From 48bd1dd75f378050213216daeaf50f1096d0c2c8 Mon Sep 17 00:00:00 2001 From: Martin Kim <46072231+martinkim0@users.noreply.github.com> Date: Thu, 7 Dec 2023 11:28:58 -0800 Subject: [PATCH] Fix autotune tutorial (#200) --- tuning/autotune_scvi.ipynb | 332 +++---------------------------------- 1 file changed, 25 insertions(+), 307 deletions(-) diff --git a/tuning/autotune_scvi.ipynb b/tuning/autotune_scvi.ipynb index 10c2f6e..3a5f5a2 100644 --- a/tuning/autotune_scvi.ipynb +++ b/tuning/autotune_scvi.ipynb @@ -53,7 +53,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -65,7 +65,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -81,24 +81,9 @@ }, { "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Global seed set to 0\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Last run with scvi-tools version: 1.0.3\n" - ] - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "scvi.settings.seed = 0\n", "print(\"Last run with scvi-tools version:\", scvi.__version__)" @@ -113,13 +98,14 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ "sc.set_figure_params(figsize=(4, 4), frameon=False)\n", "torch.set_float32_matmul_precision(\"high\")\n", "save_dir = tempfile.TemporaryDirectory()\n", + "scvi.settings.logging_dir = save_dir.name\n", "\n", "%config InlineBackend.print_figure_kwargs={\"facecolor\" : \"w\"}\n", "%config InlineBackend.figure_format=\"retina\"" @@ -135,31 +121,9 @@ }, { "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\u001b[34mINFO \u001b[0m Downloading file at \u001b[35m/tmp/tmp51dvndw4/\u001b[0m\u001b[95mhca_subsampled_20k.h5ad\u001b[0m \n", - "Downloading...: 100%|██████████| 65714/65714.0 [00:00<00:00, 110628.59it/s]\n" - ] - }, - { - "data": { - "text/plain": [ - "AnnData object with n_obs × n_vars = 18641 × 26662\n", - " obs: 'NRP', 'age_group', 'cell_source', 'cell_type', 'donor', 'gender', 'n_counts', 'n_genes', 'percent_mito', 'percent_ribo', 'region', 'sample', 'scrublet_score', 'source', 'type', 'version', 'cell_states', 'Used'\n", - " var: 'gene_ids-Harvard-Nuclei', 'feature_types-Harvard-Nuclei', 'gene_ids-Sanger-Nuclei', 'feature_types-Sanger-Nuclei', 'gene_ids-Sanger-Cells', 'feature_types-Sanger-Cells', 'gene_ids-Sanger-CD45', 'feature_types-Sanger-CD45', 'n_counts'\n", - " uns: 'cell_type_colors'" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "adata = scvi.data.heart_cell_atlas_subsampled(save_path=save_dir.name)\n", "adata" @@ -175,23 +139,9 @@ }, { "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "AnnData object with n_obs × n_vars = 18641 × 2000\n", - " obs: 'NRP', 'age_group', 'cell_source', 'cell_type', 'donor', 'gender', 'n_counts', 'n_genes', 'percent_mito', 'percent_ribo', 'region', 'sample', 'scrublet_score', 'source', 'type', 'version', 'cell_states', 'Used'\n", - " var: 'gene_ids-Harvard-Nuclei', 'feature_types-Harvard-Nuclei', 'gene_ids-Sanger-Nuclei', 'feature_types-Sanger-Nuclei', 'gene_ids-Sanger-Cells', 'feature_types-Sanger-Cells', 'gene_ids-Sanger-CD45', 'feature_types-Sanger-CD45', 'n_counts', 'highly_variable', 'highly_variable_rank', 'means', 'variances', 'variances_norm'\n", - " uns: 'cell_type_colors', 'hvg'" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "sc.pp.highly_variable_genes(adata, n_top_genes=2000, flavor=\"seurat_v3\", subset=True)\n", "adata" @@ -215,7 +165,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -233,7 +183,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -254,144 +204,9 @@ }, { "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
ModelTuner registry for SCVI\n",
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                  Tunable hyperparameters                  \n",
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-       "┃      Hyperparameter      ┃ Default value ┃    Source    ┃\n",
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       Available metrics        \n",
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-       "┃     Metric      ┃    Mode    ┃\n",
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-       "┃ Hyperparameter ┃ Sample function ┃  Arguments  ┃ Keyword arguments ┃\n",
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Tune Status

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Current time:2023-07-27 03:16:53
Running for: 00:02:40.69
Memory: 34.8/125.7 GiB
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System Info

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Bracket: Iter 64.000: -451.93446350097656 | Iter 32.000: -453.1311798095703 | Iter 16.000: -459.6698303222656 | Iter 8.000: -469.3856506347656 | Iter 4.000: -481.6686248779297 | Iter 2.000: -517.1959228515625 | Iter 1.000: -642.4600219726562
Logical resource usage: 10.0/20 CPUs, 1.0/1 GPUs (0.0/1.0 accelerator_type:G)\n", - "
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Trial Status

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Trial name status loc n_hidden n_layers lr validation_loss
_trainable_9ca2fa7cTERMINATED128.32.142.133:965309 256 30.000589003 455.212
_trainable_7d98a8b2TERMINATED128.32.142.133:965309 64 20.000350049 737.187
_trainable_ff1772f6TERMINATED128.32.142.133:965309 64 30.000918661 556.365
_trainable_5fa3a6f6TERMINATED128.32.142.133:965309 256 30.000161977 770.872
_trainable_53fa3aa1TERMINATED128.32.142.133:965309 128 10.00122786 452.142
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