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We propose a new framework for the study of continuous time dynamical systems on networks. We view such dynamical systems as collections of interacting control systems. We show that a class of maps between graphs called graph fibrations give rise to maps between dynamical systems on networks. This allows us to produce conjugacy between dynamical systems out of combinatorial data. In particular we show that surjective graph fibrations lead to synchrony subspaces in networks. The injective graph fibrations, on the other hand, give rise to surjective maps from large dynamical systems to smaller ones. One can view these surjections as a kind of fast/slow variable decompositions or as abstractions in the computer science sense of the word.
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Neural Networks (NNs) have been identified as a potentially powerful tool in the study of complex dynamical systems. A good example is the NN differential equation (DE) solver, which provides closed form, differentiable, functional approximations for the evolution of a wide variety of dynamical systems. A major disadvantage of such NN solvers can be the amount of computational resources needed to achieve accuracy comparable to existing numerical solvers. We present new strategies for existing dynamical system NN DE solvers, making efficient use of the textit{learnt} information, to speed up their training process, while still pursuing a completely unsupervised approach. We establish a fundamental connection between NN theory and dynamical systems theory via Koopman Operator Theory (KOT), by showing that the usual training processes for Neural Nets are fertile ground for identifying multiple Koopman operators of interest. We end by illuminating certain applications that KOT might have for NNs in general.
In the study of reaction networks and the polynomial dynamical systems that they generate, special classes of networks with important properties have been identified. These include reversible, weakly reversible}, and, more recently, endotactic networks. While some inclusions between these network types are clear, such as the fact that all reversible networks are weakly reversible, other relationships are more complicated. Adding to this complexity is the possibility that inclusions be at the level of the dynamical systems generated by the networks rather than at the level of the networks themselves. We completely characterize the inclusions between reversible, weakly reversible, endotactic, and strongly endotactic network, as well as other less well studied network types. In particular, we show that every strongly endotactic network in two dimensions can be generated by an extremally weakly reversible network. We also introduce a new class of source-only networks, which is a computationally convenient property for networks to have, and show how this class relates to the above mentioned network types.
The topological analysis of biological networks has been a prolific topic in network science during the last decade. A persistent problem with this approach is the inherent uncertainty and noisy nature of the data. One of the cases in which this situation is more marked is that of transcriptional regulatory networks (TRNs) in bacteria. The datasets are incomplete because regulatory pathways associated to a relevant fraction of bacterial genes remain unknown. Furthermore, direction, strengths and signs of the links are sometimes unknown or simply overlooked. Finally, the experimental approaches to infer the regulations are highly heterogeneous, in a way that induces the appearance of systematic experimental-topological correlations. And yet, the quality of the available data increases constantly. In this work we capitalize on these advances to point out the influence of data (in)completeness and quality on some classical results on topological analysis of TRNs, specially regarding modularity at different levels. In doing so, we identify the most relevant factors affecting the validity of previous findings, highlighting important caveats to future prokaryotic TRNs topological analysis.
Motivated by the dynamical uniform boundedness conjecture of Morton and Silverman, specifically in the case of quadratic polynomials, we give a formal construction of a certain class of dynamical analogues of classical modular curves. The preperiodic points for a quadratic polynomial map may be endowed with the structure of a directed graph satisfying certain strict conditions; we call such a graph admissible. Given an admissible graph $G$, we construct a curve $X_1(G)$ whose points parametrize quadratic polynomial maps -- which, up to equivalence, form a one-parameter family -- together with a collection of marked preperiodic points that form a graph isomorphic to $G$. Building on work of Bousch and Morton, we show that these curves are irreducible in characteristic zero, and we give an application of irreducibility in the setting of number fields. We end with a discussion of the Galois theory associated to the preperiodic points of quadratic polynomials, including a certain Galois representation that arises naturally in this setting.
In cellular reprogramming, almost all epigenetic memories of differentiated cells are erased by the overexpression of few genes, regaining pluripotency, potentiality for differentiation. Considering the interplay between oscillatory gene expression and slower epigenetic modifications, such reprogramming is perceived as an unintuitive, global attraction to the unstable manifold of a saddle, which represents pluripotency. The universality of this scheme is confirmed by the repressilator model, and by gene regulatory networks randomly generated and those extracted from embryonic stem cells.
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