Related papers: Foundations of a Compositional Systems Biology

Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…

All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support…

Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…

Examining individual components of cellular systems has been successful in uncovering molecular reactions and interactions. However, the challenge lies in integrating these components into a comprehensive system-scale map. This difficulty…

Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…

Living systems, particularly multicellular systems, often seem hopelessly complex. But recent studies have suggested that beneath this complexity, there may be unifying quantitative principles that we are only now starting to unravel. All…

Computability theory is traditionally conceived as the theoretical basis of informatics. Nevertheless, numerous proposals transcend computability theory, in particular by emphasizing interaction of modules, or components, parts,…

Due to the increased complexity of software development projects more and more systems are described by models. The sheer size makes it impractical to describe these systems by a single model. Instead many models are developed that provide…

The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…

With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…

Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…

Basic problems in complex systems are surveyed in connection with Life. As a key issue for complex systems, complementarity between syntax/rule/parts and semantics/behavior/whole is stressed. To address the issue, a constructive approach…

Many real-world systems can be usefully represented as sets of interacting components. Examples include computational systems, such as query processors and compilers, natural systems, such as cells and ecosystems, and social systems, such…

A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems…

Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…

Compositional understanding is crucial for human intelligence, yet it remains unclear whether contemporary vision models exhibit it. The dominant machine learning paradigm is built on the premise that scaling data and model sizes will…

All biological systems are subject to perturbations: due to thermal fluctuations, external environments, or mutations. Yet, while biological systems are composed of thousands of interacting components, recent high-throughput experiments…

Increasingly sophisticated experiments, coupled with large-scale computational models, have the potential to systematically test biological hypotheses to drive our understanding of multicellular systems. In this short review, we explore key…

Compositionality is a key property for dealing with complexity, which has been studied from many points of view in diverse fields. Particularly, the composition of individual computations (or programs) has been widely studied almost since…

The birth of Foundation Models brought unprecedented results in a wide range of tasks, from language to vision, to robotic control. These models are able to process huge quantities of data, and can extract and develop rich representations,…