Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

update all tutorials #176

Merged
merged 1 commit into from
Nov 30, 2023
Merged

update all tutorials #176

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
52 changes: 23 additions & 29 deletions tutorials/01_small_network.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

85 changes: 28 additions & 57 deletions tutorials/02_setting_parameters.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

132 changes: 65 additions & 67 deletions tutorials/03_gradient.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@
"outputs": [],
"source": [
"# I have experienced stability issues with float32.\n",
"from jax.config import config\n",
"from jax import config\n",
"config.update(\"jax_enable_x64\", True)\n",
"config.update(\"jax_platform_name\", \"cpu\")\n",
"\n",
Expand All @@ -44,8 +44,6 @@
"metadata": {},
"outputs": [],
"source": [
"import time\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import jax\n",
"import jax.numpy as jnp\n",
Expand Down Expand Up @@ -128,7 +126,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 11,
"id": "ff784bcb",
"metadata": {},
"outputs": [],
Expand All @@ -138,7 +136,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 12,
"id": "222f9a00",
"metadata": {},
"outputs": [],
Expand All @@ -148,15 +146,15 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 13,
"id": "90affb0c-dc77-47c7-be3c-18e2829cc820",
"metadata": {},
"outputs": [],
"source": [
"for cell_ind in range(5):\n",
" network.cell(cell_ind).branch(1).comp(0.0).record()\n",
" \n",
"current = jx.step_current(i_delay, i_dur, i_amp, time_vec)\n",
"current = jx.step_current(i_delay, i_dur, i_amp, dt, t_max)\n",
"for stim_ind in range(2):\n",
" network.cell(stim_ind).branch(1).comp(0.0).stimulate(current)"
]
Expand All @@ -179,10 +177,18 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 14,
"id": "10cb5b1e",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of newly added trainable parameters: 1. Total number of trainable parameters: 1\n"
]
}
],
"source": [
"network.make_trainable(\"radius\")"
]
Expand All @@ -197,10 +203,18 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 15,
"id": "c90be7f3",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of newly added trainable parameters: 200. Total number of trainable parameters: 201\n"
]
}
],
"source": [
"network.cell(\"all\").branch(\"all\").comp(\"all\").make_trainable(\"gNa\")"
]
Expand All @@ -223,10 +237,18 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 16,
"id": "f31901bd",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of newly added trainable parameters: 1. Total number of trainable parameters: 202\n"
]
}
],
"source": [
"network.make_trainable(\"gS\")"
]
Expand All @@ -241,10 +263,18 @@
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 17,
"id": "12fe7828",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of newly added trainable parameters: 6. Total number of trainable parameters: 208\n"
]
}
],
"source": [
"network.GlutamateSynapse(\"all\").make_trainable(\"gS\")"
]
Expand All @@ -267,7 +297,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 18,
"id": "40a48eea",
"metadata": {},
"outputs": [],
Expand All @@ -286,7 +316,7 @@
},
{
"cell_type": "code",
"execution_count": 17,
"execution_count": 19,
"id": "4eb3f8f1",
"metadata": {},
"outputs": [],
Expand All @@ -312,7 +342,7 @@
},
{
"cell_type": "code",
"execution_count": 24,
"execution_count": 20,
"id": "a29f1ac2",
"metadata": {},
"outputs": [],
Expand All @@ -332,7 +362,7 @@
},
{
"cell_type": "code",
"execution_count": 25,
"execution_count": 21,
"id": "f38d61a9",
"metadata": {},
"outputs": [],
Expand All @@ -342,7 +372,7 @@
},
{
"cell_type": "code",
"execution_count": 26,
"execution_count": 22,
"id": "9ac97e04",
"metadata": {},
"outputs": [],
Expand All @@ -362,22 +392,10 @@
},
{
"cell_type": "code",
"execution_count": 27,
"execution_count": 23,
"id": "d9ccf1b6",
"metadata": {},
"outputs": [
{
"ename": "ModuleNotFoundError",
"evalue": "No module named 'optax'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m/var/folders/j9/w7ftvg_16t1f9bgp1cy4bt1r0000gn/T/ipykernel_6746/3781452166.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0moptax\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'optax'"
]
}
],
"outputs": [],
"source": [
"import optax"
]
Expand All @@ -392,7 +410,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 24,
"id": "710a1545",
"metadata": {},
"outputs": [],
Expand All @@ -413,7 +431,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 25,
"id": "800f959e",
"metadata": {},
"outputs": [],
Expand All @@ -437,51 +455,31 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 26,
"id": "9d639efa",
"metadata": {},
"outputs": [],
"source": [
"opt_params = transform.inverse(params)\n",
"optimizer = optax.adam(learning_rate=1e-2)\n",
"optimizer = optax.adam(learning_rate=1e-1)\n",
"opt_state = optimizer.init(opt_params)"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 27,
"id": "0e4aebd0-283e-4165-8c24-4b6fb811135e",
"metadata": {},
"outputs": [],
"source": [
"epoch_losses = []\n",
"\n",
"for epoch in range(5):\n",
" loss_val, gradient = jitted_grad(opt_params)\n",
" updates, opt_state = optimizer.update(gradient, opt_state)\n",
" opt_params = optax.apply_updates(opt_params, updates)\n",
"\n",
" print(f\"epoch {epoch}, loss {loss_val}\")\n",
" epoch_losses.append(loss_val)\n",
" \n",
"final_params = transform.forward(opt_params)"
]
},
{
"cell_type": "code",
"execution_count": 43,
"id": "134af3e1",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"epoch 0, loss -64.97740510297487\n",
"epoch 1, loss -64.98296369502924\n",
"epoch 2, loss -64.98846441030534\n",
"epoch 3, loss -64.99390672049375\n",
"epoch 4, loss -64.99929015505666\n"
"epoch 0, loss -64.97740512171988\n",
"epoch 1, loss -65.03050878143252\n",
"epoch 2, loss -65.07820463321355\n",
"epoch 3, loss -65.12091871011332\n",
"epoch 4, loss -65.15909222980945\n"
]
}
],
Expand Down Expand Up @@ -510,9 +508,9 @@
],
"metadata": {
"kernelspec": {
"display_name": "jax",
"display_name": "neurax",
"language": "python",
"name": "jax"
"name": "python3"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -524,7 +522,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.10.11"
}
},
"nbformat": 4,
Expand Down
38 changes: 27 additions & 11 deletions tutorials/04_groups.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@
"outputs": [],
"source": [
"# I have experienced stability issues with float32.\n",
"from jax.config import config\n",
"from jax import config\n",
"config.update(\"jax_enable_x64\", True)\n",
"config.update(\"jax_platform_name\", \"cpu\")\n",
"\n",
Expand Down Expand Up @@ -618,7 +618,15 @@
"execution_count": 14,
"id": "3a399a56",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of newly added trainable parameters: 1. Total number of trainable parameters: 1\n"
]
}
],
"source": [
"network.fast_spiking.make_trainable(\"gNa\")"
]
Expand All @@ -640,7 +648,7 @@
{
"data": {
"text/plain": [
"[{'gNa': DeviceArray([[0.4]], dtype=float64)}]"
"[{'gNa': Array([[0.4]], dtype=float64)}]"
]
},
"execution_count": 15,
Expand All @@ -665,7 +673,15 @@
"execution_count": 16,
"id": "99a6c389",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of newly added trainable parameters: 3. Total number of trainable parameters: 4\n"
]
}
],
"source": [
"network.cell([0,1,3]).make_trainable(\"axial_resistivity\")"
]
Expand All @@ -679,10 +695,10 @@
{
"data": {
"text/plain": [
"[{'gNa': DeviceArray([[0.4]], dtype=float64)},\n",
" {'axial_resistivity': DeviceArray([[5000.],\n",
" [5000.],\n",
" [5000.]], dtype=float64)}]"
"[{'gNa': Array([[0.4]], dtype=float64)},\n",
" {'axial_resistivity': Array([[5000.],\n",
" [5000.],\n",
" [5000.]], dtype=float64)}]"
]
},
"execution_count": 17,
Expand All @@ -705,9 +721,9 @@
],
"metadata": {
"kernelspec": {
"display_name": "jax",
"display_name": "neurax",
"language": "python",
"name": "jax"
"name": "python3"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -719,7 +735,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.10.11"
}
},
"nbformat": 4,
Expand Down
Loading