Volume 6 (2024)

1. Profunctor Optics, a Categorical Update

Bryce Clarke ; Derek Elkins ; Jeremy Gibbons ; Fosco Loregian ; Bartosz Milewski ; Emily Pillmore ; Mario Rom├ín.
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.

2. A compositional account of motifs, mechanisms, and dynamics in biochemical regulatory networks

Rebekah Aduddell ; James Fairbanks ; Amit Kumar ; Pablo S. Ocal ; Evan Patterson ; Brandon T. Shapiro.
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.