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Complex systems are characterized by multiple spatial and temporal scales. A natural framework to capture their multiscale nature is that of multilayer networks, where different layers represent distinct physical processes that often…
Regulatory functions are essential in both socioeconomic and biological systems, from corporate managers to regulatory genes. Regulatory functions come with substantial costs and benefits, and the balance of the two is often taken for…
Evolution Strategies (ESs) have recently become popular for training deep neural networks, in particular on reinforcement learning tasks, a special form of controller design. Compared to classic problems in continuous direct search, deep…
Many biological processes have been the source of inspiration for heuristic methods that generate high-quality solutions to solve optimization and search problems. This thesis presents an epigenetic technique for Evolutionary Algorithms,…
Ecology and evolution are inseparable. Motivated by some recent experiments, we have developed models of evolutionary ecology from the perspective of dynamic networks. In these models, in addition to the intra-node dynamics, which…
Reductions in natural habitats urge that we better understand species' interconnection and how biological communities respond to environmental changes. However, ecological studies of species' interactions are limited by their geographic and…
Meta-population networks are effective tools for capturing population movement across distinct regions, but the assumption of well-mixed regions fails to capture the reality of population higher-order interactions. As a multidimensional…
The interaction networks of biological systems are known to take on several non-random structural properties, some of which are believed to positively influence system robustness. Researchers are only starting to understand how these…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…
Continuous adaptation allows survival in an ever-changing world. Adjustments in the synaptic coupling strength between neurons are essential for this capability, setting us apart from simpler, hard-wired organisms. How these changes can be…
These notes introduce probabilistic landscape models defined on high-dimensional discrete sequence spaces. The models are motivated primarily by fitness landscapes in evolutionary biology, but links to statistical physics and computer…
The evolution of complex networks is governed by both growing rules and internal properties. Most evolving network models (e.g. preferential attachment) emphasize on the growing strategy, while neglecting the characteristics of individual…
Modeling gene regulatory networks (GRNs) is an important topic in systems biology. Although there has been much work focusing on various specific systems, the generic behavior of GRNs with continuous variables is still elusive. In…
Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
Ecological systems are complex dynamical systems. Modelling efforts on ecosystems' dynamical stability have revealed that population dynamics, being highly nonlinear, can be governed by complex fluctuations. Indeed, experimental and field…
As Evolutionary Dynamics moves from the realm of theory into application, algorithms are needed to move beyond simple models. Yet few such methods exist in the literature. Ecological and physiological factors are known to be central to…
Does an ecological community allow stable coexistence? Identifying the general principles that determine the answer to this question is a central problem of theoretical ecology. Random matrix theory approaches have uncovered the general…
Biological networks of interacting agents exhibit similar topological properties for a wide range of scales, from cellular to ecological levels, suggesting the existence of a common evolutionary origin. A general evolutionary mechanism…