This code is written in Python 2.7 and requires

• Theano 0.7

Optional but recommended if you plan to run many trials with the trained networks outside of Theano:

• Cython

Optional but recommended for analysis and visualization of the networks (including examples from the paper):

• matplotlib

The code uses (but doesn't require) one function from the NetworkX package to check if the recurrent weight matrix is connected (every unit is reachable by every other unit), which is useful if you plan to train very sparse connection matrices.

Because you will eventually want to modify the pycog source files, we recommend that you "install" by simply adding the pycog directory to your $PYTHONPATH, and building the Cython extension to (slightly) speed up Euler integration for testing the networks by typing

python setup.py build_ext --inplace

You can also perform a "standard" installation by going to the pycog directory and typing

python setup.py install

Example task specifications, including those used to generate the figures in the paper, can be found in examples/models.

Training and testing networks involves some boring logistics, especially regarding file paths. You may find the script examples/do.py helpful as you start working with your own networks. For instance, to train a new network we can just type (from the examples directory)

python do.py models/sinewave train

For this particular example we've also directly included code for training and plotting the result, so you can simply type

python models/sinewave.py

• The default recurrent noise level (used for most of the tasks in our paper) is rather high. When training a new task start with a value of var_rec that is small, then increase the noise for more robust solutions.

• A list of parameters and their default values can be found in defaults.py

• The default time step is also relatively large, so always test with a smaller time step (say 0.05) and re-train with a smaller step size if the results change.

• By default, recurrent and output biases are set to zero. If you encounter difficulties with training, try including the biases by setting train_brec = True and/or train_bout = True.

• If you still have difficulties with training, try changing the value of lambda_Omega, the multiplier for the vanishing-gradient regularizer.

• It's common to see the following warning when running Theano:

  RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility
  rval = __import__(module_name, {}, {}, [module_name])
  

  This is almost always innocuous and can be safely ignored.

This code would not be possible without

• On the difficulty of training recurrent neural networks.
  R. Pascanu, T. Mikolov, & Y. Bengio, ICML 2013.
  https://github.com/pascanur/trainingRNNs

MIT

This code is the product of work carried out in the group of Xiao-Jing Wang at New York University. If you find our code helpful to your work, consider giving us a shout-out in your publications:

• Song, H. F.*, Yang, G. R.*, & Wang, X.-J. "Training Excitatory-Inhibitory Recurrent Neural Networks for Cognitive Tasks: A Simple and Flexible Framework." PLoS Comp. Bio. 12, e1004792 (2016). (* = equal contribution)