`tsodyks_synapse` and `tsodyks2_synapse` models have different behavior for short term depression
12 Dec
2024
12 Dec
'24
12:05 p.m.
Hello,
I have followed the example script comparing `tsodyks_synapse` and `tsodyks2_synapse`
models, which can be found here:
https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod…
Using the parameter set for depression instead of facilitation I found that
`tsodyks2_synapse` model leads to weird peaks of synaptic currents (at least I would not
expect that for short term depression) - during the second stimulation the weight
rescaling seems to be shifted by one spike compared to tsodyks_synapse (as if parameter
"u" would be updated after rescaling the weight instead of before).
Does anybody know why is there this difference between the two synapse models?
Thank you.
All the best,
PH
16 Dec
16 Dec
11:01 a.m.
Dear Pavel,
I can confirm you observation, and I share your surprise. Intuitively,
one would expect that the synaptic state should return to the initial
state after the long period of silence. However, after consulting the
source papers (todyks_synapse: doi:10.1523/JNEUROSCI.20-01-j0003.2000,
tsodyks2_synapse: doi:10.1016/S0893-6080(01)00144-7) and looking at the
NEST code, I conclude that what the example shows is indeed the intended
behaviour.
A key difference between tsodyks_synapse and todyks2_synapse is the
order of update steps: upon arrival of the presynaptic spike,
tsodyks_synapse first updates the synapse state (x,y,z,u; see lines
258-277 in tsodyks_synapse.h), and then reports the new weight (line 285
in tsodyks_synapse.h). In tsodyks2_synapse, this is reversed: first, the
synaptic weight is computed based on the current (i.e., the old) synapse
state (line 236 in tsodyks2_synapse.h), and then the synapse state is
updated (lines 243,244 in tsodyks2_synapse.h). When the first spike of
the second burst of presynaptic spikes arrives in the example
(https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod…),
the recovery value of tsodyks2_synapse still is where it was at the end
of the first burst of spikes (before the break). This is exactly how the
model is defined in (Maass and Markram, 2002;
doi:10.1016/S0893-6080(01)00144-7; see equations (1-5)). It needs one
more spike to really "recover".
I hope this clarifies things a bit.
Best
Tom
On 12.12.24 12:05, Pavel Haman wrote:
Hello,
I have followed the example script comparing `tsodyks_synapse` and `tsodyks2_synapse`
models, which can be found here:
https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod…
Using the parameter set for depression instead of facilitation I found that
`tsodyks2_synapse` model leads to weird peaks of synaptic currents (at least I would not
expect that for short term depression) - during the second stimulation the weight
rescaling seems to be shifted by one spike compared to tsodyks_synapse (as if parameter
"u" would be updated after rescaling the weight instead of before).
Does anybody know why is there this difference between the two synapse models?
Thank you.
All the best,
PH
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
---
Dr. Tom Tetzlaff
Institute for Advanced Simulation (IAS-6)
Computational and Systems Neuroscience
Jülich Research Centre
Jülich, Germany
https://www.fz-juelich.de/profile/tetzlaff_t
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
-----------------------------------------------------------------------
-----------------------------------------------------------------------
11:14 a.m.
Hi Tom,
Thanks for your input on this! I was just looking at the code too. It seems that the order
of updates (first update adaptation variables, then send spike, versus first send spike,
then update adaptation variables) was changed, in order to prevent the adaptation from
kicking in for the very first spike to ever go through the synapse. See
https://github.com/nest/nest-simulator/pull/1672/.) Notice that t_lastspike is initialised
to zero, rather than some "special" value like -1. It is possible that this fix
was erroneous, in that it ends up affecting not just the first-ever spike, but also
subsequent spikes. I am investigating a bit more, but if you are convinced that the
current behaviour is the correct one, then I can stop investigating.
Much obliged!
Charl
On Mon, Dec 16, 2024, at 11:01, Tom Tetzlaff wrote:
Dear Pavel,
I can confirm you observation, and I share your surprise. Intuitively,
one would expect that the synaptic state should return to the initial
state after the long period of silence. However, after consulting the
source papers (todyks_synapse: doi:10.1523/JNEUROSCI.20-01-j0003.2000,
tsodyks2_synapse: doi:10.1016/S0893-6080(01)00144-7) and looking at the
NEST code, I conclude that what the example shows is indeed the intended
behaviour.
A key difference between tsodyks_synapse and todyks2_synapse is the
order of update steps: upon arrival of the presynaptic spike,
tsodyks_synapse first updates the synapse state (x,y,z,u; see lines
258-277 in tsodyks_synapse.h), and then reports the new weight (line
285
in tsodyks_synapse.h). In tsodyks2_synapse, this is reversed: first,
the
synaptic weight is computed based on the current (i.e., the old)
synapse
state (line 236 in tsodyks2_synapse.h), and then the synapse state is
updated (lines 243,244 in tsodyks2_synapse.h). When the first spike of
the second burst of presynaptic spikes arrives in the example
(https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod…),
the recovery value of tsodyks2_synapse still is where it was at the end
of the first burst of spikes (before the break). This is exactly how
the
model is defined in (Maass and Markram, 2002;
doi:10.1016/S0893-6080(01)00144-7; see equations (1-5)). It needs one
more spike to really "recover".
I hope this clarifies things a bit.
Best
Tom
On 12.12.24 12:05, Pavel Haman wrote:
Hello,
I have followed the example script comparing `tsodyks_synapse` and `tsodyks2_synapse`
models, which can be found here:
https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod…
Using the parameter set for depression instead of facilitation I found that
`tsodyks2_synapse` model leads to weird peaks of synaptic currents (at least I would not
expect that for short term depression) - during the second stimulation the weight
rescaling seems to be shifted by one spike compared to tsodyks_synapse (as if parameter
"u" would be updated after rescaling the weight instead of before).
Does anybody know why is there this difference between the two synapse models?
Thank you.
All the best,
PH
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
---
Dr. Tom Tetzlaff
Institute for Advanced Simulation (IAS-6)
Computational and Systems Neuroscience
Jülich Research Centre
Jülich, Germany
https://www.fz-juelich.de/profile/tetzlaff_t
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
-----------------------------------------------------------------------
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Attachments:
* smime.p7s
11:41 a.m.
A little follow-up: I made a pull request with a suggested fix for this issue:
https://github.com/nest/nest-simulator/pull/3384
Tom, Pavel, would you mind having a look to see if this addresses the issue?
Again, much obliged!
Charl
On Mon, Dec 16, 2024, at 11:14, Charl Linssen wrote:
Hi Tom,
Thanks for your input on this! I was just looking at the code too. It
seems that the order of updates (first update adaptation variables,
then send spike, versus first send spike, then update adaptation
variables) was changed, in order to prevent the adaptation from kicking
in for the very first spike to ever go through the synapse. See
https://github.com/nest/nest-simulator/pull/1672/.) Notice that
t_lastspike is initialised to zero, rather than some "special" value
like -1. It is possible that this fix was erroneous, in that it ends up
affecting not just the first-ever spike, but also subsequent spikes. I
am investigating a bit more, but if you are convinced that the current
behaviour is the correct one, then I can stop investigating.
Much obliged!
Charl
On Mon, Dec 16, 2024, at 11:01, Tom Tetzlaff wrote:
Dear Pavel,
I can confirm you observation, and I share your surprise. Intuitively,
one would expect that the synaptic state should return to the initial
state after the long period of silence. However, after consulting the
source papers (todyks_synapse: doi:10.1523/JNEUROSCI.20-01-j0003.2000,
tsodyks2_synapse: doi:10.1016/S0893-6080(01)00144-7) and looking at the
NEST code, I conclude that what the example shows is indeed the intended
behaviour.
A key difference between tsodyks_synapse and todyks2_synapse is the
order of update steps: upon arrival of the presynaptic spike,
tsodyks_synapse first updates the synapse state (x,y,z,u; see lines
258-277 in tsodyks_synapse.h), and then reports the new weight (line
285
in tsodyks_synapse.h). In tsodyks2_synapse, this is reversed: first,
the
synaptic weight is computed based on the current (i.e., the old)
synapse
state (line 236 in tsodyks2_synapse.h), and then the synapse state is
updated (lines 243,244 in tsodyks2_synapse.h). When the first spike of
the second burst of presynaptic spikes arrives in the example
(https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod…),
the recovery value of tsodyks2_synapse still is where it was at the end
of the first burst of spikes (before the break). This is exactly how
the
model is defined in (Maass and Markram, 2002;
doi:10.1016/S0893-6080(01)00144-7; see equations (1-5)). It needs one
more spike to really "recover".
I hope this clarifies things a bit.
Best
Tom
On 12.12.24 12:05, Pavel Haman wrote:
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org Hello,
I have followed the example script comparing `tsodyks_synapse` and `tsodyks2_synapse`
models, which can be found here:
https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod…
Using the parameter set for depression instead of facilitation I found that
`tsodyks2_synapse` model leads to weird peaks of synaptic currents (at least I would not
expect that for short term depression) - during the second stimulation the weight
rescaling seems to be shifted by one spike compared to tsodyks_synapse (as if parameter
"u" would be updated after rescaling the weight instead of before).
Does anybody know why is there this difference between the two synapse models?
Thank you.
All the best,
PH
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
---
Dr. Tom Tetzlaff
Institute for Advanced Simulation (IAS-6)
Computational and Systems Neuroscience
Jülich Research Centre
Jülich, Germany
https://www.fz-juelich.de/profile/tetzlaff_t
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
-----------------------------------------------------------------------
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Attachments:
* smime.p7s
17 Dec
17 Dec
12:22 p.m.
Hello Tom and Charl,
thank you for your time, explanations and replies. You confirmed what I
thought was happening.
I quickly checked the paper (Maass and Markram, 2002;
doi:10.1016/S0893-6080(01)00144-7) and equations (1-5).
I think that the model should not update weights with delay of one spike,
since $\Delta t_n$ in the equations is actually $t_{n+1}-t_{n}$, i.e.
referring to the new spike (it is explained in the sentence before
equations), not to older spikes. (I believe here could be the issue, since
interpreting $\Delta t_n$, as I would naturally do, as $t_{n}-t_{n-1}$
leads to this one spike delay of updates)
Effective weight for spike $n+1$, $A_{n+1}$ is given as
$A_{n+1}= A u_{n+1} R_{n+1}$
and $u_{n+1}$ depends on the times of the new spike $t_{n+1}$ and previous
spike $t_{n}$
I will check Charl's PR later this week.
All the best,
Pavel
po 16. 12. 2024 v 22:19 odesílatel Charl Linssen <nest-users(a)turingbirds.com>
napsal:
A little follow-up: I made a pull request with a
suggested fix for this
issue: https://github.com/nest/nest-simulator/pull/3384
Tom, Pavel, would you mind having a look to see if this addresses the
issue?
Again, much obliged!
Charl
On Mon, Dec 16, 2024, at 11:14, Charl Linssen wrote:
Hi Tom,
Thanks for your input on this! I was just looking at the code too. It
seems that the order of updates (first update adaptation variables,
then send spike, versus first send spike, then update adaptation
variables) was changed, in order to prevent the adaptation from kicking
in for the very first spike to ever go through the synapse. See
https://github.com/nest/nest-simulator/pull/1672/.) Notice that
t_lastspike is initialised to zero, rather than some "special" value
like -1. It is possible that this fix was erroneous, in that it ends up
affecting not just the first-ever spike, but also subsequent spikes. I
am investigating a bit more, but if you are convinced that the current
behaviour is the correct one, then I can stop investigating.
Much obliged!
Charl
On Mon, Dec 16, 2024, at 11:01, Tom Tetzlaff wrote:
> Dear Pavel,
>
> I can confirm you observation, and I share your surprise. Intuitively,
> one would expect that the synaptic state should return to the initial
> state after the long period of silence. However, after consulting the
> source papers (todyks_synapse: doi:10.1523/JNEUROSCI.20-01-j0003.2000,
> tsodyks2_synapse: doi:10.1016/S0893-6080(01)00144-7) and looking at the
> NEST code, I conclude that what the example shows is indeed the
intended
> behaviour.
>
> A key difference between tsodyks_synapse and todyks2_synapse is the
> order of update steps: upon arrival of the presynaptic spike,
> tsodyks_synapse first updates the synapse state (x,y,z,u; see lines
> 258-277 in tsodyks_synapse.h), and then reports the new weight (line
> 285
> in tsodyks_synapse.h). In tsodyks2_synapse, this is reversed: first,
> the
> synaptic weight is computed based on the current (i.e., the old)
> synapse
> state (line 236 in tsodyks2_synapse.h), and then the synapse state is
> updated (lines 243,244 in tsodyks2_synapse.h). When the first spike of
> the second burst of presynaptic spikes arrives in the example
> (
https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod…),
> the recovery value of tsodyks2_synapse still
is where it was at the end
> of the first burst of spikes (before the break). This is exactly how
> the
> model is defined in (Maass and Markram, 2002;
> doi:10.1016/S0893-6080(01)00144-7; see equations (1-5)). It needs one
> more spike to really "recover".
>
> I hope this clarifies things a bit.
>
> Best
> Tom
>
>
>
> On 12.12.24 12:05, Pavel Haman wrote:
>> Hello,
>>
>> I have followed the example script comparing `tsodyks_synapse` and
`tsodyks2_synapse` models, which can be found here:
>>
https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod…
>>
>>> Using the parameter
set for depression instead of facilitation I found
that `tsodyks2_synapse` model leads to weird peaks of synaptic currents (at
least I would not expect that for short term depression) - during the
second stimulation the weight rescaling seems to be shifted by one spike
compared to tsodyks_synapse (as if parameter "u" would be updated after
rescaling the weight instead of before).
>>
>>> Does anybody know why
is there this difference between the two synapse
models?
>>
>>> Thank you.
>>
>>> All the best,
>>> PH
>>> _______________________________________________
>>> NEST Users mailing list -- users(a)nest-simulator.org
>>> To unsubscribe send an email to users-leave(a)nest-simulator.org
>>
>> --
>> ---
>>
>> Dr. Tom Tetzlaff
>> Institute for Advanced Simulation (IAS-6)
>> Computational and Systems Neuroscience
>> Jülich Research Centre
>> Jülich, Germany
>>
>> https://www.fz-juelich.de/profile/tetzlaff_t
>>
>>
>> -----------------------------------------------------------------------
>> -----------------------------------------------------------------------
>> Forschungszentrum Jülich GmbH
>> 52425 Jülich
>> Sitz der Gesellschaft: Jülich
>> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
>> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
>> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
>> Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
>> -----------------------------------------------------------------------
>> -----------------------------------------------------------------------
>>
>> _______________________________________________
>> NEST Users mailing list -- users(a)nest-simulator.org
>> To unsubscribe send an email to users-leave(a)nest-simulator.org
>>
>> Attachments:
>> * smime.p7s
> _______________________________________________
> 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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2:06 p.m.
Hi Pavel,
you are right. Indeed, I assumed that $\Delta{}t_n=t_n-t_{n-1}$, rather
than $\Delta{}t_n=t_{n+1}-t_n$, as used in the paper. Well spotted. This
makes much more sense now. Sorry for the confusion. I agree that the
current NEST implementation is hence wrong, obviously the result of an
earlier "fix", as Charl explained. I had a quick look at Charl's PR and
think this will solve the problem.
Best
Tom
On 17.12.24 12:22, Pavel Haman wrote:
Hello Tom and Charl,
thank you for your time, explanations and replies. You confirmed what I
thought was happening.
I quickly checked the paper (Maass and Markram, 2002;
doi:10.1016/S0893-6080(01)00144-7) and equations (1-5).
I think that the model should not update weights with delay of one
spike, since $\Delta t_n$ in the equations is actually $t_{n+1}-t_{n}$,
i.e. referring to the new spike (it is explained in the sentence before
equations), not to older spikes. (I believe here could be the issue,
since interpreting $\Delta t_n$, as I would naturally do, as
$t_{n}-t_{n-1}$ leads to this one spike delay of updates)
Effective weight for spike $n+1$, $A_{n+1}$ is given as
$A_{n+1}= A u_{n+1} R_{n+1}$
and $u_{n+1}$ depends on the times of the new spike $t_{n+1}$ and
previous spike $t_{n}$
I will check Charl's PR later this week.
All the best,
Pavel
po 16. 12. 2024 v 22:19 odesílatel Charl Linssen
<nest-users(a)turingbirds.com <mailto:nest-users@turingbirds.com>> napsal:
A little follow-up: I made a pull request with a suggested fix for
this issue: https://github.com/nest/nest-simulator/pull/3384
<https://github.com/nest/nest-simulator/pull/3384>
Tom, Pavel, would you mind having a look to see if this addresses
the issue?
Again, much obliged!
Charl
On Mon, Dec 16, 2024, at 11:14, Charl Linssen wrote:
--
---
Dr. Tom Tetzlaff
Institute for Advanced Simulation (IAS-6)
Computational and Systems Neuroscience
Jülich Research Centre
Jülich, Germany
https://www.fz-juelich.de/profile/tetzlaff_t
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
-----------------------------------------------------------------------
-----------------------------------------------------------------------
Hi Tom,
Thanks for your input on this! I was just looking at the code
too. It
seems that the order of updates (first update
adaptation variables,
then send spike, versus first send spike, then update adaptation
variables) was changed, in order to prevent the adaptation from
kicking
in for the very first spike to ever go through
the synapse. See
https://github.com/nest/nest-simulator/pull/1672/
<https://github.com/nest/nest-simulator/pull/1672/>.) Notice that
t_lastspike is initialised to zero, rather than
some "special" value
like -1. It is possible that this fix was erroneous, in that it
ends up
affecting not just the first-ever spike, but also
subsequent
spikes. I
am investigating a bit more, but if you are
convinced that the
current
behaviour is the correct one, then I can stop
investigating.
Much obliged!
Charl
On Mon, Dec 16, 2024, at 11:01, Tom Tetzlaff wrote:
> Dear Pavel,
>
> I can confirm you observation, and I share your surprise.
Intuitively,
> one would expect that the synaptic state
should return to the
initial
> state after the long period of silence.
However, after
consulting the
> source papers (todyks_synapse:
doi:10.1523/JNEUROSCI.20-01-j0003.2000,
> tsodyks2_synapse:
doi:10.1016/S0893-6080(01)00144-7) and looking
at the
> NEST code, I conclude that what the example
shows is indeed the
intended
> behaviour.
>
> A key difference between tsodyks_synapse and todyks2_synapse is the
> order of update steps: upon arrival of the presynaptic spike,
> tsodyks_synapse first updates the synapse state (x,y,z,u; see lines
> 258-277 in tsodyks_synapse.h), and then reports the new weight
(line
> 285
> in tsodyks_synapse.h). In tsodyks2_synapse, this is reversed:
first,
> the
> synaptic weight is computed based on the current (i.e., the old)
> synapse
> state (line 236 in tsodyks2_synapse.h), and then the synapse
state is
> updated (lines 243,244 in
tsodyks2_synapse.h). When the first
spike of
> the second burst of presynaptic spikes
arrives in the example
>
(https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod…
<https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsodyks2_synapse.html>),
> the recovery value of tsodyks2_synapse still
is where it was at
the end
> of the first burst of spikes (before the
break). This is exactly
how
> the
> model is defined in (Maass and Markram, 2002;
> doi:10.1016/S0893-6080(01)00144-7; see equations (1-5)). It
needs one
> more spike to really "recover".
>
> I hope this clarifies things a bit.
>
> Best
> Tom
>
>
>
> On 12.12.24 12:05, Pavel Haman wrote:
>> Hello,
>>
>> I have followed the example script comparing `tsodyks_synapse`
and `tsodyks2_synapse` models, which can be found here:
>>
https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod…
<https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsodyks2_synapse.html>
>>
>>> Using the parameter set for depression instead of facilitation
I found that `tsodyks2_synapse` model leads to weird peaks of
synaptic currents (at least I would not expect that for short term
depression) - during the second stimulation the weight rescaling
seems to be shifted by one spike compared to tsodyks_synapse (as if
parameter "u" would be updated after rescaling the weight instead of
before).
>>
>>> Does anybody know why is there this difference between the two
synapse models?
>>
>>> Thank you.
>>
>>> All the best,
>>> PH
>>> _______________________________________________
>>> 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>
>
> --
> ---
>
> Dr. Tom Tetzlaff
> Institute for Advanced Simulation (IAS-6)
> Computational and Systems Neuroscience
> Jülich Research Centre
> Jülich, Germany
>
> https://www.fz-juelich.de/profile/tetzlaff_t
<https://www.fz-juelich.de/profile/tetzlaff_t>
>
>
>
-----------------------------------------------------------------------
>
-----------------------------------------------------------------------
>> Forschungszentrum Jülich GmbH
>> 52425 Jülich
>> Sitz der Gesellschaft: Jülich
>> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
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16 Dec
16 Dec
2:44 p.m.
Hi Charl,
this is interesting. What I meant was that the tsodyks2 synapse is --as
far as I can tell-- implemented in NEST exactly as it is described in
the original publication (Maass and Markram, 2002), in particular the
order of reporting the weight (sending the spike) and updating the
synapse state. In this sense, the NEST implementation does the right
thing. If this order has been changed in the past in NEST, then this was
good in this respect. Whether it is perhaps more meaningful to swap this
order is a different question. Changing this would lead to a different
model.
Best
Tom
On 16.12.24 11:14, Charl Linssen wrote:
Hi Tom,
Thanks for your input on this! I was just looking at the code too. It seems that the
order of updates (first update adaptation variables, then send spike, versus first send
spike, then update adaptation variables) was changed, in order to prevent the adaptation
from kicking in for the very first spike to ever go through the synapse. See
https://github.com/nest/nest-simulator/pull/1672/.) Notice that t_lastspike is initialised
to zero, rather than some "special" value like -1. It is possible that this fix
was erroneous, in that it ends up affecting not just the first-ever spike, but also
subsequent spikes. I am investigating a bit more, but if you are convinced that the
current behaviour is the correct one, then I can stop investigating.
Much obliged!
Charl
On Mon, Dec 16, 2024, at 11:01, Tom Tetzlaff wrote:
--
---
Dr. Tom Tetzlaff
Institute for Advanced Simulation (IAS-6)
Computational and Systems Neuroscience
Jülich Research Centre
Jülich, Germany
https://www.fz-juelich.de/profile/tetzlaff_t
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Dear Pavel,
I can confirm you observation, and I share your surprise. Intuitively,
one would expect that the synaptic state should return to the initial
state after the long period of silence. However, after consulting the
source papers (todyks_synapse: doi:10.1523/JNEUROSCI.20-01-j0003.2000,
tsodyks2_synapse: doi:10.1016/S0893-6080(01)00144-7) and looking at the
NEST code, I conclude that what the example shows is indeed the intended
behaviour.
A key difference between tsodyks_synapse and todyks2_synapse is the
order of update steps: upon arrival of the presynaptic spike,
tsodyks_synapse first updates the synapse state (x,y,z,u; see lines
258-277 in tsodyks_synapse.h), and then reports the new weight (line
285
in tsodyks_synapse.h). In tsodyks2_synapse, this is reversed: first,
the
synaptic weight is computed based on the current (i.e., the old)
synapse
state (line 236 in tsodyks2_synapse.h), and then the synapse state is
updated (lines 243,244 in tsodyks2_synapse.h). When the first spike of
the second burst of presynaptic spikes arrives in the example
(https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod…),
the recovery value of tsodyks2_synapse still is where it was at the end
of the first burst of spikes (before the break). This is exactly how
the
model is defined in (Maass and Markram, 2002;
doi:10.1016/S0893-6080(01)00144-7; see equations (1-5)). It needs one
more spike to really "recover".
I hope this clarifies things a bit.
Best
Tom
On 12.12.24 12:05, Pavel Haman wrote:
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Hello,
I have followed the example script comparing `tsodyks_synapse` and `tsodyks2_synapse`
models, which can be found here:
https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod…
Using the parameter set for depression instead of facilitation I found that
`tsodyks2_synapse` model leads to weird peaks of synaptic currents (at least I would not
expect that for short term depression) - during the second stimulation the weight
rescaling seems to be shifted by one spike compared to tsodyks_synapse (as if parameter
"u" would be updated after rescaling the weight instead of before).
Does anybody know why is there this difference between the two synapse models?
Thank you.
All the best,
PH
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Dr. Tom Tetzlaff
Institute for Advanced Simulation (IAS-6)
Computational and Systems Neuroscience
Jülich Research Centre
Jülich, Germany
https://www.fz-juelich.de/profile/tetzlaff_t
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Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
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Tom Tetzlaff