Related papers: Fitch Graph Completion
Symmetry breaking for graphs and other combinatorial objects is notoriously hard. On the one hand, complete symmetry breaks are exponential in size. On the other hand, current, state-of-the-art, partial symmetry breaks are often considered…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
Graph signals are functions of the underlying graph. When the edge-weight between a pair of nodes is high, the corresponding signals generally have a higher correlation. As a result, the signals can be represented in terms of a graph-based…
Reciprocal best match graphs (RBMGs) are vertex colored graphs whose vertices represent genes and the colors the species where the genes reside. Edges identify pairs of genes that are most closely related with respect to an underlying…
This paper presents several algorithms for hashing directed graphs. The algorithms given are capable of hashing entire graphs as well as assigning hash values to specific nodes in a given graph. The notion of node symmetry is made precise…
For a graph with edge ordering, a linear order on the edge set, we obtain a permutation of vertices by considering the edges as transpositions of endvertices. It is known from D\'enes' results that the permutation of a tree is a full cyclic…
Many scientific problems require to process data in the form of geometric graphs. Unlike generic graph data, geometric graphs exhibit symmetries of translations, rotations, and/or reflections. Researchers have leveraged such inductive bias…
We consider complete graphs with edge weights and/or node weights taking values in some set. In the first part of this paper, we show that a large number of graphs are completely determined, up to isomorphism, by the distribution of their…
Say that an edge of a graph G dominates itself and every other edge adjacent to it. An edge dominating set of a graph G = (V,E) is a subset of edges E' of E which dominates all edges of G. In particular, if every edge of G is dominated by…
In the companion paper [Linear rank-width of distance-hereditary graphs I. A polynomial-time algorithm, Algorithmica 78(1):342--377, 2017], we presented a characterization of the linear rank-width of distance-hereditary graphs, from which…
In a short article submitted to ArXiv [1], Maddamsetti et al. argue that the variation in the neutral mutation rate among genes in Escherichia coli that we recently reported [2] might be explained by horizontal gene transfer (HGT). To…
Since Darwin, species trees have been used as a simplified description of the relationships which summarize the complicated network $N$ of reality. Recent evidence of hybridization and lateral gene transfer, however, suggest that there are…
Graphlets are subgraphs rooted at a fixed vertex. The number of occurrences of graphlets aligned to a particular vertex, called graphlet degree sequence (gds), gives a topological description of the surrounding of the analyzed vertex.…
The design of Graph Transformers (GTs) generally neglects considerations for fairness, resulting in biased outcomes against certain sensitive subgroups. Since GTs encode graph information without relying on message-passing mechanisms,…
Phylogenetic trees are often constructed by using a metric on the set of taxa that label the leaves of the tree. While there are a number of methods for constructing a tree using a given metric, such trees will only display the metric if it…
The Persistent Perfect phylogeny, also known as Dollo-1, has been introduced as a generalization of the well-known perfect phylogenetic model for binary characters to deal with the potential loss of characters. The problem of deciding the…
Distance-hereditary graphs form an important class of graphs, from the theoretical point of view, due to the fact that they are the totally decomposable graphs for the split-decomposition. The previous best enumerative result for these…
Graph Neural Networks (GNNs) typically operate by message-passing, where the state of a node is updated based on the information received from its neighbours. Most message-passing models act as graph convolutions, where features are mixed…
In a (two-type) Wright-Fisher diffusion with directional selection and two-way mutation, let $x$ denote today's frequency of the beneficial type, and given $x$, let $h(x)$ be the probability that, among all individuals of today's…