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47b015aa · Didi Hou · Administrator · 3ac823ad · 47b015aa
Commit 47b015aa authored 1 year ago by Didi Hou Committed by Administrator 1 year ago
--- 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}"
   ]
  },

 %% Cell type:markdown id:b1331599 tags:

 # Down-scaled multi-area model

 %% Cell type:markdown id:3e163b35-5330-48ca-8c7e-9e0a884520ca tags:

 ## Import dependencies

 %% Cell type:code id:96517739 tags:

 ``` python
 %matplotlib inline
 import matplotlib.pyplot as plt
 import numpy as np
 import os
 ```

 %% Cell type:code id:7e07b0d0 tags:

 ``` python
 !pip install nested_dict dicthash
 ```

+%% Cell type:code id:1d440c07-9b69-4e52-8573-26b13493bc5a tags:
+
+``` python
+%%html
+<style>
+table {float:left}
+</style>
+```
+
+%% Output
+
+
 %% Cell type:markdown id:98555af1-a5c5-4db6-85dc-6d07e40f38cc tags:

 ## Create config file

 %% Cell type:code id:72c170e4 tags:

 ``` python
 with open('config.py', 'w') as fp:
    fp.write(
 '''import os
 base_path = os.path.abspath(".")
 data_path = os.path.abspath("simulations")
 jobscript_template = "python {base_path}/run_simulation.py {label}"
 submit_cmd = "bash -c"
 ''')
 ```

 %% Cell type:code id:2784f76b tags:

 ``` python
 from multiarea_model import MultiAreaModel
 ```

 %% Cell type:markdown id:df83f5ea-1c4b-44d3-9926-01786aa46e14 tags:

 ## Specify paramters of model

 %% Cell type:markdown id:2cedd26b tags:

 ### 1. Scaling parameter
+**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>
 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.**

 %% Cell type:code id:e940bb6b tags:

 ``` python
 scale_down_to = 0.005
 ```

 %% Cell type:markdown id:d53f1eab tags:

 ### 2. Model and simulation parameters

+%% Cell type:markdown id:14bac1ce-4ba0-47ec-84b2-9d3c72bc96ec tags:
+
+#### 2.1 Connection parameters (conn_params)
+
+%% Cell type:markdown id:41d80271-f60e-49f4-9759-f8ad26097b2d tags:
+
+| Parameter | Parameter description | Variable                    | Value              | Value description |
+|:---------:|:----------------------|:---------------------------:|:------------------:|:------------------|
+|           |                       | replace_non_simulated_areas | 'het_poisson_stat' |                   |
+|           |                       | g                           | -11.               |                   |
+|           |                       | K_stable                    | 'K_stable.npy'     |                   |
+|           |                       | fac_nu_ext_TH               | 1.2                |                   |
+|           |                       | fac_nu_ext_5E               | 1.125              |                   |
+|           |                       | fac_nu_ext_6E               | 1.41666667         |                   |
+|           |                       | av_indegree_V1              | 3950.              |                   |
+
 %% Cell type:code id:7af3a191 tags:

 ``` python
 conn_params = {'replace_non_simulated_areas': 'het_poisson_stat',
               'g': -11.,

               'K_stable': 'K_stable.npy',
               'fac_nu_ext_TH': 1.2,
               'fac_nu_ext_5E': 1.125,
               'fac_nu_ext_6E': 1.41666667,
               'av_indegree_V1': 3950.}
+```
+
+%% Cell type:markdown id:1688ef55-2fdb-4800-97af-7ea62442c684 tags:
+
+#### 2.2 Input parameters (input_params)
+
+%% Cell type:markdown id:5127920c-2a89-42d0-9d87-889f7b7474d9 tags:
+
+| Parameter | Parameter description | Variable                      | Value                | Value description |
+|:---------:|:----------------------|:-----------------------------:|:--------------------:|:------------------|
+|           |                       | rate_ext                      |      10.             |                   |
+
+%% Cell type:code id:2195cddb-bd82-47a8-ba74-cf0169a6801d tags:
+
+``` python
 input_params = {'rate_ext': 10.}
+```
+
+%% Cell type:markdown id:aefa84c8-baaa-4afa-96c6-5d57d174b286 tags:
+
+#### 2.3 Neuron parameters (neuron_params)
+
+%% Cell type:markdown id:ab5eb287-e638-401f-9e2c-892f88c3ee90 tags:
+
+| Parameter | Parameter description | Variable                    | Value              | Value description |
+|:---------:|:----------------------|:---------------------------:|:------------------:|:------------------|
+|           |                       | V0_mean                     | -150.              |                   |
+|           |                       | V0_sd                       | 50.                |                   |
+
+%% Cell type:code id:f69ad836-70b8-4ebe-b46a-25f48dc3ca7c tags:
+
+``` python
 neuron_params = {'V0_mean': -150.,
                 'V0_sd': 50.}
+```
+
+%% Cell type:markdown id:cdb50fb3-4bb9-446a-ab1c-d008b7e5bfa4 tags:
+
+#### 2.4 Network parameters (network_params)
+
+%% Cell type:markdown id:3e437aca-1fd0-4296-a0f6-a346b1319903 tags:
+
+| Parameter | Parameter description | Variable              | Value                         | Value description |
+|:---------:|:----------------------|:---------------------:|:-----------------------------:|:------------------|
+|           |                       | N_scaling             | scale_down_to                 |                   |
+|           |                       | K_scaling             | scale_down_to                 |                   |
+|           |                       | fullscale_rates       | 'tests/fullscale_rates.json'  |                   |
+|           |                       | input_params          | input_params                  |                   |
+|           |                       | connection_params     | conn_params                   |                   |
+|           |                       | neuron_params         | neuron_params                 |                   |
+
+%% Cell type:code id:0aa9a9bf-b95d-4643-82a0-e29a49bb58df tags:
+
+``` python
 network_params = {'N_scaling': scale_down_to,
                  'K_scaling': scale_down_to,
                  'fullscale_rates': 'tests/fullscale_rates.json',
                  'input_params': input_params,
                  'connection_params': conn_params,
                  'neuron_params': neuron_params}
 ```

 %% Cell type:markdown id:a0730f70-ed9b-4664-b677-3dda965a01ef tags:

-### 3. Simulation paramters
+### 3. Simulation paramters (sim_params)
+
+%% Cell type:markdown id:c989ee79-fa3d-405c-a1bf-da8ec884d878 tags:
+
+| Parameter | Parameter description | Variable             | Value              | Value description |
+|:---------:|:----------------------|:--------------------:|:------------------:|:------------------|
+|           |                       |t_sim                 |2000.               |                   |
+|           |                       |num_processes         |1                   |                   |
+|           |                       |local_num_threads     |1                   |                   |
+|           |                       |recording_dict        |input_params        |                   |
+|           |                       |record_vm             |False               |                   |

 %% Cell type:code id:21484ed3-295f-4d06-b757-2969aac429a4 tags:

 ``` python
 sim_params = {'t_sim': 2000.,
              'num_processes': 1,
              'local_num_threads': 1,
              'recording_dict': {'record_vm': False}}
+```
+
+%% Cell type:markdown id:79596d77-c105-45d0-9a57-2d15e31f1189 tags:

+### 4. Theory paramters (theory_params)
+
+%% Cell type:markdown id:18e0deda-1dec-4df8-b994-ef641b3c5aac tags:
+
+| Parameter | Parameter description | Variable              | Value                         | Value description |
+|:---------:|:----------------------|:---------------------:|:-----------------------------:|:------------------|
+|           |                       | dt                    | 0.1                           |                   |
+
+%% Cell type:code id:41edb350-36c3-4e19-829e-40d6ca9633a0 tags:
+
+``` python
 theory_params = {'dt': 0.1}
 ```

 %% Cell type:markdown id:de4a6703 tags:

 ## Instantiate a multi-area model, predict firing rates from theroy

 %% Cell type:code id:d409be95 tags:

 ``` python
 M = MultiAreaModel(network_params, simulation=True,
                   sim_spec=sim_params,
                   theory=True,
                   theory_spec=theory_params)
 ```

 %% Cell type:code id:918d907f tags:

 ``` python
 p, r = M.theory.integrate_siegert()
 print("Mean-field theory predicts an average "
      "rate of {0:.3f} spikes/s across all populations.".format(np.mean(r[:, -1])))
 ```

 %% Cell type:markdown id:0c1cad59-81d0-4e24-ac33-13c4ca8c6dec tags:

 ## Run the simulation

 %% Cell type:code id:15778e9c tags:

 ``` python
 M.simulation.simulate()
 ```

 %% Cell type:markdown id:9be9287d-4891-4b4b-bd19-cfc2ebed02ac tags:

 ## Load and process simulation results data

 %% Cell type:markdown id:8726a93d tags:

 ### 1. Load spike data

 %% Cell type:code id:cb8e3edd tags:

 ``` python
 data = np.loadtxt(M.simulation.data_dir + '/recordings/' + M.simulation.label + "-spikes-1-0.dat", skiprows=3)
 ```

 %% Cell type:markdown id:8793e033 tags:

 ### 2. Compute instantaneous rate per neuron across all populations

 %% Cell type:code id:9590223b tags:

 ``` python
 tsteps, spikecount = np.unique(data[:,1], return_counts=True)
 rate = spikecount / M.simulation.params['dt'] * 1e3 / np.sum(M.N_vec)
 ```

 %% Cell type:markdown id:57ff902c-d6ce-4f96-9e4f-8e3e7166ab66 tags:

 ## Simulation results visualization

 %% Cell type:markdown id:38ddd973 tags:

 ### 1. Instantaneous and mean rate

 %% Cell type:code id:bea30fc8 tags:

 ``` python
 fig, ax = plt.subplots()
 ax.plot(tsteps, rate)
 ax.plot(tsteps, np.average(rate)*np.ones(len(tsteps)), label='mean')
 ax.set_title('instantaneous rate across all populations')
 ax.set_xlabel('time (ms)')
 ax.set_ylabel('rate (spikes / s)')
 ax.set_xlim(0, sim_params['t_sim'])
 ax.set_ylim(0, 50)
 ax.legend()
 ```