Related papers: Inference of ecological interaction networks
Understanding the causes and consequences of, and devising countermeasures to, global warming is a profoundly complex problem. Network representations are sometimes the only way forward, and sometimes able to reduce the complexity of the…
Many animals live in societies where individuals frequently interact socially with each other. The social structures of these systems can be studied in depth by means of network analysis. A large number of studies on animal social networks…
Inferring network topology from dynamical observations is a fundamental problem pervading research on complex systems. Here, we present a simple, direct method to infer the structural connection topology of a network, given an observation…
For many networks of scientific interest we know both the connections of the network and information about the network nodes, such as the age or gender of individuals in a social network, geographic location of nodes in the Internet, or…
Exploring the effects a chemical compound has on a species takes a considerable experimental effort. Appropriate methods for estimating and suggesting new effects can dramatically reduce the work needed to be done by a laboratory. In this…
An estimate of the net direction of climate interactions in different geographical regions is made by constructing a directed climate network from a regular latitude-longitude grid of nodes, using a directionality index (DI) based on…
Network cascade refers to diffusion processes in which outcome changes within part of an interconnected population trigger a sequence of changes across the entire network. These cascades are governed by underlying diffusion networks, which…
Detecting the interactions of genetic compounds like genes, SNPs, proteins, metabolites, etc. can potentially unravel the mechanisms behind complex traits and common genetic disorders. Several methods have been taken into consideration for…
Networks - collections of interacting elements or nodes - abound in the natural and manmade worlds. For many networks, complex spatiotemporal dynamics stem from patterns of physical interactions unknown to us. To infer these interactions,…
Earth observation from satellites offers the possibility to monitor our planet with unprecedented accuracy. Radiative transfer models (RTMs) encode the energy transfer through the atmosphere, and are used to model and understand the Earth…
Topology inference is a powerful tool to better understand the behaviours of network systems (NSs). Different from most of prior works, this paper is dedicated to inferring the directed topology of NSs from noisy observations, where the…
In order to use the advanced inference techniques available for Ising models, we transform complex data (real vectors) into binary strings, by local averaging and thresholding. This transformation introduces parameters, which must be varied…
Indirect effects are powerful influences in ecosystems that may maintain species diversity and alter apparent relationships between species in surprising ways. Here, we applied Network Environ Analysis to 50 empirically-based trophic…
Several recent experiments in biology study systems composed of several interacting elements, for example neuron networks. Normally, measurements describe only the collective behavior of the system, even if in most cases we would like to…
Species networks generalize the notion of species trees to allow for hybridization or other lateral gene transfer. Under the Network Multispecies Coalescent Model, individual gene trees arising from a network can have any topology, but…
Capsule networks (see e.g. Hinton et al., 2018) aim to encode knowledge and reason about the relationship between an object and its parts. In this paper we specify a \emph{generative} model for such data, and derive a variational algorithm…
Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational…
In this paper we introduce a method for determining local interaction rules in animal swarms. The method is based on the assumption that the behavior of individuals in a swarm can be treated as a set of mechanistic rules. The principal idea…
Many economic activities are embedded in networks: sets of agents and the (often) rivalrous relationships connecting them to one another. Input sourcing by firms, interbank lending, scientific research, and job search are four examples,…
Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this…