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Most classification methods are based on the assumption that data conforms to a stationary distribution. The machine learning domain currently suffers from a lack of classification techniques that are able to detect the occurrence of a…
A model of the urban agglomeration and segregation is formulated, in which two types of agents move around on the square-lattice aligned cells. The model is shown to exhibit, when the density of agents are varied as the control parameter,…
When it is polarised, a cell develops an asymmetric distribution of specific molecular markers, cytoskeleton and cell membrane shape. Polarisation can occur spontaneously or be triggered by external signals, like gradients of signalling…
In an increasingly interconnected world, a key scientific challenge is to examine mechanisms that lead to the widespread propagation of contagions, such as misinformation and pathogens, and identify risk factors that can trigger large-scale…
Many real networks can be understood as two complementary networks with two kind of nodes. This is the case of metabolic networks where the first network has chemical compounds as nodes and the second one has nodes as reactions. The second…
Many real-world complex systems rely on cluster synchronization to function properly. A cluster of nodes exhibits synchronous behavior while others behave erratically. Predicting the emergence of these clusters and understanding the…
This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…
Distillation is the task of replacing a complicated machine learning model with a simpler model that approximates the original [BCNM06,HVD15]. Despite many practical applications, basic questions about the extent to which models can be…
We propose a statistical model of a large random network with high connectivity in order to describe the behavior of {\it E.\,coli} cells after exposure to acute stress. The building blocks of this network are feedback cycles typical of the…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
Diffusion is a fundamental phenomenon that occurs ubiquitously in nature and remains the subject of continuous research interest. Understanding diffusion is a key to understanding leaving systems. In this Chapter, I discuss diffusion of…
We study the emergence of cell differentiation under the assumption of the existence of a given number of tradeoffs between genes encoding different functions. In the model the viability of colonies is determined by the capability of their…
All life, including cells and artificial protocells, must integrate diverse molecules into a single unit in order to reproduce. Despite expected pressure to evolve a simple system with the fastest replication speed, the mechanism by which…
We study the dynamics of phase synchronization in growing populations of discrete phase oscillatory systems when the division process is coupled to the distribution of oscillator phases. Using mean field theory, linear stability analysis,…
Presented with sensory challenges, living cells employ extensive noisy, fluctuating signalling and communication among themselves to compute a physiologically proper response which often results in symmetry breaking. We propose, based on…
It has been hypothesized that some form of "modular" structure in artificial neural networks should be useful for learning, compositionality, and generalization. However, defining and quantifying modularity remains an open problem. We cast…
Complex network dynamics have been analyzed with models of systems of coupled switches or systems of coupled oscillators. However, many complex systems are composed of components with diverse dynamics whose interactions drive the system's…
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…
We study synchronization of two cardiomyocytes mediated by elastic interactions through the substrate. Modeling each cell as an oscillating force dipole governed by a Rayleigh-type equation, we derive an effective mechanical coupling from…
Relationship between agents can be conveniently represented by graphs. When these relationships have different modalities, they are better modelled by multilayer graphs where each layer is associated with one modality. Such graphs arise…