Hi,
At least for me having the convention (https://nest-simulator.readthedocs.io/en/nest-2.20.1/ref_material/pynest_apis.html):
Such as:
Connect(pre,
post, conn_spec=None,
syn_spec=None,
model=None)
Got me kind of locked in “pre-post” …. But again, it is a convention and for me it is fine now that I know (I will be more careful …).
Best,
Ing
From: Markus Diesmann <diesmann@fz-juelich.de>
Sent: 19 January 2021 14:43
To: users@nest-simulator.org <users@nest-simulator.org>
Subject: [NEST Users] Re: Plot weight matrices example
Hi,
to remember the convention it is useful to think about
matrix multiplication
x_t+1 = W x_t
The weight matrix W projects (or propagates) the the old state at t
to the new state at t+1, where x is the state vector.
That's it.
Regards,
Markus
On 1/19/21 2:35 PM, Jochen Martin Eppler wrote:
> Dear Renato, dear Ing,
>
> While I agree with Renato about the fact that this convention is commonly used, I also agree with Ing that it might be not clear to everyone.
>
> Would one of you be willing (and able) to create a small pull request fixing the order and adding a short comment along the lines Ing presented, so other users don't get confused in the same way?
>
> Many thanks,
> Jochen!
>
>
> On 19.01.21 13:21, Ing Jyh Tsang wrote:
>>
>> Hi,
>>
>> Right, in that case I would switch the order when assigning :
>>
>> W_EE = np.zeros([len(E_neurons), len(E_neurons)])
>>
>> W_IE = np.zeros([len(E_neurons), len(I_neurons)])
>>
>> W_EI = np.zeros([len(I_neurons), len(E_neurons)])
>>
>> W_II = np.zeros([len(I_neurons), len(I_neurons)])
>>
>> So it would give a hint of the convention (at least for me), but as you said it is a convention, and indeed I was confused by it.
>>
>> Thanks a lot.
>>
>> *From:*Renato Duarte <rcfduarte@gmail.com>
>> *Sent:* Tuesday, 19 January 2021 13:04
>> *To:* NEST User Mailing List <users@nest-simulator.org>
>> *Subject:* [NEST Users] Re: Plot weight matrices example
>>
>> Hello,
>>
>> The use of "post-pre" notation when referring to synaptic connections is common practice in computational neuroscience.
>>
>> It does often give rise to some confusion, but it is common, for example, to refer to a synaptic connection from neuron j to neuron i as ij (post<-pre).
>>
>> This is the notation used in this example, where we refer to the connection from inhibitory to excitatory neurons (I->E) as EI (post-pre) and connections from excitatory to inhibitory neurons (E->I) as IE (post-pre).
>>
>> It is just a matter of convention.
>>
>> Best regards,
>>
>> Renato Duarte
>>
>> On Jan 19 2021, at 12:43 pm, Ing Jyh Tsang <ingjyh.tsang@uantwerpen.be <mailto:ingjyh.tsang@uantwerpen.be>> wrote:
>>
>> HI,
>>
>> I may be mistaken, but isn't the EI and IE index switched (https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnest-simulator.readthedocs.io%2Fen%2Fstable%2Fauto_examples%2Fplot_weight_matrices.html&data=04%7C01%7Cingjyh.tsang%40uantwerpen.be%7C5764feb7e87540d76bcb08d8bc803967%7C792e08fb2d544a8eaf72202548136ef6%7C0%7C0%7C637466606906760985%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=JP5sD3gnOT3bTcQ35ob83TCVgoOvHcbyWpxnfeXbqJw%3D&reserved=0
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnest-simulator.readthedocs.io%2Fen%2Fstable%2Fauto_examples%2Fplot_weight_matrices.html&data=04%7C01%7Cingjyh.tsang%40uantwerpen.be%7C5764feb7e87540d76bcb08d8bc803967%7C792e08fb2d544a8eaf72202548136ef6%7C0%7C0%7C637466606906760985%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=JP5sD3gnOT3bTcQ35ob83TCVgoOvHcbyWpxnfeXbqJw%3D&reserved=0>)
?
>>
>> a_EI = nest.GetConnections(I_neurons, E_neurons)
>>
>> c_EI = nest.GetStatus(a_EI, keys='weight')
>>
>> a_IE = nest.GetConnections(E_neurons, I_neurons)
>>
>> c_IE = nest.GetStatus(a_IE, keys='weight')
>>
>> for idx, n in enumerate(a_EI):
>>
>> W_EI[n[0] - min(I_neurons), n[1] - min(E_neurons)] += c_EI[idx]
>>
>> for idx, n in enumerate(a_IE):
>>
>> W_IE[n[0] - min(E_neurons), n[1] - min(I_neurons)] += c_IE[idx]
>>
>> Thanks,
>>
>> _______________________________________________
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>>
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>
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> Institute for Advanced Simulation
>
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