute a maximum-size subset $S'\subseteq S$ such that the intersection graph of the…
Modellers of large scale genome rearrangement events, in which segments of DNA are inverted, moved, swapped, or even inserted or deleted, have found a natural syntax in the language of permutations. Despite this, there has been a wide range…
Finding dense subgraphs of a large graph is a standard problem in graph mining that has been studied extensively both for its theoretical richness and its many practical applications. In this paper we introduce a new family of dense…
The MEG (minimum equivalent graph) problem is, given a directed graph, to find a small subset of the edges that maintains all reachability relations between nodes. The problem is NP-hard. This paper gives a proof that, for graphs where each…