Code for the computational model to avoid catastrophic forgetting as in Rikhye, Gilra and Halassa, Nature Neuroscience 2018, Fig. 5b-d and Supplementary Fig. 16b-d.

The medio-dorsal thalamus (MD) switches subsets of cortical (medial Pre-Frontal Cortex mPFC) neurons on and off depending on context, enabling other context weights to remain stable.

Installation:

You need to install python, numpy, scipy and matplotlib. The simulations were run on Ubuntu 18.04 on a server with CPU: Intel Xeon E5-2680 v3 (Haswell) 2x 12 cores, 24 threads, 2.5 GHz, 30 MB cache.
The code only uses 1 core and takes around 30 min for the task in Fig 5b-d, and around 1 hour for the xor task in Suppl. Fig 16b-d (for one network instance).

Running an instance:

First cd to the directory in which you've clone this github repo.
Then mkdir dataPFCMD where the data files will be saved.
Run python reservoir_PFCMD_simple.py. By default, it runs with MD present on the standard task in the paper (Fig 5b-d).
This runs 1000 cycles of context 1, 1000 cycles of context 2, and then 200 cycles of context 1 again (a cycle is one presentation of all cues of the current context).
This will generate 4 figures: (a) cues, a few reservoir PFC neural activity for each cue subset, MD neural activity and output activity vs time; (b) mean squared error versus cycle num; (c) evolution of a few output weights for cues A and B versus cycle number; and (d) mean activity of each neuron during a few context 1 cycles.

To turn MD off, set self.MDstrength = 0. instead of 1. in reservoir_PFCMD_simple.py.
To run the xor task (Suppl Fig 16b-d), set self.xorTask = True in reservoir_PFCMD_simple.py.

To reproduce Figure 5b-d:

1. Set seeds 0 to 9 in reservoir_PFCMD_simple.py by modifying line: self.RNGSEED = 0.
2. Run twice for each seed setting self.MDstrength = 0. and self.MDstrength = 1..
3. Finally, run python plot_PFCMD_figs.py which is save a fig_paper.eps file corresponding to Fig 5b-d.

To reproduce Suppl. Figure 16b-d:

Repeat as above, except set self.xorTask = True in reservoir_PFCMD_simple.py and set xorStr = '_xor' in plot_PFCMD_figs.py.