Related papers: Modeling and Inferring Metacommunity Dynamics with…
Sequential Monte Carlo (SMC) algorithms represent a suite of robust computational methodologies utilized for state estimation and parameter inference within dynamical systems, particularly in real-time or online environments where data…
Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and…
Ecosystems are governed by dynamic processes such as competition for resources, reproduction and dispersal. These shape their biodiversity and how the system responds to change. Current approaches to modelling ecosystems, especially plants,…
Across many fields, a problem of interest is to predict the transition rates between nodes of a network, given limited stationary state and dynamical information. We give a solution using the principle of Maximum Caliber. We find the…
Many systems across the sciences evolve through a combination of multiplicative growth and diffusive transport. In the presence of disorder, these systems tend to form localized structures which alternate between long periods of relative…
Metapopulation epidemic models are a valuable tool for studying large-scale outbreaks. With the limited availability of epidemic tracing data, it is challenging to infer the essential constituents of these models, namely, the epidemic…
Ecosystems often undergo abrupt regime shifts in response to gradual external changes. These shifts are theoretically understood as a regime switch between alternative stable states of the ecosystem dynamical response to smooth changes in…
Stochastic agent-based models can account for millions of cells with spatiotemporal movement that can be a function of different factors. However, these simulations can be computationally expensive. In this work, we develop a novel…
Community finding algorithms for networks have recently been extended to dynamic data. Most of these recent methods aim at exhibiting community partitions from successive graph snapshots and thereafter connecting or smoothing these…
Predicting competitive outcomes typically requires fitting dynamical models to data, from which interaction strengths and coexistence indicators such as invasion criteria can be produced. Methods that allow to propagate parameter…
Recently we have introduced a simplified model of ecosystem assembly (Capitan et al., 2009) for which we are able to map out all assembly pathways generated by external invasions in an exact manner. In this paper we provide a deeper…
This paper provides an overview of the research on the metastable behavior of the Ising model. We analyze the transition times from the set of metastable states to the set of the stable states by identifying the critical configurations that…
Spatial ecological networks are widely used to model interactions between georeferenced biological entities (e.g., populations or communities). The analysis of such data often leads to a two-step approach where groups containing similar…
Recent advances in metagenomics have revealed macroecological patterns or "laws" describing robust statistical regularities across microbial communities. Stochastic logistic models (SLMs), which treat species as independent -- akin to ideal…
Species interactions (ranging from direct predator prey relationships to indirect effects mediated by the environment) are central to ecosystem balance and biodiversity. While empirical methods for measuring these interactions exist, their…
We analyse metapopulation dynamics in terms of an individual-based, stochastic model of a finite metapopulation. We suggest a new approach, using the number of patches in the population as a large parameter. This approach does not require…
The internal behaviour of a population is an important feature to take account of when modelling their dynamics. In line with kin selection theory, many social species tend to cluster into distinct groups in order to enhance their overall…
Standard epidemic models based on compartmental differential equations are investigated under continuous parameter change as external forcing. We show that seasonal modulation of the contact parameter superimposed a monotonic decay needs a…
Recent measurements of durations of non-equilibrium processes provide valuable information on microscopic mechanisms and energetics. Comprehensive theory for corresponding experiments so far is well developed for single-particle systems…
Extreme weather is one of the main mechanisms through which climate change will directly impact human society. Coping with such change as a global community requires markedly improved understanding of how global warming drives extreme…