From 47b015aa0d74254d293c0e81124d55f8467beb5d Mon Sep 17 00:00:00 2001
From: didihou <didi.hou@rwth-aachen.de>
Date: Fri, 11 Aug 2023 14:15:17 +0200
Subject: [PATCH] /
---
multi-area-model.ipynb | 200 +++++++++++++++++++++++++++++++++++++++--
1 file changed, 192 insertions(+), 8 deletions(-)
diff --git a/multi-area-model.ipynb b/multi-area-model.ipynb
index f7ba497..92ec9be 100644
--- a/multi-area-model.ipynb
+++ b/multi-area-model.ipynb
@@ -39,6 +39,34 @@
"!pip install nested_dict dicthash"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "id": "1d440c07-9b69-4e52-8573-26b13493bc5a",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<style>\n",
+ "table {float:left}\n",
+ "</style>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "%%html\n",
+ "<style>\n",
+ "table {float:left}\n",
+ "</style>"
+ ]
+ },
{
"cell_type": "markdown",
"id": "98555af1-a5c5-4db6-85dc-6d07e40f38cc",
@@ -77,7 +105,9 @@
{
"cell_type": "markdown",
"id": "df83f5ea-1c4b-44d3-9926-01786aa46e14",
- "metadata": {},
+ "metadata": {
+ "tags": []
+ },
"source": [
"## Specify paramters of model"
]
@@ -85,9 +115,12 @@
{
"cell_type": "markdown",
"id": "2cedd26b",
- "metadata": {},
+ "metadata": {
+ "tags": []
+ },
"source": [
"### 1. Scaling parameter\n",
+ "**Scaling parameter** (scale_down_to) is the parameter defines the the ratio of the full scale multi-area model being down-scaled to a model with fewer neurons and indegrees so as to be simulated on machines with lower computational ability and the simulation results can be obtained in relative shorter period of time.<br> <br> \n",
"Neurons and indegrees are both scaled down to 0.5%, where the model can usually be simulated on a local machine.<br> **Warning: This will not yield reasonable dynamical results from the network and is only meant to demonstrate the simulation workflow.**"
]
},
@@ -109,6 +142,30 @@
"### 2. Model and simulation parameters"
]
},
+ {
+ "cell_type": "markdown",
+ "id": "14bac1ce-4ba0-47ec-84b2-9d3c72bc96ec",
+ "metadata": {},
+ "source": [
+ "#### 2.1 Connection parameters (conn_params)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "41d80271-f60e-49f4-9759-f8ad26097b2d",
+ "metadata": {},
+ "source": [
+ "| Parameter | Parameter description | Variable | Value | Value description |\n",
+ "|:---------:|:----------------------|:---------------------------:|:------------------:|:------------------|\n",
+ "| | | replace_non_simulated_areas | 'het_poisson_stat' | |\n",
+ "| | | g | -11. | |\n",
+ "| | | K_stable | 'K_stable.npy' | |\n",
+ "| | | fac_nu_ext_TH | 1.2 | |\n",
+ "| | | fac_nu_ext_5E | 1.125 | |\n",
+ "| | | fac_nu_ext_6E | 1.41666667 | |\n",
+ "| | | av_indegree_V1 | 3950. | |"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -123,10 +180,97 @@
" 'fac_nu_ext_TH': 1.2,\n",
" 'fac_nu_ext_5E': 1.125,\n",
" 'fac_nu_ext_6E': 1.41666667,\n",
- " 'av_indegree_V1': 3950.}\n",
- "input_params = {'rate_ext': 10.}\n",
+ " 'av_indegree_V1': 3950.}"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "1688ef55-2fdb-4800-97af-7ea62442c684",
+ "metadata": {},
+ "source": [
+ "#### 2.2 Input parameters (input_params)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "5127920c-2a89-42d0-9d87-889f7b7474d9",
+ "metadata": {},
+ "source": [
+ "| Parameter | Parameter description | Variable | Value | Value description |\n",
+ "|:---------:|:----------------------|:-----------------------------:|:--------------------:|:------------------|\n",
+ "| | | rate_ext | 10. | |"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "2195cddb-bd82-47a8-ba74-cf0169a6801d",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "input_params = {'rate_ext': 10.}"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "aefa84c8-baaa-4afa-96c6-5d57d174b286",
+ "metadata": {},
+ "source": [
+ "#### 2.3 Neuron parameters (neuron_params)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "ab5eb287-e638-401f-9e2c-892f88c3ee90",
+ "metadata": {},
+ "source": [
+ "| Parameter | Parameter description | Variable | Value | Value description |\n",
+ "|:---------:|:----------------------|:---------------------------:|:------------------:|:------------------|\n",
+ "| | | V0_mean | -150. | |\n",
+ "| | | V0_sd | 50. | |"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "f69ad836-70b8-4ebe-b46a-25f48dc3ca7c",
+ "metadata": {},
+ "outputs": [],
+ "source": [
"neuron_params = {'V0_mean': -150.,\n",
- " 'V0_sd': 50.}\n",
+ " 'V0_sd': 50.}"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "cdb50fb3-4bb9-446a-ab1c-d008b7e5bfa4",
+ "metadata": {},
+ "source": [
+ "#### 2.4 Network parameters (network_params)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "3e437aca-1fd0-4296-a0f6-a346b1319903",
+ "metadata": {},
+ "source": [
+ "| Parameter | Parameter description | Variable | Value | Value description |\n",
+ "|:---------:|:----------------------|:---------------------:|:-----------------------------:|:------------------|\n",
+ "| | | N_scaling | scale_down_to | |\n",
+ "| | | K_scaling | scale_down_to | |\n",
+ "| | | fullscale_rates | 'tests/fullscale_rates.json' | |\n",
+ "| | | input_params | input_params | |\n",
+ "| | | connection_params | conn_params | |\n",
+ "| | | neuron_params | neuron_params | |"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "0aa9a9bf-b95d-4643-82a0-e29a49bb58df",
+ "metadata": {},
+ "outputs": [],
+ "source": [
"network_params = {'N_scaling': scale_down_to,\n",
" 'K_scaling': scale_down_to,\n",
" 'fullscale_rates': 'tests/fullscale_rates.json',\n",
@@ -140,7 +284,21 @@
"id": "a0730f70-ed9b-4664-b677-3dda965a01ef",
"metadata": {},
"source": [
- "### 3. Simulation paramters"
+ "### 3. Simulation paramters (sim_params)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "c989ee79-fa3d-405c-a1bf-da8ec884d878",
+ "metadata": {},
+ "source": [
+ "| Parameter | Parameter description | Variable | Value | Value description |\n",
+ "|:---------:|:----------------------|:--------------------:|:------------------:|:------------------|\n",
+ "| | |t_sim |2000. | |\n",
+ "| | |num_processes |1 | |\n",
+ "| | |local_num_threads |1 | |\n",
+ "| | |recording_dict |input_params | |\n",
+ "| | |record_vm |False | |"
]
},
{
@@ -153,8 +311,34 @@
"sim_params = {'t_sim': 2000.,\n",
" 'num_processes': 1,\n",
" 'local_num_threads': 1,\n",
- " 'recording_dict': {'record_vm': False}}\n",
- "\n",
+ " 'recording_dict': {'record_vm': False}}"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "79596d77-c105-45d0-9a57-2d15e31f1189",
+ "metadata": {},
+ "source": [
+ "### 4. Theory paramters (theory_params)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "18e0deda-1dec-4df8-b994-ef641b3c5aac",
+ "metadata": {},
+ "source": [
+ "| Parameter | Parameter description | Variable | Value | Value description |\n",
+ "|:---------:|:----------------------|:---------------------:|:-----------------------------:|:------------------|\n",
+ "| | | dt | 0.1 | |"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "41edb350-36c3-4e19-829e-40d6ca9633a0",
+ "metadata": {},
+ "outputs": [],
+ "source": [
"theory_params = {'dt': 0.1}"
]
},
--
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