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We propose a theoretical model for species that is focused on intrinsic organization and processes. Specifically, we regard species to be networks of organisms integrated by reproductive mechanisms (e.g., conjugation, meiosis, syngamy)…
Context. Generative models open up the possibility to interrogate scientific data in a more data-driven way. Aims: We propose a method that uses generative models to explore hypotheses in astrophysics and other areas. We use a neural…
The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are…
In this work, we introduce a spatial branching process to model the growth of the mycelial network of a filamentous fungus. In this model, each filament is described by the position of its tip, the trajectory of which is solution to a…
Patterns often appear in a variety of large, real-world networks, and interesting physical phenomena are often explained by network topology as in the case of the bow-tie structure of the World Wide Web, or the small world phenomenon in…
One explanation for the impressive recent boom in network theory might be that it provides a promising tool for an understanding of complex systems. Network theory is mainly focusing on discrete large-scale topological structures rather…
We introduce a framework to intertwine dynamical processes of different nature, each with its own distinct network topology, using a multilayer network approach. As an example of collective phenomena emerging from the interactions of…
The propagations of diseases, behaviors and information in real systems are rarely independent of each other, but they are coevolving with strong interactions. To uncover the dynamical mechanisms, the evolving spatiotemporal patterns and…
Modularity structures are common in various social and biological networks. However, its dynamical origin remains an open question. In this work, we set up a dynamical model describing the evolution of a social network. Based on the…
Although networks provide a powerful approach to study a large variety of ecological systems, their formulation does not typically account for multiple interaction types, interactions that vary in space and time, and interconnected systems…
The world of network science is fascinating and filled with complex phenomena that we aspire to understand. One of them is the dynamics of spreading processes over complex networked structures. Building the knowledge-base in the field where…
To comprehend the multipartite organization of large-scale biological and social systems, we introduce a new information theoretic approach that reveals community structure in weighted and directed networks. The method decomposes a network…
Recently, evolving networks are becoming a suitable form to model many real-world complex systems, due to their peculiarities to represent the systems and their constituting entities, the interactions between the entities and the…
To understand the structure of a large-scale biological, social, or technological network, it can be helpful to decompose the network into smaller subunits or modules. In this article, we develop an information-theoretic foundation for the…
As one of the main subjects of investigation in data science, network science has been demonstrated a wide range of applications to real-world networks analysis and modeling. For example, the pervasive presence of structural or topological…
Methods that generate networks sharing a given degree distribution and global clustering can induce changes in structural properties other than that controlled for. Diversity in structural properties, in turn, can affect the outcomes of…
Self-organization, the ability of a system of microscopically interacting entities to shape macroscopically ordered structures, is ubiquitous in Nature. Spatio-temporal patterns are abundantly observed in a large plethora of applications,…
Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…
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…
Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and…