Leo Lobski

We develop layered monoidal theories – a generalisation of monoidal theories combining formal descriptions of a system at different levels of abstraction. Via their representation as string diagrams , monoidal theories provide a graphical formalism to reason algebraically about information flow in models across different fields of science. Layered monoidal theories allow mixing several monoidal theories (together with translations between them) within the same string diagram, while retaining mathematical precision and semantic interpretability. We develop the mathematical foundations of layered monoidal theories, as well as providing several instances of our approach, including digital and electrical circuits, quantum processes, chemical reactions, concurrent processes, and probability theory.

We provide a category theoretical framework capturing two approaches to graph-based models of chemistry: formal reactions and disconnection rules. We model a translation from the latter to the former as a functor, which is faithful, and full up to isomorphism. This allows us to state, as our main result, that the disconnection rules are sound, complete and universal with respect to the reactions. Concretely, this means that every reaction can be decomposed into a sequence of disconnection rules in an essentially unique way. This provides a uniform way to store reaction data, and gives an algorithmic interface between (forward) reaction prediction and (backward) reaction search or retrosynthesis.

We introduce a mathematical framework for retrosynthetic analysis, an important research method in synthetic chemistry. Our approach represents molecules and their interaction using string diagrams in layered props - a recently introduced categorical model for partial explanations in scientific reasoning. Such principled approach allows one to model features currently not available in automated retrosynthesis tools, such as chirality, reaction environment and protection-deprotection steps.