Related papers: Popping Bubbles in Pangenome Graphs

Many-to-one maps are ubiquitous in machine learning, from the image recognition model that assigns a multitude of distinct images to the concept of "cat" to the time series forecasting model which assigns a range of distinct time-series to…

Graphs are quickly emerging as a leading abstraction for the representation of data. One important application domain originates from an emerging discipline called "connectomics". Connectomics studies the brain as a graph; vertices…

In non-linear systems, where explicit analytic solutions usually can't be found, visualisation is a powerful approach which can give insights into the dynamical behaviour of models; it is also crucial for teaching this area of mathematics.…

Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the machine-readable newick format. There are thus thousands of published trees in the scientific literature…

A graphical model is a statistical model that is associated to a graph whose nodes correspond to variables of interest. The edges of the graph reflect allowed conditional dependencies among the variables. Graphical models admit…

Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of…

Bounded model checking of pointer programs is a debugging technique for programs that manipulate dynamically allocated pointer structures on the heap. It is based on the following four observations. First, error conditions like dereference…

Tanglegrams are a special class of graphs appearing in applications concerning cospeciation and coevolution in biology and computer science. They are formed by identifying the leaves of two rooted binary trees. We give an explicit formula…

We address the problem of form understanding: finding text entities and the relationships/links between them in form images. The proposed FUDGE model formulates this problem on a graph of text elements (the vertices) and uses a Graph…

We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph…

A graph is a $k$-leaf power of a tree $T$ if its vertices are leaves of $T$ and two vertices are adjacent in $T$ if and only if their distance in $T$ is at most $k$. Then $T$ is a $k$-leaf root of $G$. This notion was introduced by…

A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…

Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…

The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also…

Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that…

Inspired by the human ability to learn and organize knowledge into hierarchical taxonomies with prototypes, this paper addresses key limitations in current deep hierarchical clustering methods. Existing methods often tie the structure to…

In this paper, we study the graph classification problem from the graph homomorphism perspective. We consider the homomorphisms from $F$ to $G$, where $G$ is a graph of interest (e.g. molecules or social networks) and $F$ belongs to some…

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…

Given a graph with millions of nodes, what patterns exist in the distributions of node characteristics, and how can we detect them and separate anomalous nodes in a way similar to human vision? In this paper, we propose a vision-guided…