Brendan Fong finished his thesis a while ago, and here it is!

• Brendan Fong, *The Algebra of Open and Interconnected Systems*, Ph.D. thesis, Department of Computer Science, University of Oxford, 2016.

This material is close to my heart, since I’ve informally served as Brendan’s advisor since 2011, when he came to Singapore to work with me on chemical reaction networks. We’ve been collaborating intensely ever since. I just looked at our correspondence, and I see it consists of 880 emails!

At some point I gave him a project: *describe the category whose morphisms are electrical circuits*. He took up the challenge much more ambitiously than I’d ever expected, developing powerful general frameworks to solve not only this problem but also many others. He did this in a number of papers, most of which I’ve already discussed:

• Brendan Fong, Decorated cospans, *Th. Appl. Cat.* **30** (2015), 1096–1120. (Blog article here.)

• Brendan Fong and John Baez, A compositional framework for passive linear circuits. (Blog article here.)

• Brendan Fong, John Baez and Blake Pollard, A compositional framework for Markov processes. (Blog article here.)

• Brendan Fong and Brandon Coya, Corelations are the prop for extraspecial commutative Frobenius monoids. (Blog article here.)

• Brendan Fong, Paolo Rapisarda and Paweł Sobociński,

A categorical approach to open and interconnected dynamical systems.

But Brendan’s thesis is the best place to see a lot of this material in one place, integrated and clearly explained.

I wanted to write a summary of his thesis. But since he did that himself very nicely in the preface, I’m going to be lazy and just quote that! (I’ll leave out the references, which are crucial in scholarly prose but a bit off-putting in a blog.)

### Preface

This is a thesis in the mathematical sciences, with emphasis on the mathematics. But before we get to the category theory, I want to say a few words about the scientific tradition in which this thesis is situated.

Mathematics is the language of science. Twinned so intimately with physics, over the past centuries mathematics has become a superb—indeed, unreasonably effective—language for understanding planets moving in space, particles in a vacuum, the structure of spacetime, and so on. Yet, while Wigner speaks of the unreasonable effectiveness of mathematics in the natural sciences, equally eminent mathematicians, not least Gelfand, speak of the unreasonable *ineffectiveness* of mathematics in biology and related fields. Why such a difference?

A contrast between physics and biology is that while physical systems can often be studied in isolation—the proverbial particle in a vacuum—biological systems are necessarily situated in their environment. A heart belongs in a body, an ant in a colony. One of the first to draw attention to this contrast was Ludwig von Bertalanffy, biologist and founder of general systems theory, who articulated the difference as one between closed and open systems:

Conventional physics deals only with closed systems, i.e. systems which are considered to be isolated from their environment. […] However, we find systems which by their very nature and definition are not closed systems. Every living organism is essentially an open system. It maintains itself in a continuous inflow and outflow, a building up and breaking down of components, never being, so long as it is alive, in a state of chemical and thermodynamic equilibrium but maintained in a so-called ‘steady state’ which is distinct from the latter.

While the ambitious generality of general systems theory has proved difficult, von Bertalanffy’s philosophy has had great impact in his home field of biology, leading to the modern field of systems biology. Half a century later, Dennis Noble, another great pioneer of systems biology and the originator of the first mathematical model of a working heart, describes the shift as one from reduction to integration.

Systems biology […] is about putting together rather than taking apart, integration rather than reduction. It requires that we develop ways of thinking about integration that are as rigorous as our reductionist programmes, but different. It means changing our philosophy, in the full sense of the term.

In this thesis we develop rigorous ways of thinking about integration or, as we refer to it, interconnection.

Interconnection and openness are tightly related. Indeed, openness implies that a system may be interconnected with its environment. But what is an environment but comprised of other systems? Thus the study of open systems becomes the study of how a system changes under interconnection with other systems.

To model this, we must begin by creating language to describe theinterconnection of systems. While reductionism hopes that phenomena can be explained by reducing them to “elementary units investigable independently of each other” (in the words of von Bertalanffy), this philosophy of integration introduces as an additional and equal priority the investigation of the way these units are interconnected. As such, this thesis is predicated on the hope that the meaning of an expression in our new language is determined by the meanings of its constituent expressions together with the syntactic rules combining them. This is known as the principle of compositionality.

Also commonly known as Frege’s principle, the principle of compositionality both dates back to Ancient Greek and Vedic philosophy, and is still the subject of active research today. More recently, through the work of Montague in natural language semantics and Strachey and Scott in programming language semantics, the principle of compositionality has found formal expression as the dictum that the interpretation of a language should be given by a homomorphism from an algebra of syntactic representations to an algebra of semantic objects. We too shall follow this route.

The question then arises: what do we mean by algebra? This mathematical question leads us back to our scientific objectives: what do we mean by system? Here we must narrow, or at least define, our scope. We give some examples. The investigations of this thesis began with electrical circuits and their diagrams, and we will devote significant time to exploring their compositional formulation. We discussed biological systems above, and our notion of system

includes these, modelled say in the form of chemical reaction networks or Markov processes, or the compartmental models of epidemiology, population biology, and ecology. From computer science, we consider Petri nets, automata, logic circuits, and the like. More abstractly, our notion of system encompasses matrices and systems of differential equations.

Drawing together these notions of system are well-developed diagrammatic representations based on network diagrams— that is, topological graphs. We call these network-style diagrammatic languages. In abstract, by ‘system’ we shall simply mean that which can be represented by a box with a collection of terminals, perhaps of different types, through which it interfaces with the surroundings. Concretely, one might envision a circuit diagram with terminals, such as

or

The algebraic structure of interconnection is then simply the structure that results from the ability to connect terminals of one system with terminals of another. This graphical approach motivates our language of interconnection: indeed, these diagrams will be the expressions of our language.

We claim that the existence of a network-style diagrammatic language to represent a system implies that interconnection is inherently important in understanding the system. Yet, while each of these example notions of system are well-studied in and of themselves, their compositional, or algebraic, structure has received scant attention. In this thesis, we study an algebraic structure called a ‘hypergraph category’, and argue that this is the relevant algebraic structure for modelling interconnection of open systems.

Given these pre-existing diagrammatic formalisms and our visual intuition, constructing algebras of syntactic representations is thus rather straightforward. The semantics and their algebraic structure are more subtle.

In some sense our semantics is already given to us too: in studying these systems as closed systems, scientists have already formalised the meaning of these diagrams. But we have shifted from a closed perspective to an open one, and we need our semantics to also account for points of interconnection.

Taking inspiration from Willems’ behavioural approach and Deutsch’s constructor theory, in this thesis I advocate the following position. First, at each terminal of an open system we may make measurements appropriate to the type of terminal. Given a collection of terminals, the **universum** is then the set of all possible measurement outcomes. Each open system has a collection of terminals, and hence a universum. The semantics of an open system is the subset of measurement outcomes on the terminals that are permitted by the system. This is known as the **behaviour** of the system.

For example, consider a resistor of resistance This has two terminals—the two ends of the resistor—and at each terminal, we may measure the potential and the current. Thus the universum of this system is the set where the summands represent respectively the potentials and currents at each of the two terminals. The resistor is governed by Kirchhoff’s current law, or conservation of charge,

and Ohm’s law. Conservation of charge states that the current flowing into one terminal must equal the current flowing out of the other terminal, while Ohm’s law states that this current will be proportional to the potential difference, with constant of proportionality Thus the behaviour of the resistor is the set

Note that in this perspective a law such as Ohm’s law is a mechanism for partitioning *behaviours* into possible and impossible behaviours.

Interconnection of terminals then asserts the identification of the variables at the identified terminals. Fixing some notion of open system and subsequently an algebra of syntactic representations for these systems, our approach, based on the principle of compositionality, requires this to define an algebra of semantic objects and a homomorphism from syntax to semantics. The first part of this thesis develops the mathematical tools necessary to pursue this vision for modelling open systems and their interconnection.

The next goal is to demonstrate the efficacy of this philosophy in applications. At core, this work is done in the faith that the right language allows deeper insight into the underlying structure. Indeed, after setting up such a language for open systems there are many questions to be asked: Can we find a sound and complete logic for determining when two syntactic expressions have the same semantics? Suppose we have systems that have some property, for example controllability. In what ways can we interconnect controllable systems so that the combined system is also controllable? Can we compute the semantics of a large system quicker by computing the semantics of subsystems and then composing them? If I want a given system to achieve a specified trajectory, can we interconnect another system to make it do so? How do two different notions of system, such as circuit diagrams and signal flow graphs, relate to each other? Can we find homomorphisms between their syntactic and semantic algebras? In the second part of this thesis we explore some applications in depth, providing answers to questions of the above sort.

### Outline of the thesis

The thesis is divided into two parts. Part I, comprising

Chapters 1 to 4, focuses on mathematical foundations. In it we develop the theory of hypergraph categories and a powerful tool for constructing and manipulating them: decorated corelations. Part II, comprising Chapters 5 to 7, then discusses applications of this theory to examples of open systems.

The central refrain of this thesis is that the syntax and semantics of network-style diagrammatic languages can be modelled by hypergraph categories. These are introduced in Chapter 1. **Hypergraph categories** are symmetric monoidal categories in which every object is equipped with the structure of a special commutative Frobenius monoid in a way compatible with the monoidal product. As we will rely heavily on properties of monoidal categories, their functors, and their graphical calculus, we begin with a whirlwind review of these ideas. We then provide a definition of hypergraph categories and their functors, a strictification theorem, and an important example: the category of cospans in a category with finite colimits.

A **cospan** is a pair of morphisms

with a common codomain. In Chapter 2 we introduce the idea of a ‘decorated cospan’, which equips the apex with extra structure. Our motivating example is cospans of finite sets decorated by graphs, as in this picture:

Here graphs are a proxy for expressions in a network-style diagrammatic language. To give a bit more formal detail, let be a category with finite colimits, writing its as coproduct as and let be a braided monoidal category. Decorated cospans provide a method of producing a hypergraph category from a lax braided monoidal functor

The objects of these categories are simply the objects of while the morphisms are pairs comprising a cospan in together with an element in —the so-called **decoration**. We will also describe how to construct hypergraph functors between decorated cospan categories. In particular, this provides a useful tool for constructing a hypergraph category that captures the syntax of a network-style diagrammatic language.

Having developed a method to construct a category where the morphisms are expressions in a diagrammatic language, we turn our attention to categories of semantics. This leads us to the notion of a corelation, to which we devote Chapter 3. Given a factorisation system on a category we define a **corelation** to be a cospan such that the copairing of the two maps, a map is a morphism in Factorising maps using the factorisation system leads to a notion of equivalence on cospans, and this helps us describe when two diagrams are equivalent. Like cospans, corelations form hypergraph categories.

In Chapter 4 we decorate corelations. Like decorated cospans,

decorated corelations are corelations together with some additional structure on the apex. We again use a lax braided monoidal functor to specify the sorts of extra structure allowed. Moreover, decorated corelations too form the morphisms of a hypergraph category. The culmination of our theoretical work is to show that every hypergraph category and every hypergraph functor can be constructe using decorated corelations. This implies that we can use decorated corelations to construct a semantic hypergraph category for any network-style diagrammatic language, as well as a hypergraph functor from its syntactic category that interprets each diagram. We also discuss how the intuitions behind decorated corelations guide construction of these categories and functors.

Having developed these theoretical tools, in the second part we turn to demonstrating that they have useful applications. Chapter 5 uses corelations to formalise signal flow diagrams representing linear time-invariant discrete dynamical systems as morphisms in a category. Our main result gives an intuitive sound and fully complete equational theory for reasoning about these linear time-invariant systems. Using this framework, we derive a novel structural characterisation of controllability, and consequently provide a methodology for analysing controllability of networked and interconnected systems.

Chapter 6 studies passive linear networks. Passive linear

networks are used in a wide variety of engineering applications, but the best studied are electrical circuits made of resistors, inductors and capacitors. The goal is to construct what we call the ‘black box functor’, a hypergraph functor from a category of open circuit diagrams to a category of behaviours of circuits. We construct the former as a decorated cospan category, with each morphism a cospan of finite sets decorated by a circuit diagram on the apex. In this category, composition describes the process of attaching the outputs of one circuit to the inputs of another. The behaviour of a circuit is the relation it imposes between currents and potentials at their terminals. The space of these currents and potentials naturally has the structure of a symplectic vector space, and the relation imposed by a circuit is a Lagrangian linear relation. Thus, the black box functor goes from our category of circuits to the category of symplectic vector spaces and Lagrangian linear relations. Decorated corelations provide a critical tool for constructing these hypergraph categories and the black box functor.

Finally, in Chapter 7 we mention two further research directions. The first is the idea of a ‘bound colimit’, which aims to describe why epi-mono factorisation systems are useful for constructing corelation categories of semantics for open systems. The second research direction pertains to applications of the black box functor for passive linear networks, discussing the work of Jekel on the inverse problem for electric circuits and the work of Baez, Fong, and Pollard on open Markov processes.

That presupposes that it is always possible to have available and/or to find means to build corresponding interfaces.

Yes, by definition: no interfaces = closed system.

“Interface” here is meant rather broadly. For example water in a cup sitting on a table is an open system. Water can evaporate and leave the cup, it exchanges heat with the table and the rest of the room and so on.

Closed system means the system has no interfaces but if you have a system with interfaces (i.e. its “open”) than this doesn’t imply that the interfaces of the given environment match.

I’m not familiar with a definition of open systems that cares about the existence of unused potential interfaces. A thermodynamic system of a gas in a closed room is not considered open if it has a hatch which

couldopen, but is currently jammed shut. Then the system is just closed, end of story.If it is in fact impossible to find means to interface the system with its environment, then the system is just closed. It could be turned into an open system later when the means are developed, but that’s then considered a different system.

As I also tried to explain below, I would prefer to say the system is closed with respect to its environment.

Maybe a better way to think of open systems is not in terms of interfaces but in terms of dynamics. The dynamics of a (continuous time) closed system depends only on its state. The dynamics of a (continuous time) open system depends on its state and the state of something else, which we may call the environment.

Imagine you have e.g. an animal in a closed space ship in outer space which lives by utilizing radiation of a specific wavelength. (Laika didnt survive on radiation but this is a different subject). If this wavelength is not existing in that outer space (i.e. the environment of the closed system space ship) than the survival of that animal

doesn’t dependon having an open window which would let (only) this radiation into the spaceship, it would still rot away as if the space ship would be closed.I think I now see what you concern is.

Being mathematician I think of closed systems as a special class of open systems: closed systems are those where the influence of the “environment” is zero. There is a precise way to say that in terms of surjective submersions. I am not sure if you’d like to see that.

I don’t know who came up with this definition but I think it is misleading. And other mathematicians would eventually come up with a different definition.

First a system usually also has an influence on the respective environment.

Moreover as I tried to point out above it is rather that a system is closed

with respect toan environment, than just closed “as a system”. Everbody knows that if you put “systems” in a different environment than “influences” might change.I don’t have much time anymore for trying to understand lenghty math constructs and let’s put it this way – if the definition had already missed out those (what I think) important aspects than the probability that there are more problemes lurking in the construct is not too small.