Information Processing in Chemical Networks

4 January, 2017

There’s a workshop this summer:

Dynamics, Thermodynamics and Information Processing in Chemical Networks, 13-16 June 2017, Complex Systems and Statistical Mechanics Group, University of Luxembourg. Organized by Massimiliano Esposito and Matteo Polettini.

They write, “The idea of the workshop is to bring in contact a small number of high-profile research groups working at the frontier between physics and biochemistry, with particular emphasis on the role of Chemical Networks.”

The speakers include John Baez, Sophie de Buyl, Massimiliano Esposito, Arren Bar-Even, Christoff Flamm, Ronan Fleming, Christian Gaspard, Daniel Merkle, Philippe Nge, Thomas Ouldridge, Luca Peliti, Matteo Polettini, Hong Qian, Stefan Schuster, Alexander Skupin, Pieter Rein ten Wolde. I believe attendance is by invitation only, so I’ll endeavor to make some of the ideas presented available here at this blog.

Some of the people involved

I’m looking forward to this, in part because there will be a mix of speakers I’ve met, speakers I know but haven’t met, and speakers I don’t know yet. I feel like reminiscing a bit, and I hope you’ll forgive me these reminiscences, since if you try the links you’ll get an introduction to the interface between computation and chemical reaction networks.

In part 25 of the network theory series here, I imagined an arbitrary chemical reaction network and said:

We could try to use these reactions to build a ‘chemical computer’. But how powerful can such a computer be? I don’t know the answer.

Luca Cardelli answered my question in part 26. This was just my first introduction to the wonderful world of chemical computing. Erik Winfree has a DNA and Natural Algorithms Group at Caltech, practically next door to Riverside, and the people there do a lot of great work on this subject. David Soloveichik, now at U. T. Austin, is an alumnus of this group.

In 2014 I met all three of these folks, and many other cool people working on these theme, at a workshop I tried to summarize here:

Programming with chemical reaction networks, Azimuth, 23 March 2014.

The computational power of chemical reaction networks, 10 June 2014.

Chemical reaction network talks, 26 June 2014.

I met Matteo Polettini about a year later, at a really big workshop on chemical reaction networks run by Elisenda Feliu and Carsten Wiuf:

Trends in reaction network theory (part 1), Azimuth, 27 January 2015.

Trends in reaction network theory (part 2), Azimuth, 1 July 2015.

Polettini has his own blog, very much worth visiting. For example, you can see his view of the same workshop here:

• Matteo Polettini, Mathematical trends in reaction network theory: part 1 and part 2, Out of Equilibrium, 1 July 2015.

Finally, I met Massimiliano Esposito and Christoph Flamm recently at the Santa Fe Institute, at a workshop summarized here:

Information processing and biology, Azimuth, 7 November 2016.

So, I’ve gradually become educated in this area, and I hope that by June I’ll be ready to say something interesting about the semantics of chemical reaction networks. Blake Pollard and I are writing a paper about this now.


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:


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, 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:

Screenshot of Globular

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
, 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: In a monoidal category, if multiplication and comultiplication morphisms are unital, counital and Frobenius, then they are associative and coassociative.

Strengthening an equivalence: In a 2-category, an equivalence gives rise to an adjoint equivalence, satisfying the snake equations.

Swallowtail comes for free: 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: 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.

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.


Compositional Frameworks for Open Systems

27 November, 2016


Here are the slides of Blake Pollard’s talk at the Santa Fe Institute workshop on Statistical Physics, Information Processing and Biology:

• Blake Pollard, Compositional frameworks for open systems, 17 November 2016.

He gave a really nice introduction to how we can use categories to study open systems, with his main example being ‘open Markov processes’, where probability can flow in and out of the set of states. People liked it a lot!


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’:

Monoidal categories of networks.

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


Monday, December 5th, 2016
9 – 9:20 am
Coffee and Check-In
9:20 – 9:30 am
Opening Remarks
9:30 – 10:30 am
10:30 – 11 am
11 – 11:35 am
11:40 am – 12:15 pm
12:20 – 2 pm
2 – 2:35 pm
2:40 – 3:15 pm
3:30 – 4 pm
4 – 5 pm
5 – 6 pm


Tuesday, December 6th, 2016
9 – 9:30 am
Coffee and Check-In
9:30 – 10:30 am
10:30 – 11 am
11 – 11:35 am
11:40 am – 12 pm
12:05 – 12:25 pm
12:30 – 2 pm
2 – 2:35 pm
2:40 – 3:15 pm
3:30 – 4 pm
4 – 5 pm


Wednesday, December 7th, 2016
9 – 9:30 am
Coffee and Check-In
9:30 – 10:30 am
10:30 – 11 am
11 – 11:20 am
11:25 – 11:45 am
11:50 am – 12:25 pm
12:30 – 2 pm


Thursday, December 8th, 2016
9 – 9:30 am
Coffee and Check-In
9:30 – 10:05 am
10:10 – 10:30 am
10:35 – 11 am
11 – 11:20 am
11 am – 11:45 am
11 am – 12:10 pm
12 pm – 2 pm
2 – 2:35 pm
2:40 – 3:15 pm
3 pm – 3:50 pm
3:50 – 4:25 pm
4:30 – 4:50 pm


Friday, December 9th, 2016
9:30 – 10:05 am
10 am – 10:45 am
10:50 – 11:20 am
11:20 – 11:55 am
12 – 12:35 pm
12:40 – 2 pm
2 – 3 pm
3 – 3:40 pm