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The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…

In complex systems, groups of interacting objects may form prevalent and persistent spatiotemporal patterns, which we refer to as motifs. These motifs can exhibit features that reveal how individual objects interact with one another.…

Given the large size and complexity of most biochemical regulation and signaling networks, there is a non-trivial relationship between the micro-level logic of component interactions and the observed macro-dynamics. Here we address this…

The abundance of data affords researchers to pursue more powerful computational tools to learn the dynamics of complex system, such as neural networks, engineered systems and social networks. Traditional machine learning approaches capture…

Indirect reciprocity is a foundational mechanism of human cooperation. Existing models of indirect reciprocity fail to robustly support social cooperation: image scoring models fail to provide robust incentives, while social standing models…

Recent progress in diverse intelligence has shown simple learning capacities below the organism level - single cells and even molecular networks. However, there are still many knowledge gaps around learning capacity above the organism…

We address the problem of retrieving relevant experiments given a query experiment, motivated by the public databases of datasets in molecular biology and other experimental sciences, and the need of scientists to relate to earlier work on…

Complex networks are an important paradigm of modern complex systems sciences which allows quantitatively assessing the structural properties of systems composed of different interacting entities. During the last years, intensive efforts…

Networked systems are systems of interconnected components, in which the dynamics of each component are influenced by the behavior of neighboring components. Examples of networked systems include biological networks, critical…

Biomolecular feedback systems are now a central application area of interest within control theory. While classical control techniques provide invaluable insight into the function and design of both natural and synthetic biomolecular…

Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and…

The interplay between causal mechanisms and emerging collective behaviors is a central aspect of understanding, controlling, and predicting complex networked systems. In our work, we investigate the relationship between higher-order…

Sequential activation of neurons is a common feature of network activity during a variety of behaviors, including working memory and decision making. Previous network models for sequences and memory emphasized specialized architectures in…

Imitation is an important learning heuristic in animal and human societies. Previous explorations report that the fate of individuals with cooperative strategies is sensitive to the protocol of imitation, leading to a conundrum about how…

Recent advances in human mobility research have revealed consistent pairwise characteristics in movement behavior, yet existing mobility models often overlook the spatial and topological structure of mobility networks. By analyzing millions…

Behavioral changes in animals and humans, as a consequence of an error or a verbal instruction, can be extremely rapid. Improvement in behavioral performances are usually associated in machine learning and reinforcement learning to synaptic…

A hallmark of living systems is the ability to employ a common set of versatile building blocks that can self-organize into a multitude of different structures, in a way that can be controlled with minimal cost. This capability can only be…

Models of the dynamics of cellular interaction networks have become increasingly larger in recent years. Formal verification based on model checking provides a powerful technology to keep up with this increase in scale and complexity. The…

The study of interacting dynamical systems continues to attract research interest in various fields of science and engineering. In a collection of interacting particles, the interaction network contains information about how various…

Representing social systems as networks, starting from the interactions between individuals, sheds light on the mechanisms governing their dynamics. However, networks encode only pairwise interactions, while most social interactions occur…