相关论文: Abstract relational structures in models of biolog…
As data structures and mathematical objects used for complex systems modeling, hypergraphs sit nicely poised between on the one hand the world of network models, and on the other that of higher-order mathematical abstractions from algebra,…
Many real-world phenomena are naturally modeled by graphs and networks. However, classical graph models are often limited to pairwise interactions and may not adequately capture the richer structures that arise in practice. Higher-order…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
The representation of complex systems as networks is inappropriate for the study of certain problems. We show several examples of social, biological, ecological and technological systems where the use of complex networks gives very limited…
Providing an abstract representation of natural and human complex structures is a challenging problem. Accounting for the system heterogenous components while allowing for analytical tractability is a difficult balance. Here I introduce…
To make progress in science, we often build abstract representations of physical systems that meaningfully encode information about the systems. The representations learnt by most current machine learning techniques reflect statistical…
We demonstrate that graph-based models are fully capable of representing higher-order interactions, and have a long history of being used for precisely this purpose. This stands in contrast to a common claim in the recent literature on…
The complexity of many biological, social and technological systems stems from the richness of the interactions among their units. Over the past decades, a great variety of complex systems has been successfully described as networks whose…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a…
Abstract separation systems provide a simple general framework in which both tree-shape and high cohesion of many combinatorial structures can be expressed, and their duality proved. Applications range from tangle-type duality and tree…
Abstraction is a powerful idea widely used in science, to model, reason and explain the behavior of systems in a more tractable search space, by omitting irrelevant details. While notions of abstraction have matured for deterministic…
Complex systems are often driven by higher-order interactions among multiple units, naturally represented as hypergraphs. Understanding dependency structures within these hypergraphs is crucial for understanding and predicting the behavior…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
The behavior of complex systems is determined not only by the topological organization of their interconnections but also by the dynamical processes taking place among their constituents. A faithful modeling of the dynamics is essential…
Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence,…
Complex networks are universal, arising in fields as disparate as sociology, physics, and biology. In the past decade, extensive research into the properties and behaviors of complex systems has uncovered surprising commonalities among the…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
This article presents formalistic tool for description of structural and biochemical relations between cells in the course of development of the body of plants. This is flexible formalistic space, based on the Category theory and the Petri…
This thesis (defended 10/07/2019) develops a theory of networks of hybrid open systems and morphisms. It builds upon a framework of networks of continuous-time open systems as product and interconnection. We work out categorical notions for…