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Merged
merged 1 commit into from
Jul 27, 2023
Merged

Update and rerun autotune #153

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65 changes: 35 additions & 30 deletions tuning/autotune_new_model.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -42,33 +42,30 @@
"## Installing required packages"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Uncomment the following lines in Google Colab in order to install `scvi-tools`:"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"!pip install --quiet hyperopt\n",
"!pip install --quiet \"ray[tune]\"\n",
"!pip install --quiet scvi-colab\n",
"from scvi_colab import install\n",
"# !pip install --quiet scvi-colab\n",
"# from scvi_colab import install\n",
"\n",
"install()"
"# install()"
]
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Global seed set to 0\n"
]
}
],
"outputs": [],
"source": [
"import jax\n",
"import jax.numpy as jnp\n",
Expand All @@ -81,9 +78,17 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Last run with scvi-tools version: 1.0.3\n"
]
}
],
"source": [
"scvi.settings.seed = 0\n",
"print(\"Last run with scvi-tools version:\", scvi.__version__)"
Expand All @@ -107,7 +112,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -176,7 +181,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -217,15 +222,15 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/martin/dev/scvi-tools/scvi/autotune/_manager.py:74: UserWarning: No default search space available for LassoTunable.\n",
" warnings.warn(\n"
"/home/martin/dev/scvi-tools/scvi/autotune/_manager.py:60: UserWarning: No default search space available for LassoTunable.\n",
" self._defaults = self._get_defaults(self._model_cls)\n"
]
},
{
Expand Down Expand Up @@ -334,7 +339,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -385,7 +390,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 8,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -496,7 +501,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -526,15 +531,15 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/martin/dev/scvi-tools/scvi/autotune/_manager.py:74: UserWarning: No default search space available for LassoModel.\n",
" warnings.warn(\n"
"/home/martin/dev/scvi-tools/scvi/autotune/_manager.py:60: UserWarning: No default search space available for LassoModel.\n",
" self._defaults = self._get_defaults(self._model_cls)\n"
]
},
{
Expand Down Expand Up @@ -649,7 +654,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.8"
"version": "3.11.4"
},
"orig_nbformat": 4,
"vscode": {
Expand Down
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