## Globular

14 December, 2016

One of my goals is to turn category theory, and even higher category theory, into a practical tool for science. For this we need good scientific ideas—but we also need good software.

My friend Jamie Vicary has been developing some of this software, together with Aleks Kissinger and Krzysztof Bar and others. Jamie demonstrated it at the Simons Institute workshop on compositionality. You can watch his demonstration here:

But since Globular runs on a web browser, you can also try it out yourself here:

Globular.

You can see his talk slides:

• Jamie Vicary, Data structures for quasistrict higher categories. (Talk slides here.)

Abstract. Higher category theory is one of the most general approaches to compositionality, with broad and striking applications across computer science, mathematics and physics. We present a new, simple way to define higher categories, in which many important compositional properties emerge as theorems, rather than axioms. Our approach is amenable to computer implementation, and we present a new proof assistant we have developed, with a powerful graphical calculus. In particular, we will outline a substantial new proof we have developed in our setting.

And in December 2015, he wrote an article about this software on the n-Category Café. It’s been improved since then, but it can’t hurt to read what he wrote—so I append it here!

### Globular: the basic idea

When you’re trying to prove something in a monoidal category, or a higher category, string diagrams are a really useful technique, especially when you’re trying to get an intuition for what you’re doing. But when it comes to writing up your results, the problems start to mount. For a complex proof, it’s hard to be sure your result is correct—a slip of the pen could lead to a false proof, and an error that’s hard to find. And writing up your results can be a huge time-sink, requiring weeks or months using a graphics package, all just for some nice pictures that tell you little about the correctness of the proof, and become useless if you decide to change your approach. Computers should be able help with all these things, in the way that proof assistants like Coq and Agda are allowing us to work with traditional syntactic proofs in a more sophisticated way.

The purpose of this post is to introduce Globular, a new proof assistant for working with higher-categorical proofs using string diagrams. It’s available at http://globular.science, with documentation on the nab. It’s web-based, so everything happens right in your browser: build formal proofs, visualize and step through them; keep your proofs private, share them with collaborators, or make them publicly available.

Before we get into the technical details, here’s a screenshot of Globular in action:

The main part of the screen shows a diagram, which in this case is 2-dimensional. It represents a composite 2-cell in a finitely-presented 2-category, with the blue and red regions representing objects, the lines representing 1-cells, and the vertices representing 2-cells. In fact, this 2d diagram is just an intermediate state of a 3d proof, through which we’re navigating with the ‘Slice’ controls in the top-right. The proof itself has been built up by composing the generators listed in the signature, down the left-hand side of the screen. (If you want to take a look at this proof yourself, you can go straight there; in the top-right, set ‘Project’ to 0, then increment the second ‘Slice’ counter to scroll through the proof.)

Globular has been developed so far in the Quantum Group in
the Oxford Computer Science department, by Krzysztof
Bar
, Katherine Casey, Aleks Kissinger, Jamie Vicary and Caspar Wylie. We haven’t quite got around to it yet, but Globular will be open-source, and we’re really keen for people to get involved and help build the software—there’s a huge amount to do! If you want to help out, get in touch.

### Mathematical foundations

Globular is based on the theory of finitely-presented semistrict n-categories; at the moment, it works up to the level of 3-categories, with an extension to 4-categories actively in development. (You can build cells of any dimension, but from 4-cells and up, some structures are missing.)

Definitions of n-category vary in how strict they are; a definition is semistrict when it’s as strict as possible, while still having the property that every weak n-category satisfies it, up to equivalence. Definitions of semistrict n-category are not unique: in dimension 3, Gray categories put all the weak structure in the interchangers, while Simpson snucategories put it all in the unitors. Globular implements the axioms of a Gray category, because this is the most appropriate for the graphical calculus: the interchangers can be seen graphically, as changes in height of the components of the diagram. By the theory of k-tuply monoidal n-categories, this also lets you build proofs in a monoidal category, or a braided monoidal category, or a monoidal 2-category.

The only things that Globular understands are $k$-cells, for some value of $k$. So if you want to build an n-category where an equation $f=g$ holds between n-cells, you have to do it by adding $(n+1)$-cells $a:f \to g$ and $b:g \to f$. If you then build some composite $C(f)$ involving $f$, you can apply the cell $a$ to obtain $C(g)$, and we interpret this as the equation $C(f) = C(g)$. In a slogan, this is equality via rewriting. This is consistent with the basic premise of homotopy type theory: treat your proofs as first-order structures, which can in turn be reasoned about themselves.

Globular can also handle invertibility in a nice way. For a cell $F:A \to B$ to be invertible, indicated by ticking a box in the signature, means that there also exists an invertible cell $F^{-1}: B \to A$, and invertible cells $\text{id}_A \to F . F^{-1}$ and $\text{id}_B \to F^{-1} . F$. This is a coinductive definition (see Mike Shulman’s nice post on this topic), since we’re defining the notion of invertibility in terms of itself in a higher dimension. This sort of a definition is great for proof assistants to work with, as it allows a lot of structure to be generated from a single compact definition.

### How it works

For a lot more details, take a look at the nLab page. Everything that happens in Globular involves in interaction between the signature on the left-hand side, and the diagram in the main part of the screen. The signature stores the ‘library’ of cells you have available, and the diagram is a particular composite of cells that you have constructed.

To construct a new diagram, clear whatever is currently displayed by clicking the ‘Clear’ button on the right, or pressing ‘c’. Then start by clicking the icon of a n-cell in your signature, which will make a diagram consisting just of that cell. Clicking on the icons of other $k$-generators for $0 < k \leq n$ will display a list of ways the cell can be attached, and when you choose one of these ways, the attachment will be performed, growing your n-diagram. (If you’re starting with a blank workspace you will only have a single 0-cell available, so you won’t be able to do this yet!) Clicking an $(n+1)$-cell $G$ displays a list of ways that your n-diagram $D$ can be rewritten, by identifying the source of $G$ as a subdiagram of $D$. Selecting one of these ways will implement the rewrite, by ‘cutting out’ the chosen subdiagram of $D$, and replacing it with the target of $G$.

Another way to modify the diagram is to click directly on it. Clicking near the edge of the diagram performs an attachment, while clicking in the interior of the diagram performs a rewrite. If more than one attachment or rewrite is consistent with your click, a little menu will pop up for you to choose what you want to do. When you move your mouse pointer over the diagram, a little label pops up to show you what your cursor is hovering over, which is helpful when choosing where to click.

You can also click-and-drag on the diagram. This will attach or rewrite with an interchanger, or naturality for an interchanger, or invertibility for an interchanger, depending on where you have clicked and the direction of the drag. Clicking and dragging is designed to work as if you were really ‘touching’ the strings. So if you want to braid one strand over another, click the strand to ‘grab’ it, and ‘pull’ it to one side. If you want to pull a vertex through a braiding, click the vertex to ‘grab’ it, and ‘pull’ it up or down through its adjacent braiding. Of course, Globular will only carry out the command if the move you are attempting to make is actually valid in that location.

### Example theorems

Here are four worked examples of nontrivial proofs in Globular:

Frobenius implies associative: http://globular.science/1512.004. In a monoidal category, if multiplication and comultiplication morphisms are unital, counital and Frobenius, then they are associative and coassociative.

Strengthening an equivalence: http://globular.science/1512.007. In a 2-category, an equivalence gives rise to an adjoint equivalence, satisfying the snake equations.

Swallowtail comes for free: http://globular.science/1512.006. In a monoidal 2-category, a weakly-dual pair of objects gives rise to a strongly-dual pair, satisfying the swallowtail equations.

Pentagon and triangle implies $\lambda_I = \rho_I$: http://globular.science/1512.002. In a monoidal 2-category, if a pseudomonoid object satisfies pentagon and triangle equations, then it satisfies $\lambda_I = \rho_I$.

We’ll focus on the second example project “Strengthening an equivalence” listed above, and see how it was constructed. This project investigates the factthat every equivalence in a 2-category gives rise to an adjoint equivalence. To start, we therefore need the basic data that exhibits an equivalence in a 2-category: two 0-cells $A$ and $B$, and an invertible 1-cell $F:A \to B$, by the weak definition of ‘invertible’ discussed above. This gives us the following signature:

The 2-cells that witness invertibility of $F$ look like cups and caps in the graphical calculus, but they won’t satisfy the snake equations that define an adjoint equivalence. The idea of this proof is to define a new cap, built out of the invertible structure of $F$, which does satisfy the snake equations with the existing cup.

By starting with a diagram consisting of $F$ alone, pressing ‘i’ to take the identity diagram, and clicking-and-dragging, we build the following 2-diagram, out of the invertible structure associated to $F$:

This is our candidate for our redefined cup. Its source is the identity on $A$, and its target is $F$ composed with $F^{-1}$. It looks a bit like the curved end of a hockey stick.

To store it for later use, we now click the ‘Theorem’ button. Writing $D$ for the 2-diagram we have constructed, this does two things. First, it creates a 2-cell generator that we call “New Cup”, whose source is $s(D)$, and whose target is $t(D)$. This is the redefined cup that we can use in future expressions. Second, it creates an invertible 3-cell generator that we call “New Cup Definition”, with source given by “New Cup”, and with target given by our hockey-stick diagram $D$. This says what “New Cup” means in terms of our original structure. This adds the following cells to our signature:

Because “New Cup Definition” is a 3-cell, by default we see two little icons: one for its source, and one for its target. See how its source is a little picture of “New Cup”, and its target is a little picture of the hockey stick, just as we defined it.

We’re now ready to prove one of the snake equations. We start by building the snake composite, using “New Cup” for the cup, and the invertible structure of $F$ for the cap:

Now have to prove that this equals the identity. Since equality is implemented by rewriting, we must construct a 3-diagram whose source is this snake composite, and whose target is the identity on $F$. To start, we click the ‘Identity’ button to convert our diagram into an identity 3-diagram. The only apparent effect this has is to add a number scroller to the ‘Slice’ area of the controls in the top-right. At the moment we can set this to ‘0’ and ‘1’, representing the source and target of our identity 3-diagram respectively. We set it to ‘1’, because we want to compose things to the target.

We now build up our proof. First, we click on the pink vertex that represents “New Cup”. This will attach our 3-cell “New Cup Definition”, replacing “New Cup” with our hockey-stick picture. By clicking-and-dragging on the diagram, we obtain the following sequence
of pictures:

Pictures 3 to 10 were created by attaching interchangers, and pictures 11 to 15 were created by attaching higher structure generated by the invertibility of $F$. In all cases, this structure was attached just by clicking-and-dragging on the appropriate vertices of the diagram. We’ve turned the snake into the identity, so we’ve finished our proof, which required 14 3-cells. By using the ‘Slice’ control in the top-right, we can navigate through the 15 slices that make up our proof, and review what we just did. Even better, turning the ‘Project’ control to the value ‘1’ tells Globular to project out the lowest dimension. This means that our entire 3-diagram proof can be viewed as a single 2-dimensional diagram, as follows:

This is just like the Morse singularity graphics used by topologists to study the structure of higher-dimensional manifolds. In this picture, the vertices are 3-cells, the lines are 2-cells, and the regions are 1-cells (in fact, every region is the 1-cell $F$.) By moving your mouse pointer over the different parts of the diagram, you can see what the different components are. Interchangers are represented in this projection by braidings.

Now we can do something cool: we can modify our proof, by clicking-and-dragging on the Morse projection. For example, just to the right of centre, there is a crossing, out of which emerge two long vertical lines that travel up a long way before annihilating with one another. Our proof would be much simpler if these two lines just annihilated with each other right after the interchanger. So, we click the vertex at the top of the lines, and drag it down repeatedly, until it gets to where we want it:

We’ve simplified our proof. By clicking-and-dragging some more, you can change the proof in lots of different ways, although you probably won’t get it much simpler than this. Putting the ‘Project’ control back to ‘0’, and navigating through the stages of the proof with the ‘Slice’ control as we were doing before, we can see that our proof has indeed been modified.

This project has been in development for about 18 months, so it feels great to finally launch. We hope the whole community will get clicking-and-dragging, and let us know how easy it is to use, and what other features would be useful. There are certain to still be bugs, so let us know about them too, and we’ll get right on them.

## Modelling Interconnected Systems with Decorated Corelations

9 December, 2016

Here at the Simons Institute workshop on compositionality, my talk on network theory explained how to use ‘decorated cospans’ as a general model of open systems. These were invented by Brendan Fong, and are nicely explained in his thesis:

• Brendan Fong, The Algebra of Open and Interconnected Systems. (Blog article here.)

But he went further: to understand the externally observable behavior of an open system we often want to simplify a decorated cospan and get another sort of structure, which he calls a ‘decorated corelation’.

In this talk, Brendan explained decorated corelations and what they’re good for:

• Brendan Fong, Modelling interconnected systems with decorated corelations. (Talk slides here.)

Abstract. Hypergraph categories are monoidal categories in which every object is equipped with a special commutative Frobenius monoid. Morphisms in a hypergraph category can hence be represented by string diagrams in which strings can branch and split: diagrams that are reminiscent of electrical circuit diagrams. As such they provide a framework for formalising the syntax and semantics of circuit-type diagrammatic languages. In this talk I will introduce decorated corelations as a tool for building hypergraph categories and hypergraph functors, drawing examples from linear algebra and dynamical systems.

## Semantics for Physicists

7 December, 2016

I once complained that my student Brendan Fong said ‘semantics’ too much. You see, I’m in a math department, but he was actually in the computer science department at Oxford: I was his informal supervisor. Theoretical computer scientists love talking about syntax versus semantics—that is, written expressions versus what those expressions actually mean, or programs versus what those programs actually do. So Brendan was very comfortable with that distinction. But my other grad students, coming from a math department didn’t understand it… and he was mentioning it in practically ever other sentence.

In 1963, in his PhD thesis, Bill Lawvere figured out a way to talk about syntax versus semantics that even mathematicians—well, even category theorists—could understand. It’s called ‘functorial semantics’. The idea is that things you write are morphisms in some category $X,$ while their meanings are morphisms in some other category $Y.$ There’s a functor $F \colon X \to Y$ which sends things you write to their meanings. This functor sends syntax to semantics!

But physicists may not enjoy this idea unless they see it at work in physics. In physics, too, the distinction is important! But it takes a while to understand. I hope Prakash Panangaden’s talk at the start of the Simons Institute workshop on compositionality is helpful. Check it out:

## Compositionality in Network Theory

29 November, 2016

I gave a talk at the workshop on compositionality at the Simons Institute for the Theory of Computing next week. I spoke about some new work with Blake Pollard. You can see the slides here:

• John Baez, Compositionality in network theory, 6 December 2016.

and a video here:

Abstract. To describe systems composed of interacting parts, scientists and engineers draw diagrams of networks: flow charts, Petri nets, electrical circuit diagrams, signal-flow graphs, chemical reaction networks, Feynman diagrams and the like. In principle all these different diagrams fit into a common framework: the mathematics of symmetric monoidal categories. This has been known for some time. However, the details are more challenging, and ultimately more rewarding, than this basic insight. Two complementary approaches are presentations of symmetric monoidal categories using generators and relations (which are more algebraic in flavor) and decorated cospan categories (which are more geometrical). In this talk we focus on the latter.

This talk assumes considerable familiarity with category theory. For a much gentler talk on the same theme, see:

## Monoidal Categories of Networks

12 November, 2016

Here are the slides of my colloquium talk at the Santa Fe Institute at 11 am on Tuesday, November 15th. I’ll explain some not-yet-published work with Blake Pollard on a monoidal category of ‘open Petri nets’:

Nature and the world of human technology are full of networks. People like to draw diagrams of networks: flow charts, electrical circuit diagrams, chemical reaction networks, signal-flow graphs, Bayesian networks, food webs, Feynman diagrams and the like. Far from mere informal tools, many of these diagrammatic languages fit into a rigorous framework: category theory. I will explain a bit of how this works and discuss some applications.

There I will be using the vaguer, less scary title ‘The mathematics of networks’. In fact, all the monoidal categories I discuss are symmetric monoidal, but I decided that too many definitions will make people unhappy.

The main new thing in this talk is my work with Blake Pollard on symmetric monoidal categories where the morphisms are ‘open Petri nets’. This allows us to describe ‘open’ chemical reactions, where chemical flow in and out. Composing these morphisms then corresponds to sticking together open Petri nets to form larger open Petri nets.

## Compositionality Workshop

1 November, 2016

I’m excited! In early December I’m going to a workshop on ‘compositionality’, meaning how big complex things can be built by sticking together smaller, simpler parts:

Compositionality, 5-9 December 2016, workshop at the Simons Institute for the Theory of Computing, Berkeley. Organized by Samson Abramsky, Lucien Hardy and Michael Mislove.

In 2007 Jim Simons, the guy who helped invent Chern–Simons theory and then went on to make billions using math to run a hedge fund, founded a research center for geometry and physics on Long Island. More recently he’s also set up this institute for theoretical computer science, in Berkeley. I’ve never been there before.

‘Compositionality’ sounds like an incredibly broad topic, but since it’s part of a semester-long program on Logical structures in computation, this workshop will be aimed at theoretical computer scientists, who have specific ideas about compositionality. And these theoretical computer scientists tend to like category theory. After all, category theory is about morphisms, which you can compose.

Here’s the idea:

The compositional description of complex objects is a fundamental feature of the logical structure of computation. The use of logical languages in database theory and in algorithmic and finite model theory provides a basic level of compositionality, but establishing systematic relationships between compositional descriptions and complexity remains elusive. Compositional models of probabilistic systems and languages have been developed, but inferring probabilistic properties of systems in a compositional fashion is an important challenge. In quantum computation, the phenomenon of entanglement poses a challenge at a fundamental level to the scope of compositional descriptions. At the same time, compositionally has been proposed as a fundamental principle for the development of physical theories. This workshop will focus on the common structures and methods centered on compositionality that run through all these areas.

So, some physics and quantum computation will get into the mix!

A lot of people working on categories and computation will be at this workshop. Here’s what I know about the talks so far. If you click on the talk titles you’ll get abstracts, at least for most of them.

### The program

 9 – 9:20 am Coffee and Check-In 9:20 – 9:30 am Opening Remarks 9:30 – 10:30 am Compositionally, Adequacy, and Full Abstraction Gordon Plotkin, University of Edinburgh 10:30 – 11 am Break 11 – 11:35 am An Operadic Approach to Compositionality David Spivak, MIT 11:40 am – 12:15 pm Data Structures for Quasistrict Higher Categories Jamie Vicary, University of Oxford 12:20 – 2 pm Lunch 2 – 2:35 pm From Linearizability to Eventual Consistency Radha Jagadeesan, DePaul University 2:40 – 3:15 pm Compositionality and Session Types Nobuko Yoshida, Imperial College London 3:30 – 4 pm Break 4 – 5 pm Discussion 5 – 6 pm Reception

 9 – 9:30 am Coffee and Check-In 9:30 – 10:30 am The Mathematics of Networks John Baez, UC Riverside 10:30 – 11 am Break 11 – 11:35 am Composition in Categorical Distributional Models of Natural Language Mehrnoosh Sadrzadeh, Queen Mary University of London 11:40 am – 12 pm Modelling Interconnected Systems with Decorated Corelations Brendan Fong, University of Pennsylvania 12:05 – 12:25 pm Custom Compact Closed Categories via Relations Dan Marsden, University of Oxford 12:30 – 2 pm Lunch 2 – 2:35 pm Some Thoughts on Inferring System Structure Tobias Fritz, Max Planck Institute, Leipzig 2:40 – 3:15 pm TBD Alexandra Silva, University College London 3:30 – 4 pm Break 4 – 5 pm Discussion

 9 – 9:30 am Coffee and Check-In 9:30 – 10:30 am Compositional Thermodynamics Giulio Chiribella, The University of Hong Kong 10:30 – 11 am Break 11 – 11:20 am Composition and Quantum Theory: A Conjecture, and How it Could Fail Markus Mueller, Western University 11:25 – 11:45 am Multipartite Composition of Contextuality Scenarios Ana Belen Sainz, University of Bristol 11:50 am – 12:25 pm Compositionality in Categorical Quantum Computing Ross Duncan, University of Strathclyde 12:30 – 2 pm Lunch

 9 – 9:30 am Coffee and Check-In 9:30 – 10:05 am Canonical Representations of Measurements for Contextuality Analysis Ehtibar Dzhafarov, Purdue University 10:10 – 10:30 am TBD Rui Soares Barbosa, University of Oxford 10:35 – 11 am Break 11 – 11:20 am Modelling Interfaces in Distributed Systems: Some First Steps David Pym, University College London 11 am – 11:45 am Compositionality in Cybersecurity Pasquale Malacaria, Queen Mary University of London 11 am – 12:10 pm A Topological Approach for Exploiting Compositionality in Complex Systems Emanuela Merelli, University of Camerino 12 pm – 2 pm Lunch 2 – 2:35 pm Nominal Games: A Semantics Paradigm for Effectful Languages Nikos Tzevelekos, Queen Mary University of London 2:40 – 3:15 pm Probabilistic Call By Push Value Christine Tasson, Université Paris Diderot 3 pm – 3:50 pm Break 3:50 – 4:25 pm TBD Kohei Kishida, University of Oxford 4:30 – 4:50 pm Linear Logic, Session Types and Deadlock-Freedom Simon Gay, University of Glasgow

 9:30 – 10:05 am Composing Schema Mappings: An Overview 10 am – 10:45 am TBD Val Tannen, University of Pennsylvania 10:50 – 11:20 am Break 11:20 – 11:55 am A Compositional Quantum Programming Language Peter Selinger, Dalhousie University 12 – 12:35 pm Programming Recurrence Relations Pawel Sobocinski, University of Southampton 12:40 – 2 pm Lunch 2 – 3 pm Discussion 3 – 3:40 pm TBD Dana Scott, Carnegie Mellon University

## Open and Interconnected Systems

23 October, 2016

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 $r.$ 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 $\mathbb{R}\oplus\mathbb{R}\oplus\mathbb{R}\oplus\mathbb{R},$ 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 $1/r.$ Thus the behaviour of the resistor is the set

$\displaystyle{ \big\{\big(\phi_1,\phi_2, -\tfrac1r(\phi_2-\phi_1),\tfrac1r(\phi_2-\phi_1)\big)\,\big\vert\, \phi_1,\phi_2 \in \mathbb{R}\big\} }$

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

$X \to N \leftarrow Y$

with a common codomain. In Chapter 2 we introduce the idea of a ‘decorated cospan’, which equips the apex $N$ 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 $\mathcal C$ be a category with finite colimits, writing its as coproduct as $+,$ and let $(\mathcal D, \otimes)$ be a braided monoidal category. Decorated cospans provide a method of producing a hypergraph category from a lax braided monoidal functor

$F\colon (\mathcal C,+) \to (\mathcal D, \otimes)$

The objects of these categories are simply the objects of $\mathcal C,$ while the morphisms are pairs comprising a cospan $X \rightarrow N \leftarrow Y$ in $\mathcal C$ together with an element $I \to FN$ in $\mathcal D$—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 $(\mathcal{E},\mathcal{M})$ on a category $\mathcal{C},$ we define a corelation to be a cospan $X \to N \leftarrow Y$ such that the copairing of the two maps, a map $X+Y \to N,$ is a morphism in $\mathcal{E}.$ Factorising maps $X+Y \to N$ 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.