Related papers: Matrix and graph representations of vine copula st…
Forbidden characterizations may sometimes be the most natural way to describe families of graphs, and yet these characterizations are usually very hard to exploit for enumerative purposes. By building on the work of Gioan and Paul (2012)…
A monotone drawing of a graph G is a straight-line drawing of G such that every pair of vertices is connected by a path that is monotone with respect to some direction. Trees, as a special class of graphs, have been the focus of several…
Regular vine distributions which constitute a flexible class of multivariate dependence models are discussed. Since multivariate copulae constructed through pair-copula decompositions were introduced to the statistical community, interest…
Motion planning is an important and well-studied field of robotics. A typical approach to finding a route is to construct a {\em cell graph} representing a scene and then to find a path in such a graph. In this paper we present and analyze…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
The topological (or graph) structures of real-world networks are known to be predictive of multiple dynamic properties of the networks. Conventionally, a graph structure is represented using an adjacency matrix or a set of hand-crafted…
In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…
Important graph mining problems such as Clustering are computationally demanding. To significantly accelerate these problems, we propose ProbGraph: a graph representation that enables simple and fast approximate parallel graph mining with…
Context: Edge graphs are graphs whose edges are labelled with identifiers, and nodes can have multiple edges between them. They are used to model a wide range of systems, including networks with distances or degrees of connection and…
The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle…
Structured prediction can be thought of as a simultaneous prediction of multiple labels. This is often done by maximizing a score function on the space of labels, which decomposes as a sum of pairwise and unary potentials. The above is…
Reciprocal best matches play an important role in numerous applications in computational biology, in particular as the basis of many widely used tools for orthology assessment. Nevertheless, very little is known about their mathematical…
An arborescence of a directed graph $\Gamma$ is a spanning tree directed toward a particular vertex $v$. The arborescences of a graph rooted at a particular vertex may be encoded as a polynomial $A_v(\Gamma)$ representing the sum of the…
Machine learning on graphs is an important and ubiquitous task with applications ranging from drug design to friendship recommendation in social networks. The primary challenge in this domain is finding a way to represent, or encode, graph…
A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the…
Graph-structured data are pervasive across domains including social networks, biological networks, and knowledge graphs. Due to their non-Euclidean nature, such data pose significant challenges to conventional machine learning methods. This…
This thesis presents a number of results related to path traversal in trees and graphs. In particular, we focus on data structures which allow such traversals to be performed efficiently in the external memory setting. In addition, for…
In this article we discuss a data structure, which combines advantages of two different ways for representing graphs: adjacency matrix and collection of adjacency lists. This data structure can fast add and search edges (advantages of…
In social networks, information and influence diffuse among users as cascades. While the importance of studying cascades has been recognized in various applications, it is difficult to observe the complete structure of cascades in practice.…
Accurate 3D modelling of grapevines is crucial for precision viticulture, particularly for informed pruning decisions and automated management techniques. However, the intricate structure of grapevines poses significant challenges for…