Welcome to the Computational Neuroscience Research Group (CNRG) site. We are one of the labs in the Waterloo Centre for Theoretical Neuroscience.

We are interested in understanding how the brain works. We research perception, action, cognition, and basic theoretical issues from a neural perspective. Most of this research is carried out by building large-scale models (usually simulating single neurons) of various brain areas. The main software tool we use and developed for this purpose is Nengo. The books Neural Engineering and How to build a brain summarize the main theoretical approaches we take. We recently proposed the Legendre Memory Unit (LMU) and Spatial Semantic Pointers (SSPs) based on our understanding of brain function. Both are helping to improve deep learning.

We are currently offering the Nengo summer school on how to use Nengo to build large-scale brain models.

You can find and download our publications on this site.

Lab Photo

After the release of our paper about Spaun in the journal Science, we hosted an Ask Me Anything thread on reddit. We got a lot of great questions, the most common of which we have archived on this page.

Basic summary of the model:

Xuan: Spaun is comprised of different modules (parts of the brain if you will), that do different things. There is a vision module, a motor module, memory, and a decision making module.

The basic run-down of how it works is: It gets visual input, processes said visual input, and based on the visual input, decides what to do with it. It could put it in memory, or change it in some way, or move the information from one part of the brain to another, and so forth. By following a set of appropriate actions it can answer basic tasks: e.g. - get visual input - store in memory - take item in memory, add 1, put back in memory - do this 3 times - send memory to output.

The cool thing about Spaun is that it is simulated entirely with spiking neurons, the basic processing units in the brain.

You can find a picture of the high-level architecture of Spaun here.

The stuff in the memory modules of spaun are points in a high dimensional space. If you think about a point on a 2D plane, then on a 3D plane. Now extend that to a 512D hyperspace. It's hard to imagine.

Terry: "Functional" here means that it does tasks. There are eight different tasks (memorizing lists, adding digits, completing a pattern, etc) and we can tell it different tasks to do by showing it different visual stimuli. It takes in visual input, routes it to the relevant brain areas, combines results, and produces motor responses, all using spiking neurons. Projects like IBM Synapse and Blue Brain are definitely working in that direction, but they're generally starting with doing one particular brain component in great detail, rather than our approach of doing less-detailed models of many brain areas, and then connecting them all together.

What is your hardware/software setup?

Xuan: The core simulation code is in Java. Done so mainly for cross-compatibility between different operating systems. The model itself is coded in Python (because Python is so much easier to write), and all it does it hook into the Java code and construct the model that way.

To simulate Spaun, we used both an in-house GPU server, as well as the supercomputing resource that we have available in Ontario, Canada. Sharcnet if you want to know what it is. It's available to all universities in Ontario I believe.

Terry: The core research software is just a simple Java application [http://nengo.ca], so that it can be easily run by any researcher anywhere (we do tutorials on it at various conferences, and there's tutorials online).

But, once we've got a model defined, we can that run that model on pretty much any hardware we feel like. We have a CUDA version for GPUs, we're working on an FPGA version, a Theano [http://deeplearning.net/software/theano/] version (Python compiled to C), and we can upload it into SpiNNaker [http://apt.cs.man.ac.uk/projects/SpiNNaker/], which is a giant supercomputer filled with ARM processors.

Terry: We're actually working directly with Kwabena Boahen, and have a paper with him using this sort of model to do brain-machine interfacing for prosthetic limbs: [http://books.nips.cc/papers/files/nips24/NIPS2011_1225.pdf]

The great thing is that there are a whole bunch of projects right now to build dedicated hardware for simulating neurons extremely quickly. Kwabena takes one approach (using custom analog chips that actually physically model the voltage flowing in neurons), while others like SpiNNaker [http://apt.cs.man.ac.uk/projects/SpiNNaker/] just put a whole bunch of ARM processors together into one giant parallel system. We're definitely supporting both approaches.

I should also note that, while there is a lot of work building these large simulators, the question we are most interested in is figuring out what the connections should be set to in order to produce human-like behaviour. Once we get those connections figured out, then we can feed those connections into whatever large-scale computing hardware is around.

How do I get into your field?

Travis: I would say that your best bet is to find the neuroscience people at your school and start attending talks. Approaching and asking if there's a way you can get involved too is a great idea. It won't be anything fancy, but especially if you have good programming skills you'll be useful in some way off the bat, and as you develop a rapport with the people in the lab you'll be able to work on more interesting things and have good recommendations for when you apply to grad school! And that's huge.

I would start by learning Python, it's a straightforward language with really nice syntax. And you can look up simple reinforcement learning algorithm cat vs mouse examples and the such! Just throw it into google and a million tutorials / courses will pop up!  It'd be a great place to start. Find projects that interest you and then figure out how to do them. Being able to implement your own models / ideas is clutch in this stuff.

The math you’ll need to learn will depend a bit on the kinds of modeling you're going to be doing specifically, but calculus in general is always useful, especially when you're modeling dynamical systems, and probability theory / stats understanding will definitely come in handy for the electrophysiology work! Anything you can do to start giving yourself a leg up now you'll really appreciate later. Things like watching Khan academy videos on intro to calculus is a big help.

Travis: Dr. Eliasmith's book 'The Neural Engineering Framework' is definitely on all our reading lists, but we take a course with him to get through it. And it's very painful. Aside from that, as more of an introductory book I'm a fan of this bad boy by Kandel http://www.amazon.com/Search-Memory-Emergence-Science-Mind/dp/0393329372 It's an easy read / intro to neuroscience. Most of what we do here is reading papers and then coding up ideas / models that we develop, as things are becoming more open access or if you have access to a campus internet connection you can definitely do these things on your own as well to get into things! For more specific reading list though, I would recommend checking out our lab page, looking through our member's list and then if someone's work interests you send them an email! Should be able to provide a nice set of papers related to their area.

How can I get involved in this project?

Trevor: Oh boy! Lots of people wanting to help! Well, the first step is to (attempt to) learn our software, and the theory behind it. There's a course for doing this at the University of Waterloo -- we're looking into ways that we can offer this to people outside of the university in something like Coursera (not for credit). Take an experimental neuroscience paper and try to model it!

Trevor: Our simulator is up on github and our models are up here. We would definitely welcome code contributions! Start with the tutorials and go from there!

What’s next?

Travis: One of the major focuses of the lab right now is incorporating more learning into the model. A couple of us are specifically looking at hierarchical reinforcement learning and building systems that are capable of completing novel tasks using previously learned solutions, and adding learned solutions to its repertoire!

One of the profs at UWaterloo is actually working on incorporating robotics into our models, and having robot eyes / arm being controlled by the spiking neuron models built in Nengo!

Terry: The project I'm currently working on is getting a bit more linguistics into the model. The goal is to be able to describe a new task to the model, and have it do that. Right now it's "hard-coded" to do particular tasks (i.e. we manually set the connections between the cortex and the basal ganglia to be what they would be if someone was already an expert at those tasks).

Xuan: It has always been my goal to make a system navigate a maze, with only visual input from a screen (or video device of some sort), and motor output to a mouse (or similar device).

What's your opinion on the Singularity?  When will we have human-level AI?

Xuan: This is a rather hard question to answer. The definition of "Singularity" is different everywhere. If you are asking when we are going to have machines that have the same level of intelligence as a human being, I'd have to say that we are still a long ways away from that. (I don't like to make predictions about this, because my predictions would most certainly be wrong.

Terry: Who knows. This sort of research is more about understanding human intelligence, rather than creating AI in general. Still, I believe that trying to figure out the algorithms behind human intelligence will definitely help towards the task of making human-like AI. A big part of what comes out of our work is finding that some algorithms are very easy to implement in neurons, and other algorithms are not. For example, circular convolution is an easy operation to implement, but a simple max() function is extremely difficult. Knowing this will, I believe, help guide future research into human cognition.

Terry: I would be extremely surprised if the first human-equivalent AI happened in the next 20 years. I have two main reasons for this.

  1. We've only just begun to try to pin down the algorithms that different parts of the brain are using. They don't look anything like standard computing algorithms (they're much closer to control theory), and it's a very interesting challenge to try to map those on to psychological phenomena. So it feels to me like we're at the beginnings of a field, rather than in the "quickly ramping up" part.
  2. AI has constantly been "20 years away". There are predictions of AI being 20 years away all the way back to when this field started.

That said, the main reason that I got extremely excited about this work and joined this lab is that I think this approach of actually building complex biologically realistic models is the way forward. And I think that if it turned out that everything we're doing in Spaun is right (unlikely) and if all the other researchers in this field abandoned what they were doing and started building Spaun-type models (even more unlikely), then it feels to me human-level AI could happen in 20 years. But, as I make that prediction, I'm very aware that I may be falling into the prediction trap that lots of other AI researchers have made in the past.

How did you train it? Is this just a giant backprop network?

Xuan: Only the visual system in Spaun is trained, and that is so that it could categorize the handwritten digits. More accurately though, it grouped similar looking digits together in a high dimensional vector space. We trained it on the MNIST database (I think it was on the order of 60,000 training examples; 10,000 test examples).

The rest of Spaun is however, untrained. We took a different approach than most neural network models out there. Rather than have a gigantic network which is trained, we infer the functionality of the different parts of the model from behavioural data (i.e. we look at a part of the brain, take a guess at what it does, and hook it up to other parts of the brain).

The analogy is trying to figure out how a car works. Rather than assembling a random number of parts and swapping them out until they work, we try to figure out the necessary parts for a working car and then put those together. While this might not give us a 100% accurate facsimile, it does help us understand the system a whole lot better than traditional "training" techniques.

Additionally, with the size of Spaun, there are no techniques right now that will allow us to train that big of a model in any reasonable amount of time.

Terry: There's a bit of tension right now between machine learning and computational neuroscience. For the most part, machine learning is just focused on solving problems, rather than figuring out how the brain solves those problems. So ML tends to ignore neuroscience, but then every now and then someone in ML uses neuroscience inspiration to make the next big machine learning algorithm breakthrough (I'm thinking right now of Geoff Hinton's deep belief networks [http://www.cs.toronto.edu/\~hinton/]). I also think computational neuroscience needs to be very familiar with ML, so we can make use of any algorithms that show up there that might be a good hypothesis for what the brain is doing.

The model is not started with a blank slate -- in fact, our approach is pretty unique in terms of neural modelling in that we compute what the connection weights should be, rather than rely on a learning rule (although we can also add in a learning rule afterward).

How is this approach similar/dissimilar to things like the Blue Brain project?

Trevor: We definitely know of the Blue Brain project, but we don't have any collaborations with them; they are trying to build a brain bottom-up, figuring out all the details and simulating it. We are trying to build a brain top-down, figuring out the functions we want it to perform and building that with biologically plausible tools. Eventually I hope that both projects will meet somewhere in the middle and it will the best collaboration ever.

Travis: The Blue Brain project really has a different goal than our work, I think. Their goal (as I understand it) is to simulate, as realistically as possible, the number of neurons in a human brain. What we're more concerned with here is how to hook up those neurons to each other such that we get interesting function out of our models, so we're very concerned with the overall system architecture and structure. And that's how we can get out these really neat results with only 2.5 million neurons (which is just a fraction of the 10 billion a human brain has). We are definitely interested in scaling up the number of neurons we can simulate, but it's secondary to producing function.

Xuan: In order to understand the brain (or any complex system), there are multiple ways of approaching the problem.  There is the bottom-up approach - this is similar to the approach used by the Blue Brain project - build as detailed and as complex a model as possible and hope something meaningful emerges. There is the top-down approach - this is the approach used by philosophers and psychologists. These models are usually high level abstractions of behavioural data.

Then there are approaches that come in from the middle, i.e., everything else in between.

You could say that our properties are "weakly constrained", but all of the neuron properties are within those found in a real brain. The main question we were trying to answer was "can we use what we understand functionally about how the brain does things to construct a model that does these things?"

It's similar to understanding how a car works. You can

  1. Replicate it in as much detail as possible and hope it works.
  2. Attempt to understand how each part of the car works, and what function each part has, and then construct your own version of it. The thing is, your construct may not be a 100% accurate facsimile, but it does tell us about our understanding of how a car works.

How do you model individual neurons?

Xuan: The models in spaun are simulated using a leaky-integrate-and-fire (LIF) neuron model. All of the neuron parameters (max firing rate, etc) are chosen from a random distribution, but no extra randomness is added in calculating the voltage levels within each cell.

Travis: Our neural simulation uses Leaky Integrate and Fire neurons, but yes! It is possible to use more complex neural models, and it's actually been something we've been considering, to make it possible to communicate with programs like Neuron that simulate on a much more realistic level. But the LIF neurons do capture like 95% of the features of better simulations, so we are content to use them (as they are also very fast to simulate!)

Terry: The main thing we worry about for neuron types is the neurotransmitter reabsorption rate. This varies wildly across different types of neurons (from 2ms to 200ms), and that's very important for our model. However, right now other than that we have all one neuron type: the standard leaky-integrate-and-fire neuron. We've done some exploring of other neuron types, but that work's not part of Spaun yet.

Ethical questions:

Terry: Being able to simulate a particular person's brain is incredibly far away. There aren't any particularly good ideas as to how we might be able to reasonably read out that sort of information from a person's brain.

That said, there are also lots of uses that a repressive state would have for any intelligent system (think of automatically scanning all surveillence camera footage). But, you don't want a realistic model of the brain to do that -- it'd get bored exactly as fast as people do. That's part of why I a) feel that the vast majority of direct medium-term applications of this sort of work are positive (medicine, education), and b) make sure that all of the work is open-source and made public, so any negative uses can be identified and publicly discussed.

My biggest hope, though, is that by understanding how the mind works, we might be able to figure out what is it about people that lets repressive states take them over, and find ways to subvert that process.

Do you know Jeff Hawkins’ work and Numenta? How does this compare?

Terry: Definitely, and I've even fiddled with some of his Hierarchical Temporal Memory models. It may be possible to build interesting AI out of his version of cortical columns (although my instinct is that that sort of processing is only one of many types of processing found in the brain). But our goal is to try to understand how the human brain works, not build brain-like AI in general. We're working at the level of neurons (rather than cortical columns) because a) neurons are pretty well understood, and b) there seems to be a lot of representational power in the sorts of distributed representations neurons use.

Of course, future models may have to include even finer details about proteins and whatnot, if those details turn out to have important behavioural effects for understanding human cognition.

Reddit AMA, with lots more questions and answers


Less frequently asked questions

What are your thoughts on the connectome project?

Terry: We're definitely keeping a close eye on the connectome project. My hope is that it'll progress along to a point where we might be able to compare the connections that we compute are needed to the actual connections for a particular part of the brain. However, right now the main thing we can get from the connectome project is the sort of high-level gross connectivity (part A connects to part B, but not to part C) rather than the low-level details (neuron #1,543,234 connects to neuron # 34,213,764 with strength 0.275).

How is your work different than Jeff Krichmar’s work on neurorobotics?

Terry: Jeff's work focuses on real-time robotics. We focus on trying to figure out how the human brain works. We do this by making sure the components in the model (simulated neurons) map on to components in the real brain (neurons), so that we can use the simulation as a way of testing our understanding. So our models are constrained to have the same organization as the human brain, and since we have more realistic neurons, the models run slower.

We also have components in our model specifically for doing human-style reasoning (memorizing lists, finding patterns in numbers, adding by counting), which aren't a priority for Jeff's group.

What do you think is the nature of the connection between the cells? Would you say they are best characterized as a computational symbol manipulation network or would a connectionist neural network actually be more appropriate?

Terry: We go with a third approach, and we actually have a paper in the Oxford Handbook of Compositionality on exactly this topic: [http://ctnsrv.uwaterloo.ca/cnrglab/node/276]. Basically, we're making use of a neural representation approach that allows for symbol-like manipulations while still being completely connectionist. But when building the models, it makes more sense to think about it as symbol-like, rather than neural.

How can the brain be thought of as a computer and how this might be consistent with things like emotion and consciousness?

Terry: It definitely cannot be thought of as a classical computer (or at least it's not useful to think of it as a classical computer). Building these sorts of models severely stretches what we think of as a "computer".

I also think it will be possible to model emotions with these systems (especially since most of the emotional centres in the brain are pretty old in evolutionary terms, so they may be simpler than the more complex recent things like language). We're not researching in that direction at the moment, but I don't see why these techniques wouldn't apply.

That said, even if we build these full simulations of the brain, we're still going to be left with the response "well, it's just behaving as if it had emotions, but it doesn't really feel anything". To which there's always the reply "well, how do I know you really feel anything and aren't just behaving as if you feel things?" When/if researchers ever get to that stage, that'll be a very interesting debate to have, and I tend to fall on the side of "a difference that makes no difference is no difference” -- so there's no difference between actually having feelings and behaving as if you have feelings.

What is currently the limiting the power of SPAUN?

Terry: The limit is what brain parts we know how to model. There's all sorts of parts of the brain that don't exist in Spaun. So we need to get a better theoretical understanding of what those parts do, write that as a mathematical algorithm, derive how neurons could do that computation, and then add it to the model.

There's also a lot of adaptability (i.e. learning) going on in many parts of the brain that we still don't have a good handle on, even for the parts that are in Spaun.

I think those things are limiting us much more than computational power. That said, more computational power will let us try out different algorithms more easily, which will help with the real problems.

What's your response to Noam chomsky's critique of Modern day neuroscience in this Atlantic article?

Terry: I pretty much agree with Chomsky that we need to have a theoretical understanding of what's going on in the brain, instead of just throwing stats at it. I'm a bit more positive on the stats approach than Chomsky lays out in that article, but that's because the main thing that we do is figure out how to combine the two. To understand the brain we need to figure out what the underlying structures and algorithms are, and one of the most important aspects we need to understand for human brains is how to represent and manipulate structured information. The core part of how Spaun works is a proof-of-concept of how it is possible for neurons to store and manipulate structured information, which is something that's been traditionally very difficult for neural (and statistical) approaches.

What are the hypotheses that you are testing at the moment? Anything related to the binding problem?

Terry: Good question. The main part of the research was just getting it to run and give vaguely realistic results. We did find a good match to human performance for recognizing hand-written digits and serial recall (forgetting items in the middle of a list more than the ends). For more detailed predictions, we're looking at things like the spiking patterns of neurons in particular areas when guessing a number (and comparing that to spiking patterns in rats when guessing which lever to press).

As for the binding problem, that's actually a very big part of this research -- it's what lets us do things like memorize a series of numbers (for those that don't know, the binding problem is the question of how the brain manages to represent multiple things at once at keep them straight. For example, if I have "8, 4, 7", I have to represent 8 in position 1, 4 in position 2, and 7 in position 3" all at the same time, and keep that distinct from "4, 7, 8" and other orderings). A lot of neuroscientists make the assumption that this is done by neural oscillations: first the pattern for "8 in position 1" appears, then "4 in position 2", then "7 in position 3" appears, all in a fraction of a second.

That's not what we do. Instead, we use the approach taken by Vector Symbolic Architectures [http://cogprints.org/3983/], which shows a way to combine patterns to get new patterns that you can decompress back to the original patterns. This operation (we use circular convolution) turns out to be really easy to implement in neurons.

The Computational Neuroscience Research Group (CNRG) was started in 1992 by Charles H. Anderson when he moved with David Van Essen to Washington University. In 2001, Chris Eliasmith, then a member of the Washington University group moved to the University of Waterloo and began a second CNRG. The two groups were closely affiliated and employ the same approach. The CNRG began by constructing models of the visual system, introducing the cortical shifter circuit. Concurrently, the CNRG pursued work on the probability density function (PDF) framework for neural representation. Although that framework has now been considerably extended and improved, the main goal of providing a unifying framework for understanding complex neurobiological systems remains the same (see research).

Upon the retirement of Charles H. Anderson in 2005 or so, Chris Eliasmith became the sole lab head and is located at Waterloo. The CNRG at Waterloo is part of Waterloo's Centre for Theoretical Neuroscience (CTN), which Dr. Eliasmith directs. For seminars, workshops, and other activities related to theoretical neuroscience, please visit the Centre's webpage.

Funding for the CNRG (WashU) has been provided by the National Science Foundation and the Center for Higher Brain Function. Major funding for the CNRG has been provided by the G. Harold and Leila Y. Mathers Foundation of Mt. Kisco, N.Y. Funding for the CNRG (Waterloo) has been provided by the Natural Sciences and Engineering Research Council (NSERC) of Canada, the Canadian Foundation for Innovation, the Ontario Innovation Trust, and Canada Research Chairs among others.


Chris Eliasmith (lab head): celiasmith@uwaterloo.ca

Mailing Address

Computational Neuroscience Research Group

200 University Avenue West

Waterloo, ON, Canada   N2L 3G1


Phone: +1 519 888 4567   x38842

Fax: +1 519 746 3097