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The ambitious and ultimate research purpose in Systems Biology is the understanding and modelling of the cell's system. Although a vast number of models have been developed in order to extract biological knowledge from complex systems…
Community assembly is studied using individual-based multispecies models. The models have stochastic population dynamics with mutation, migration, and extinction of species. Mutants appear as a result of mutation of the resident species,…
By default neural networks are not robust to changes in data distribution. This has been demonstrated with simple image corruptions, such as blurring or adding noise, degrading image classification performance. Many methods have been…
From a mathematical point of view self-organization can be described as patterns to which certain dynamical systems modeling social dynamics tend spontaneously to be attracted. In this paper we explore situations beyond self-organization,…
Which factors govern the evolution of mutation rates and emergence of species? Here, we address this question using a first principles model of life where population dynamics of asexual organisms is coupled to molecular properties and…
Robustness, the ability of a system to maintain performance under significant and unanticipated environmental changes, is a critical property for robotic systems. While biological systems naturally exhibit robustness, there is no…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…
The persistence of life requires populations to adapt at a rate commensurate with the dynamics of their environment. Successful populations that inhabit highly variable environments have evolved mechanisms to increase the likelihood of…
In biology, the evolution of increasingly cooperative groups has shaped the history of life. Genes collaborate in the control of cells; cells efficiently divide tasks to produce cohesive multicellular individuals; individual members of…
Transfer learning has recently become the dominant paradigm of machine learning. Pre-trained models fine-tuned for downstream tasks achieve better performance with fewer labelled examples. Nonetheless, it remains unclear how to develop…
Background. Organisms use a variety of mechanisms to protect themselves against perturbations. For example, repair mechanisms fix damage, feedback loops keep homeostatic systems at their setpoints, and biochemical filters distinguish signal…
Unambiguous identification of the rewards driving behaviours of entities operating in complex open-ended real-world environments is difficult, partly because goals and associated behaviours emerge endogenously and are dynamically updated as…
This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…
The characterization of plasticity, robustness, and evolvability, an important issue in biology, is studied in terms of phenotypic fluctuations. By numerically evolving gene regulatory networks, the proportionality between the phenotypic…
Many current robot designs prioritize efficiency and one-size-fits-all solutions, oftentimes overlooking personalization, adaptability, and sustainability. To explore alternatives, we conducted two co-design workshops with 23 participants,…
Popular hypotheses about the origins of collective adaptation are related to two basic behaviours: protection from predators and a combined search for food resources. Among the anti-predator explanations, the predator confusion hypothesis…
The structure and degree of order in soft matter and other materials is intimately connected to the nature of the interactions between the particles. One important research goal is to find suitable control mechanisms, to enhance or suppress…
Purpose and meaning are necessary concepts for understanding mind and culture, but appear to be absent from the physical world and are not part of the explanatory framework of the natural sciences. Understanding how meaning (in the broad…
Cooperation is a persistent behavioral pattern of entities pooling and sharing resources. Its ubiquity in nature poses a conundrum. Whenever two entities cooperate, one must willingly relinquish something of value to the other. Why is this…
Developing reliable mechanisms for continuous local learning is a central challenge faced by biological and artificial systems. Yet, how the environmental factors and structural constraints on the learning network influence the optimal…