Related papers: Systematizing Cellular Complexity: A Hilbertian Ap…
The knowledge of cell molecular mechanisms implicated in human diseases is expanding and should be converted into guidelines for deciphering pathological cell signaling and suggesting appropriate treatment. The basic assumption is that…
Biological systems are often modeled as a system of ordinary differential equations (ODEs) with time-invariant parameters. However, cell signaling events or pharmacological interventions may alter the cellular state and induce multi-mode…
We discuss the relevance of studying ecology within the framework of Complexity Science from a statistical mechanics approach. Ecology is concerned with understanding how systems level properties emerge out of the multitude of interactions…
Biological phenomena differ significantly from physical phenomena. At the heart of this distinction is the fact that biological entities have computational abilities and thus they are inherently difficult to predict. This is the reason why…
The word "complexity" is most often used as a meta--linguistic expression referring to certain intuitive characteristics of a natural system and/or its scientific description. These characteristics may include: sheer amount of data that…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…
This paper argues that explainability is only one facet of a broader ideal that shapes our expectations towards artificial intelligence (AI). Fundamentally, the issue is to what extent AI exhibits systematicity--not merely in being…
Many fields, such as neuroscience, are experiencing the vast proliferation of cellular data, underscoring the need for organizing and interpreting large datasets. A popular approach partitions data into manageable subsets via hierarchical…
High-throughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major…
The quest for a scientific description of consciousness has given rise to new theoretical and empirical paradigms for the investigation of phenomenological contents as well as clinical disorders of consciousness. An outstanding challenge in…
In this paper, we determine the complexity of the satisfiability problem for various logics obtained by adding numerical quantifiers, and other constructions, to the traditional syllogistic. In addition, we demonstrate the incompleteness of…
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…
We define a notion of complexity, which quantifies the nonlinearity of the computation of a neural network, as well as a complementary measure of the effective dimension of feature representations. We investigate these observables both for…
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…
This paper will introduce a theory of emergent animal social complexity using various results from computational models and empirical results. These results will be organized into a vertical model of social complexity. This will support the…
The ability of a cell to communicate with its environment is essential for key cellular functions like replication, metabolism, or cell fate decisions. The involved molecular mechanisms are highly dynamic and difficult to capture…
What makes living systems flexible so that they can react quickly and adapt easily to changing environments? This question has not only engaged biologists for decades but is also of great interest to computer scientists and engineers who…
The determination of environmentally- and economically-optimal energy system designs and operations is complex. In particular, the integration of weather-dependent renewable energy technologies into energy system optimization models…