Layered Monoidal Theories

TL;DR

This paper introduces layered monoidal theories for combining multiple levels of system descriptions with graphical string diagrams, and applies this framework to formalize retrosynthesis in synthetic chemistry, linking reaction levels and rules.

Contribution

It develops a novel layered monoidal theory framework and formalizes retrosynthesis using this approach, connecting chemical reaction levels and disconnection rules.

Findings

Layered monoidal theories enable combining multiple system descriptions visually.

The formalization of retrosynthesis links reaction schemes, disconnection rules, and reactions.

Disconnection rules are shown to be sound, complete, and universal within the framework.

Abstract

In the first part, we develop layered monoidal theories - a generalisation of monoidal theories combining descriptions of a system at several levels. Via their representation as string diagrams, monoidal theories provide a graphical syntax with a visually intuitive notions of information flow and composition. 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 define three flavours of layered monoidal theories, provide a recursively generated syntax for each, and construct a free-forgetful adjunction with respect to three closely related semantics: opfibrations, fibrations and deflations. We motivate the general theory by providing several examples from existing literature. In the second part, we develop a formal approach to retrosynthesis - the process of backwards reaction search in synthetic chemistry. Chemical processes are treated at three levels of abstraction: (1) (formal) reactions encode all chemically feasible combinatorial rearrangements of molecules, (2) reaction schemes encode transformations applicable to 'patches' of molecules (including the functional groups), and (3) disconnection rules encode local chemical rewrite rules applicable to a single bond or atom at a time. We show that the three levels are tightly linked: the reactions are generated by the reaction schemes, while there is a functorial translation from the disconnection rules to the reactions. Moreover, the translation from the disconnection rules to the reactions is shown to be sound, complete and universal - allowing one to treat the disconnection rules as a formal syntax with the semantics provided by the reactions. We tie together the two parts by providing a formalisation of retrosynthesis within a certain layered monoidal theory.