[Brian 2] automatic creation of synapses from adjacency matrix

[luc.be...@gmail.com]

Hello,

This query is specific to Brian v2. 

I understand that since multiple connections are possible between neurons, the notion of 'adjacency matrix' is problematic. 

However, what if I do want to initialise synapses from an existing adjacency matrix? 

In http://brian2.readthedocs.org/en/2.0b4/user/synapses.html it is indicated that it is possible to create synapses using code with the code being a boolean statement that should return True when a synapse must be created, where i is the pre and j the post synaptic neuron index. So I tried the following: 

A=randint(2,size=(4,4)) 

S.connect('A(i,j)==1')

However, I am getting the following error: 

In [11]: S.connect('A[i,j]==1')

  File "<string>", line unknown

SyntaxError: Unknown syntax: Subscript

Any idea? 

If this is not going to be possible at all, am I supposed to cycle through all entries of my adjacency matrix and create the connections one by one? 

This does not sound very efficient. Example above has only 4 neurons but I'm looking at much larger networks (N>1000)... 

Thanks, 

Luc Berthouze

[Marcel Stimberg]

Hi Luc,

expressions are only allowed to use a restricted subset of Python, indexing of arrays is not supported (there's an open issue for that, but it is a complicated issue and not something that is high on our list: https://github.com/brian-team/brian2/issues/388). For connecting synapses based on an existing structure, you'd not use string-based creation but instead you'd explicitly specify the list of source and target indices:
    A = randint(2,size=(4,4))
    rows, cols = nonzero(A)
    S.connect(rows, cols)  # or cols, rows...

Best,
  Marcel

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New paper about Brian 2: Stimberg M, Goodman DFM, Benichoux V, Brette R (2014).Equation-oriented specification of neural models for simulations. Frontiers Neuroinf, doi: 10.3389/fninf.2014.00006.
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[luc.be...@gmail.com]

Thanks, this is very helpful.

Luc Berthouze