Related papers: Topological phenotypes constitute a new dimension …
Complex distribution networks are pervasive in biology. Examples include nutrient transport in the slime mold \emph{Physarum polycephalum} as well as mammalian and plant venation. Adaptive rules are believed to guide development of these…
Biology presents many examples of planar distribution and structural networks having dense sets of closed loops. An archetype of this form of network organization is the vasculature of dicotyledonous leaves, which showcases a…
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
The vascular network of leaves, comprising xylem and phloem, is a highly optimized system for the delivery of water, nutrients, and sugars. The design rules for these naturally occurring networks have been studied since the time of Leonardo…
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…
Classification of large and dense networks based on topology is very difficult due to the computational challenges of extracting meaningful topological features from real-world networks. In this paper we present a computationally tractable…
The statistical mechanical approach to complex networks is the dominant paradigm in describing natural and societal complex systems. The study of network properties, and their implications on dynamical processes, mostly focus on locally…
Advances in imaging techniques enable high resolution 3D visualisation of vascular networks over time and reveal abnormal structural features such as twists and loops, and their quantification is an active area of research. Here we showcase…
Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…
We propose a new method for quantitative characterization of spatial network-like patterns with loops, such as surface fracture patterns, leaf vein networks and patterns of urban streets. Such patterns are not well characterized by purely…
The ability to reroute and control flow is vital to the function of venation networks across a wide range of organisms. By modifying individual edges in these networks, either by adjusting edge conductances or creating and destroying edges,…
A network's topology information can be given as an adjacency matrix. The bitmap of sorted adjacency matrix(BOSAM) is a network visualisation tool which can emphasise different network structures by just looking at reordered adjacent…
We present an approach to leaf level segmentation of images of Arabidopsis thaliana plants based upon detected edges. We introduce a novel approach to edge classification, which forms an important part of a method to both count the leaves…
Geometric trees are characterized by their tree-structured layout and spatially constrained nodes and edges, which significantly impacts their topological attributes. This inherent hierarchical structure plays a crucial role in domains such…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
Compound graphs are networks in which vertices can be grouped into larger subsets, with these subsets capable of further grouping, resulting in a nesting that can be many levels deep. In several applications, including biological workflows,…
Network topology is a fundamental aspect of network science that allows us to gather insights into the complicated relational architectures of the world we inhabit. We provide a first specific study of neighbourhood degree sequences in…
Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…
Latent space models for network data characterize each node through a vector of latent features whose pairwise similarities define the edge probabilities among the pairs of nodes. Although this formulation has led to successful…
Automatic detection and segmentation of overlapping leaves in dense foliage can be a difficult task, particularly for leaves with strong textures and high occlusions. We present Dense-Leaves, an image dataset with ground truth segmentation…