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We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
We propose a method for detecting significant interactions in very large multivariate spatial point patterns. This methodology develops high dimensional data understanding in the point process setting. The method is based on modelling the…
Accurate biodiversity monitoring is essential for effective environmental policy, yet current practices often rely on arbitrarily defined ecosystems, communities, and ad-hoc indicator species, limiting cost-efficiency and reproducibility.…
Discontinuous dynamical systems with grazing solutions are discussed. The group property, continuation of solutions, continuity and smoothness of motions are thoroughly analyzed. A variational system around a grazing solution which depends…
We consider an approach for community detection in time-varying networks. At its core, this approach maintains a small sketch graph to capture the essential community structure found in each snapshot of the full network. We demonstrate how…
We propose a sub-structural niching method that fully exploits the problem decomposition capability of linkage-learning methods such as the estimation of distribution algorithms and concentrate on maintaining diversity at the sub-structural…
We simulate the evolution of model protein sequences subject to mutations. A mutation is considered neutral if it conserves 1) the structure of the ground state, 2) its thermodynamic stability and 3) its kinetic accessibility. All other…
Ecosystem approach to fisheries requires a thorough understanding of fishing impacts on ecosystem status and processes as well as predictive tools such as ecosystem models to provide useful information for management. The credibility of…
The presence of one or more species at some spatial locations but not others is a central matter in ecology. This phenomenon is related to ecological pattern formation. Nonlocal interactions can be considered as one of the mechanisms…
Can evolving networks be inferred and modeled without directly observing their nodes and edges? In many applications, the edges of a dynamic network might not be observed, but one can observe the dynamics of stochastic cascading processes…
Cell tracking and segmentation assist biologists in extracting insights from large-scale microscopy time-lapse data. Driven by local accuracy metrics, current tracking approaches often suffer from a lack of long-term consistency and the…
Developments in transcriptomics techniques have caused a large demand in tailored computational methods for modelling gene expression dynamics from experimental data. Recently, so-called single-cell experiments have revolutionised genetic…
The gradual patterns that model the complex co-variations of attributes of the form "The more/less X, The more/less Y" play a crucial role in many real world applications where the amount of numerical data to manage is important, this is…
A framework is proposed to detect anomalies in multi-modal data. A deep neural network-based object detector is employed to extract counts of objects and sub-events from the data. A cyclostationary model is proposed to model regular…
Predicting dynamic behaviors is one of the goals of science in general as well as essential to many specific applications of human knowledge to real world systems. Here we introduce an analytic approach using the sigmoid growth curve to…
We propose ClusPath, a novel algorithm for detecting general evolution tendencies in a population of entities. We show how abstract notions, such as the Swedish socio-economical model (in a political dataset) or the companies fiscal…
This chapter aims to inform a practitioner about current methods for predicting potential distributions of invasive species. It mostly addresses single species models, covering the conceptual bases, touching on mechanistic models, and then…
The two dominant approaches for the analysis of species-habitat associations in animals have been shown to reach divergent conclusions. Models fitted from the viewpoint of an individual (step selection functions), once scaled up, do not…
The description of large temporal graphs requires effective methods giving an appropriate mesoscopic partition. Many approaches exist today to detect communities in static graphs. However, many networks are intrinsically dynamical, and need…
The modeling of time series is becoming increasingly critical in a wide variety of applications. Overall, data evolves by following different patterns, which are generally caused by different user behaviors. Given a time series, we define…