19 Jan
2021
19 Jan
'21
12:43 p.m.
HI,
I may be mistaken, but isn't the EI and IE index switched
(https://nest-simulator.readthedocs.io/en/stable/auto_examples/plot_weight_m…)
?
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,
19 Jan
19 Jan
1:04 p.m.
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(a)uantwerpen.be> wrote:
HI,
I may be mistaken, but isn't the EI and IE index switched
(https://nest-simulator.readthedocs.io/en/stable/auto_examples/plot_weight_m…)
?
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,
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
1:21 p.m.
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(a)gmail.com>
Sent: Tuesday, 19 January 2021 13:04
To: NEST User Mailing List <users(a)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://nest-simulator.readthedocs.io/en/stable/auto_examples/plot_weight_m…)
?
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,
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
2:35 p.m.
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:
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
2:43 p.m.
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:
--
Prof. Dr. Markus Diesmann, Director
Inst of Neuroscience and Medicine (INM-6) Tel +49-2461-61-4748 (secr)
Computational and Systems Neuroscience & +49-2461-61-9301 (lab)
Institute for Advanced Simulation (IAS-6) Fax +49-2461-61-9460
Theoretical Neuroscience Mob +49-175-290-1943
Jülich Research Centre and JARA Institute I
Jülich, Germany
Department of Psychiatry, Psychotherapy and Psychosomatics
School of Medicine, RWTH Aachen University
Aachen, Germany
www.nest-initiative.org www.csn.fz-juelich.de
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(a)gmail.com>
*Sent:* Tuesday, 19 January 2021 13:04
*To:* NEST User Mailing List <users(a)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(a)uantwerpen.be
<mailto:ingjyh.tsang@uantwerpen.be>> wrote:
HI,
I may be mistaken, but isn't the EI and IE index switched
(https://nest-simulator.readthedocs.io/en/stable/auto_examples/plot_weight_m…
<https://nest-simulator.readthedocs.io/en/stable/auto_examples/plot_weight_matrices.html>)
?
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,
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
<mailto:users@nest-simulator.org>
To unsubscribe send an email to users-leave(a)nest-simulator.org
<mailto:users-leave@nest-simulator.org>
Sent from Mailspring
_______________________________________________
NEST Users mailing list --users(a)nest-simulator.org
To unsubscribe send an email tousers-leave(a)nest-simulator.org
--
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
3:04 p.m.
Hi,
At least for me having the convention
(https://nest-simulator.readthedocs.io/en/nest-2.20.1/ref_material/pynest_ap…):
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(a)fz-juelich.de>
Sent: 19 January 2021 14:43
To: users(a)nest-simulator.org <users(a)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:
--
Prof. Dr. Markus Diesmann, Director
Inst of Neuroscience and Medicine (INM-6) Tel +49-2461-61-4748 (secr)
Computational and Systems Neuroscience & +49-2461-61-9301 (lab)
Institute for Advanced Simulation (IAS-6) Fax +49-2461-61-9460
Theoretical Neuroscience Mob +49-175-290-1943
Jülich Research Centre and JARA Institute I
Jülich, Germany
Department of Psychiatry, Psychotherapy and Psychosomatics
School of Medicine, RWTH Aachen University
Aachen, Germany
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.nest-i…
https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.csn.fz…
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(a)gmail.com>
*Sent:* Tuesday, 19 January 2021 13:04
*To:* NEST User Mailing List <users(a)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(a)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-simu…
<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,
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
<mailto:users@nest-simulator.org>
To unsubscribe send an email to users-leave(a)nest-simulator.org
<mailto:users-leave@nest-simulator.org>
Sent from Mailspring
_______________________________________________
NEST Users mailing list --users(a)nest-simulator.org
To unsubscribe send an email tousers-leave(a)nest-simulator.org
--
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
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1186
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5 comments
5 participants
participants (5)
-
Ing Jyh Tsang -
Ing Jyh Tsang
-
Jochen Martin Eppler -
Markus Diesmann -
Renato Duarte