Related papers: MI-Sim: A MATLAB Package for the Numerical Analysi…
Motivated by the results of recent laboratory experiments (Yoshida et al. Nature, 424, 303-306 (2003)) as well as many earlier field observations that evolutionary changes can take place in ecosystems over relatively short ecological time…
Better understanding the natural world is a crucial task with a wide range of applications. In environments with close proximity between humans and animals, such as zoos, it is essential to better understand the causes behind animal…
The structure of a bipartite interaction network can be described by providing a clustering for each of the two types of nodes. Such clusterings are outputted by fitting a Latent Block Model (LBM) on an observed network that comes from a…
Food webs represent the set of consumer-resource interactions among a set of species that co-occur in a habitat, but most food web studies have omitted parasites and their interactions. Recent studies have provided conflicting evidence on…
Let a collection of networks represent interactions within several (social or ecological) systems. We pursue two objectives: identifying similarities in the topological structures that are held in common between the networks and clustering…
The central nervous system is composed of many individual units -- from cells to areas -- that are connected with one another in a complex pattern of functional interactions that supports perception, action, and cognition. One natural and…
Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at…
A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex,…
Efficient and accurate extraction of microstructures in micrographs of materials is essential in process optimization and the exploration of structure-property relationships. Deep learning-based image segmentation techniques that rely on…
Frequent and structurally related subgraphs, also known as network motifs, are valuable features of many graph datasets. However, the high computational complexity of identifying motif sets in arbitrary datasets (motif mining) has limited…
Recent work suggests that cross-feeding -- the secretion and consumption of metabolic biproducts by microbes -- is essential for understanding microbial ecology. Yet how cross-feeding and competition combine to give rise to ecosystem-level…
Several natural and theoretical networks can be broken down into smaller portions, or subgraphs corresponding to neighborhoods. The more frequent of these neighborhoods can then be understood as motifs of the network, being therefore…
The nematode Caenorhabditis elegans is a well-known model organism used to investigate fundamental questions in biology. Motility assays of this small roundworm are designed to study the relationships between genes and behavior. Commonly,…
Hybrid modeling combining data-driven techniques and numerical methods is an emerging and promising research direction for efficient climate simulation. However, previous works lack practical platforms, making developing hybrid modeling a…
Visual recognition of materials and their states is essential for understanding most aspects of the world, from determining whether food is cooked, metal is rusted, or a chemical reaction has occurred. However, current image recognition…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
Food image classification models are crucial for dietary management applications because they reduce the burden of manual meal logging. However, most publicly available datasets for training such models rely on web-crawled images, which…
Movement is a fundamental aspect of animal life and plays a crucial role in determining the structure of population dynamics, communities, ecosystems, and diversity. In recent years, the recording of animal movements via GPS collars, camera…
Many real-world networks describe systems in which interactions decay with the distance between nodes. Examples include systems constrained in real space such as transportation and communication networks, as well as systems constrained in…
Advances in GPS telemetry technology have enabled analysis of animal movement in open areas. Ecologists today are utilizing modern analytic tools to study animal behaviors from large quantity of GPS coordinates. Analytic tools with…