Optics are bidirectional data accessors that capture data transformation patterns such as accessing subfields or iterating over containers. Profunctor optics are a particular choice of representation supporting modularity, meaning that we can construct accessors for complex structures by combining simpler ones. Profunctor optics have previously been studied only in an unenriched and non-mixed setting, in which both directions of access are modelled in the same category. However, functional programming languages are arguably better described by enriched categories; and we have found that some structures in the literature are actually mixed optics, with access directions modelled in different categories. Our work generalizes a classic result by Pastro and Street on Tambara theory and uses it to describe mixed V-enriched profunctor optics and to endow them with V-category structure. We provide some original families of optics and derivations, including an elementary one for traversals. Finally, we discuss a Haskell implementation.
Regulatory networks depict promoting or inhibiting interactions between molecules in a biochemical system. We introduce a category-theoretic formalism for regulatory networks, using signed graphs to model the networks and signed functors to describe occurrences of one network in another, especially occurrences of network motifs. With this foundation, we establish functorial mappings between regulatory networks and other mathematical models in biochemistry. We construct a functor from reaction networks, modeled as Petri nets with signed links, to regulatory networks, enabling us to precisely define when a reaction network could be a physical mechanism underlying a regulatory network. Turning to quantitative models, we associate a regulatory network with a Lotka-Volterra system of differential equations, defining a functor from the category of signed graphs to a category of parameterized dynamical systems. We extend this result from closed to open systems, demonstrating that Lotka-Volterra dynamics respects not only inclusions and collapsings of regulatory networks, but also the process of building up complex regulatory networks by gluing together simpler pieces. Formally, we use the theory of structured cospans to produce a lax double functor from the double category of open signed graphs to that of open parameterized dynamical systems. Throughout the paper, we ground the categorical formalism in examples inspired by systems biology.
Turing machines and spin models share a notion of universality according to which some simulate all others. Is there a theory of universality that captures this notion? We set up a categorical framework for universality which includes as instances universal Turing machines, universal spin models, NP completeness, top of a preorder, denseness of a subset, and more. By identifying necessary conditions for universality, we show that universal spin models cannot be finite. We also characterize when universality can be distinguished from a trivial one and use it to show that universal Turing machines are non-trivial in this sense. Our framework allows not only to compare universalities within each instance, but also instances themselves. We leverage a Fixed Point Theorem inspired by a result of Lawvere to establish that universality and negation give rise to unreachability (such as uncomputability). As such, this work sets the basis for a unified approach to universality and invites the study of further examples within the framework.
In this paper we develop a novel mathematical formalism for the modeling of neural information networks endowed with additional structure in the form of assignments of resources, either computational or metabolic or informational. The starting point for this construction is the notion of summing functors and of Segal's Gamma-spaces in homotopy theory. The main results in this paper include functorial assignments of concurrent/distributed computing architectures and associated binary codes to networks and their subsystems, a categorical form of the Hopfield network dynamics, which recovers the usual Hopfield equations when applied to a suitable category of weighted codes, a functorial assignment to networks of corresponding information structures and information cohomology, and a cohomological version of integrated information.
