scArches_crossspecies.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "60eae13d",
   "metadata": {},
   "source": [
    "# scArches cross-species transfer learning"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "67792820",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "os.chdir('../')\n",
    "import warnings\n",
    "warnings.simplefilter(action='ignore', category=FutureWarning)\n",
    "warnings.simplefilter(action='ignore', category=UserWarning)\n",
    "\n",
    "import scanpy as sc\n",
    "import torch\n",
    "import scarches as sca\n",
    "from scarches.dataset.trvae.data_handling import remove_sparsity\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "import gdown\n",
    "\n",
    "sc.settings.set_figure_params(dpi=200, frameon=False)\n",
    "sc.set_figure_params(dpi=200)\n",
    "sc.set_figure_params(figsize=(4, 4))\n",
    "torch.set_printoptions(precision=3, sci_mode=False, edgeitems=7)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "fc52c060",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 60976 × 2000\n",
       "    obs: 'orig.ident', 'nCount_RNA', 'nFeature_RNA', 'seurat_clusters', 'RNA_snn_res.0.5', 'RNA_snn_res.0.6', 'RNA_snn_res.0.7', 'RNA_snn_res.0.8', 'RNA_snn_res.0.9', 'RNA_snn_res.1', 'RNA_snn_res.1.1', 'RNA_snn_res.1.2', 'RNA_snn_res.1.3', 'RNA_snn_res.1.4', 'RNA_snn_res.1.5', 'RNA_snn_res.1.6', 'RNA_snn_res.1.7', 'RNA_snn_res.1.8', 'RNA_snn_res.1.9', 'RNA_snn_res.2', 'tissue', 'is_HD', 'global.cluster', 'global.cluster2', 'hpv_status', 'RNA_snn_res.2.1', 'RNA_snn_res.2.2', 'RNA_snn_res.2.3', 'RNA_snn_res.2.4', 'RNA_snn_res.2.5', 'RNA_snn_res.2.6', 'RNA_snn_res.2.7', 'RNA_snn_res.2.8', 'RNA_snn_res.2.9', 'RNA_snn_res.3', 'tissue_hpv', 'global.cluster4', 'global.cluster5', 'AEG_global.cluster'\n",
       "    var: 'vst.mean', 'vst.variance', 'vst.variance.expected', 'vst.variance.standardized', 'vst.variable'\n",
       "    obsm: 'X_harmony', 'X_pca', 'X_umap'\n",
       "    varm: 'HARMONY', 'PCs'"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "moc2 = sc.read('/Volumes/hdlab/Projects/HNC_SPORE/Mouse_to_human_comparsion/scArches_comparison/moc2_seurat.h5ad')\n",
    "moc2\n",
    "\n",
    "hnc = sc.read('/Volumes/hdlab/Projects/HNC_SPORE/Mouse_to_human_comparsion/scArches_comparison/hnc_human_seurat.h5ad')\n",
    "hnc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "484d1d33",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[34mINFO    \u001b[0m Using batches from adata.obs\u001b[1m[\u001b[0m\u001b[32m\"orig.ident\"\u001b[0m\u001b[1m]\u001b[0m                                          \n",
      "\u001b[34mINFO    \u001b[0m Using labels from adata.obs\u001b[1m[\u001b[0m\u001b[32m\"global.cluster4\"\u001b[0m\u001b[1m]\u001b[0m                                      \n",
      "\u001b[34mINFO    \u001b[0m Using data from adata.X                                                             \n",
      "\u001b[34mINFO    \u001b[0m Successfully registered anndata object containing \u001b[1;36m60976\u001b[0m cells, \u001b[1;36m2000\u001b[0m vars, \u001b[1;36m26\u001b[0m        \n",
      "         batches, \u001b[1;36m28\u001b[0m labels, and \u001b[1;36m0\u001b[0m proteins. Also registered \u001b[1;36m0\u001b[0m extra categorical covariates  \n",
      "         and \u001b[1;36m0\u001b[0m extra continuous covariates.                                                  \n",
      "\u001b[34mINFO    \u001b[0m Please do not further modify adata until model is trained.                          \n"
     ]
    }
   ],
   "source": [
    "sca.dataset.setup_anndata(hnc, batch_key= 'orig.ident', labels_key = 'global.cluster4')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "dcb1aca9",
   "metadata": {},
   "outputs": [],
   "source": [
    "vae = sca.models.SCVI(hnc)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "f0681d46",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "GPU available: False, used: False\n",
      "TPU available: False, using: 0 TPU cores\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Epoch 1/131:   0%|          | 0/131 [00:00<?, ?it/s]"
     ]
    },
    {
     "ename": "ValueError",
     "evalue": "Expected parameter loc (Tensor of shape (128, 10)) of distribution Normal(loc: torch.Size([128, 10]), scale: torch.Size([128, 10])) to satisfy the constraint Real(), but found invalid values:\ntensor([[nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        ...,\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan]],\n       grad_fn=<AddmmBackward0>)",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-24-a64959953ca9>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mvae\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtrain\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0;31m#array_sum = np.sum(hnc.X)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0;31m#array_has_nan = np.isnan(array_sum)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0;31m#print(array_sum)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/scvi/model/base/_training_mixin.py\u001b[0m in \u001b[0;36mtrain\u001b[0;34m(self, max_epochs, use_gpu, train_size, validation_size, batch_size, early_stopping, plan_kwargs, **trainer_kwargs)\u001b[0m\n\u001b[1;32m     75\u001b[0m             \u001b[0;34m**\u001b[0m\u001b[0mtrainer_kwargs\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     76\u001b[0m         )\n\u001b[0;32m---> 77\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mrunner\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/scvi/train/_trainrunner.py\u001b[0m in \u001b[0;36m__call__\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m     70\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraining_plan\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mn_obs_training\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata_splitter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mn_train\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     71\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 72\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtrainer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraining_plan\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata_splitter\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     73\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_update_history\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     74\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/scvi/train/_trainer.py\u001b[0m in \u001b[0;36mfit\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m    175\u001b[0m                     \u001b[0mmessage\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"`LightningModule.configure_optimizers` returned `None`\"\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    176\u001b[0m                 )\n\u001b[0;32m--> 177\u001b[0;31m             \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/trainer/trainer.py\u001b[0m in \u001b[0;36mfit\u001b[0;34m(self, model, train_dataloader, val_dataloaders, datamodule)\u001b[0m\n\u001b[1;32m    458\u001b[0m         )\n\u001b[1;32m    459\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 460\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_run\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodel\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    461\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    462\u001b[0m         \u001b[0;32massert\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstate\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstopped\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/trainer/trainer.py\u001b[0m in \u001b[0;36m_run\u001b[0;34m(self, model)\u001b[0m\n\u001b[1;32m    756\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    757\u001b[0m         \u001b[0;31m# dispatch `start_training` or `start_evaluating` or `start_predicting`\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 758\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdispatch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    759\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    760\u001b[0m         \u001b[0;31m# plugin will finalized fitting (e.g. ddp_spawn will load trained model)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/trainer/trainer.py\u001b[0m in \u001b[0;36mdispatch\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    797\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maccelerator\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstart_predicting\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    798\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 799\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maccelerator\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstart_training\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    800\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    801\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mrun_stage\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/accelerators/accelerator.py\u001b[0m in \u001b[0;36mstart_training\u001b[0;34m(self, trainer)\u001b[0m\n\u001b[1;32m     94\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     95\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mstart_training\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtrainer\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m'pl.Trainer'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 96\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraining_type_plugin\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstart_training\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtrainer\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     97\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     98\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mstart_evaluating\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtrainer\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m'pl.Trainer'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/plugins/training_type/training_type_plugin.py\u001b[0m in \u001b[0;36mstart_training\u001b[0;34m(self, trainer)\u001b[0m\n\u001b[1;32m    142\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mstart_training\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtrainer\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m'pl.Trainer'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    143\u001b[0m         \u001b[0;31m# double dispatch to initiate the training loop\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 144\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_results\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtrainer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_stage\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    145\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    146\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mstart_evaluating\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtrainer\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m'pl.Trainer'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/trainer/trainer.py\u001b[0m in \u001b[0;36mrun_stage\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    807\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpredicting\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    808\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_predict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 809\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_train\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    810\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    811\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_pre_training_routine\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/trainer/trainer.py\u001b[0m in \u001b[0;36mrun_train\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    869\u001b[0m                 \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprofiler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprofile\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"run_training_epoch\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    870\u001b[0m                     \u001b[0;31m# run train epoch\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 871\u001b[0;31m                     \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtrain_loop\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_training_epoch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    872\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    873\u001b[0m                 \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmax_steps\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmax_steps\u001b[0m \u001b[0;34m<=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mglobal_step\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/trainer/training_loop.py\u001b[0m in \u001b[0;36mrun_training_epoch\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    497\u001b[0m             \u001b[0;31m# ------------------------------------\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    498\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtrainer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprofiler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprofile\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"run_training_batch\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 499\u001b[0;31m                 \u001b[0mbatch_output\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_training_batch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbatch\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdataloader_idx\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    500\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    501\u001b[0m             \u001b[0;31m# when returning -1 from train_step, we end epoch early\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/trainer/training_loop.py\u001b[0m in \u001b[0;36mrun_training_batch\u001b[0;34m(self, batch, batch_idx, dataloader_idx)\u001b[0m\n\u001b[1;32m    736\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    737\u001b[0m                         \u001b[0;31m# optimizer step\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 738\u001b[0;31m                         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moptimizer_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0moptimizer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mopt_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtrain_step_and_backward_closure\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    739\u001b[0m                         \u001b[0;32mif\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtrainer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moptimizers\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    740\u001b[0m                             \u001b[0;31m# revert back to previous state\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/trainer/training_loop.py\u001b[0m in \u001b[0;36moptimizer_step\u001b[0;34m(self, optimizer, opt_idx, batch_idx, train_step_and_backward_closure)\u001b[0m\n\u001b[1;32m    432\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    433\u001b[0m         \u001b[0;31m# model hook\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 434\u001b[0;31m         model_ref.optimizer_step(\n\u001b[0m\u001b[1;32m    435\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtrainer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcurrent_epoch\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    436\u001b[0m             \u001b[0mbatch_idx\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/core/lightning.py\u001b[0m in \u001b[0;36moptimizer_step\u001b[0;34m(self, epoch, batch_idx, optimizer, optimizer_idx, optimizer_closure, on_tpu, using_native_amp, using_lbfgs)\u001b[0m\n\u001b[1;32m   1401\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1402\u001b[0m         \"\"\"\n\u001b[0;32m-> 1403\u001b[0;31m         \u001b[0moptimizer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstep\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mclosure\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0moptimizer_closure\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1404\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1405\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0moptimizer_zero_grad\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mepoch\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch_idx\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moptimizer\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mOptimizer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moptimizer_idx\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/core/optimizer.py\u001b[0m in \u001b[0;36mstep\u001b[0;34m(self, closure, *args, **kwargs)\u001b[0m\n\u001b[1;32m    212\u001b[0m             \u001b[0mprofiler_name\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34mf\"optimizer_step_and_closure_{self._optimizer_idx}\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    213\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 214\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__optimizer_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mclosure\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mclosure\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mprofiler_name\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mprofiler_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    215\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_total_optimizer_step_calls\u001b[0m \u001b[0;34m+=\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    216\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/core/optimizer.py\u001b[0m in \u001b[0;36m__optimizer_step\u001b[0;34m(self, closure, profiler_name, **kwargs)\u001b[0m\n\u001b[1;32m    132\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    133\u001b[0m         \u001b[0;32mwith\u001b[0m \u001b[0mtrainer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprofiler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprofile\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprofiler_name\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 134\u001b[0;31m             \u001b[0mtrainer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maccelerator\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moptimizer_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0moptimizer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_optimizer_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlambda_closure\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mclosure\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    135\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    136\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mstep\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mclosure\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mOptional\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mCallable\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/accelerators/accelerator.py\u001b[0m in \u001b[0;36moptimizer_step\u001b[0;34m(self, optimizer, opt_idx, lambda_closure, **kwargs)\u001b[0m\n\u001b[1;32m    327\u001b[0m         )\n\u001b[1;32m    328\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mmake_optimizer_step\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 329\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_optimizer_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0moptimizer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mopt_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlambda_closure\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    330\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprecision_plugin\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpost_optimizer_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0moptimizer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mopt_idx\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    331\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraining_type_plugin\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpost_optimizer_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0moptimizer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mopt_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/accelerators/accelerator.py\u001b[0m in \u001b[0;36mrun_optimizer_step\u001b[0;34m(self, optimizer, optimizer_idx, lambda_closure, **kwargs)\u001b[0m\n\u001b[1;32m    334\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moptimizer\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mOptimizer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moptimizer_idx\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlambda_closure\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mCallable\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mAny\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    335\u001b[0m     ) -> None:\n\u001b[0;32m--> 336\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraining_type_plugin\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moptimizer_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0moptimizer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlambda_closure\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mlambda_closure\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    337\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    338\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0moptimizer_zero_grad\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcurrent_epoch\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch_idx\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moptimizer\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mOptimizer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mopt_idx\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/plugins/training_type/training_type_plugin.py\u001b[0m in \u001b[0;36moptimizer_step\u001b[0;34m(self, optimizer, lambda_closure, **kwargs)\u001b[0m\n\u001b[1;32m    191\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    192\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0moptimizer_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moptimizer\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moptim\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mOptimizer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlambda_closure\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mCallable\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 193\u001b[0;31m         \u001b[0moptimizer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstep\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mclosure\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mlambda_closure\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    194\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    195\u001b[0m     \u001b[0;34m@\u001b[0m\u001b[0mproperty\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/torch/optim/optimizer.py\u001b[0m in \u001b[0;36mwrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m     86\u001b[0m                 \u001b[0mprofile_name\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"Optimizer.step#{}.step\"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__class__\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__name__\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     87\u001b[0m                 \u001b[0;32mwith\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mautograd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprofiler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrecord_function\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprofile_name\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 88\u001b[0;31m                     \u001b[0;32mreturn\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     89\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mwrapper\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     90\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/torch/autograd/grad_mode.py\u001b[0m in \u001b[0;36mdecorate_context\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m     26\u001b[0m         \u001b[0;32mdef\u001b[0m \u001b[0mdecorate_context\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     27\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__class__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 28\u001b[0;31m                 \u001b[0;32mreturn\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     29\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mcast\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mF\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdecorate_context\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     30\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/torch/optim/adam.py\u001b[0m in \u001b[0;36mstep\u001b[0;34m(self, closure)\u001b[0m\n\u001b[1;32m     90\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mclosure\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     91\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0menable_grad\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 92\u001b[0;31m                 \u001b[0mloss\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mclosure\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     93\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     94\u001b[0m         \u001b[0;32mfor\u001b[0m \u001b[0mgroup\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mparam_groups\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/trainer/training_loop.py\u001b[0m in \u001b[0;36mtrain_step_and_backward_closure\u001b[0;34m()\u001b[0m\n\u001b[1;32m    730\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    731\u001b[0m                         \u001b[0;32mdef\u001b[0m \u001b[0mtrain_step_and_backward_closure\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 732\u001b[0;31m                             result = self.training_step_and_backward(\n\u001b[0m\u001b[1;32m    733\u001b[0m                                 \u001b[0msplit_batch\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mopt_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moptimizer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtrainer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhiddens\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    734\u001b[0m                             )\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/trainer/training_loop.py\u001b[0m in \u001b[0;36mtraining_step_and_backward\u001b[0;34m(self, split_batch, batch_idx, opt_idx, optimizer, hiddens)\u001b[0m\n\u001b[1;32m    821\u001b[0m         \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtrainer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprofiler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprofile\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"training_step_and_backward\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    822\u001b[0m             \u001b[0;31m# lightning module hook\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 823\u001b[0;31m             \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraining_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msplit_batch\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mopt_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mhiddens\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    824\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_curr_step_result\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    825\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/trainer/training_loop.py\u001b[0m in \u001b[0;36mtraining_step\u001b[0;34m(self, split_batch, batch_idx, opt_idx, hiddens)\u001b[0m\n\u001b[1;32m    288\u001b[0m             \u001b[0mmodel_ref\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_results\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mResult\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    289\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtrainer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprofiler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprofile\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"training_step\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 290\u001b[0;31m                 \u001b[0mtraining_step_output\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtrainer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maccelerator\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraining_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    291\u001b[0m                 \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtrainer\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maccelerator\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpost_training_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    292\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/accelerators/accelerator.py\u001b[0m in \u001b[0;36mtraining_step\u001b[0;34m(self, args)\u001b[0m\n\u001b[1;32m    202\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    203\u001b[0m         \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprecision_plugin\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtrain_step_context\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraining_type_plugin\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtrain_step_context\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 204\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraining_type_plugin\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraining_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    205\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    206\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mpost_training_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/pytorch_lightning/plugins/training_type/training_type_plugin.py\u001b[0m in \u001b[0;36mtraining_step\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m    153\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    154\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mtraining_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 155\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlightning_module\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraining_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    156\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    157\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mpost_training_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/scvi/train/_trainingplans.py\u001b[0m in \u001b[0;36mtraining_step\u001b[0;34m(self, batch, batch_idx, optimizer_idx)\u001b[0m\n\u001b[1;32m    150\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;34m\"kl_weight\"\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloss_kwargs\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    151\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloss_kwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m{\u001b[0m\u001b[0;34m\"kl_weight\"\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mkl_weight\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 152\u001b[0;31m         \u001b[0m_\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mscvi_loss\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mforward\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbatch\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mloss_kwargs\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloss_kwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    153\u001b[0m         \u001b[0mreconstruction_loss\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mscvi_loss\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreconstruction_loss\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    154\u001b[0m         \u001b[0;31m# pytorch lightning automatically backprops on \"loss\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/scvi/train/_trainingplans.py\u001b[0m in \u001b[0;36mforward\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m    145\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mforward\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    146\u001b[0m         \u001b[0;34m\"\"\"Passthrough to `model.forward()`.\"\"\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 147\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodule\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    148\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    149\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mtraining_step\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moptimizer_idx\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/torch/nn/modules/module.py\u001b[0m in \u001b[0;36m_call_impl\u001b[0;34m(self, *input, **kwargs)\u001b[0m\n\u001b[1;32m   1100\u001b[0m         if not (self._backward_hooks or self._forward_hooks or self._forward_pre_hooks or _global_backward_hooks\n\u001b[1;32m   1101\u001b[0m                 or _global_forward_hooks or _global_forward_pre_hooks):\n\u001b[0;32m-> 1102\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mforward_call\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0minput\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1103\u001b[0m         \u001b[0;31m# Do not call functions when jit is used\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1104\u001b[0m         \u001b[0mfull_backward_hooks\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnon_full_backward_hooks\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/scvi/module/base/_decorators.py\u001b[0m in \u001b[0;36mauto_transfer_args\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m     30\u001b[0m         \u001b[0;31m# decorator only necessary after training\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     31\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraining\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 32\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     33\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     34\u001b[0m         \u001b[0mdevice\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdevice\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mp\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mparameters\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/scvi/module/base/_base_module.py\u001b[0m in \u001b[0;36mforward\u001b[0;34m(self, tensors, get_inference_input_kwargs, get_generative_input_kwargs, inference_kwargs, generative_kwargs, loss_kwargs, compute_loss)\u001b[0m\n\u001b[1;32m    143\u001b[0m             \u001b[0mtensors\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mget_inference_input_kwargs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    144\u001b[0m         )\n\u001b[0;32m--> 145\u001b[0;31m         \u001b[0minference_outputs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minference\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0minference_inputs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0minference_kwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    146\u001b[0m         generative_inputs = self._get_generative_input(\n\u001b[1;32m    147\u001b[0m             \u001b[0mtensors\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0minference_outputs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mget_generative_input_kwargs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/scvi/module/base/_decorators.py\u001b[0m in \u001b[0;36mauto_transfer_args\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m     30\u001b[0m         \u001b[0;31m# decorator only necessary after training\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     31\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtraining\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 32\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     33\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     34\u001b[0m         \u001b[0mdevice\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdevice\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mp\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mparameters\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/scvi/module/_vae.py\u001b[0m in \u001b[0;36minference\u001b[0;34m(self, x, batch_index, cont_covs, cat_covs, n_samples)\u001b[0m\n\u001b[1;32m    274\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    275\u001b[0m             \u001b[0mcategorical_input\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtuple\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 276\u001b[0;31m         \u001b[0mqz_m\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mqz_v\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mz\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mz_encoder\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mencoder_input\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch_index\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0mcategorical_input\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    277\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    278\u001b[0m         \u001b[0mql_m\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mql_v\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/torch/nn/modules/module.py\u001b[0m in \u001b[0;36m_call_impl\u001b[0;34m(self, *input, **kwargs)\u001b[0m\n\u001b[1;32m   1100\u001b[0m         if not (self._backward_hooks or self._forward_hooks or self._forward_pre_hooks or _global_backward_hooks\n\u001b[1;32m   1101\u001b[0m                 or _global_forward_hooks or _global_forward_pre_hooks):\n\u001b[0;32m-> 1102\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mforward_call\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0minput\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1103\u001b[0m         \u001b[0;31m# Do not call functions when jit is used\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1104\u001b[0m         \u001b[0mfull_backward_hooks\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnon_full_backward_hooks\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/scvi/nn/_base_components.py\u001b[0m in \u001b[0;36mforward\u001b[0;34m(self, x, *cat_list)\u001b[0m\n\u001b[1;32m    292\u001b[0m         \u001b[0mq_m\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmean_encoder\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mq\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    293\u001b[0m         \u001b[0mq_v\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvar_activation\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvar_encoder\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mq\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvar_eps\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 294\u001b[0;31m         \u001b[0mlatent\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mz_transformation\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mreparameterize_gaussian\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mq_m\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mq_v\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    295\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mq_m\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mq_v\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlatent\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    296\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/scvi/nn/_base_components.py\u001b[0m in \u001b[0;36mreparameterize_gaussian\u001b[0;34m(mu, var)\u001b[0m\n\u001b[1;32m     11\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     12\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mreparameterize_gaussian\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmu\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvar\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 13\u001b[0;31m     \u001b[0;32mreturn\u001b[0m \u001b[0mNormal\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmu\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvar\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msqrt\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrsample\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     14\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     15\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/torch/distributions/normal.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, loc, scale, validate_args)\u001b[0m\n\u001b[1;32m     48\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     49\u001b[0m             \u001b[0mbatch_shape\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msize\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 50\u001b[0;31m         \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mNormal\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbatch_shape\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalidate_args\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mvalidate_args\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     51\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     52\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mexpand\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch_shape\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_instance\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/anaconda3/lib/python3.8/site-packages/torch/distributions/distribution.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, batch_shape, event_shape, validate_args)\u001b[0m\n\u001b[1;32m     53\u001b[0m                 \u001b[0mvalid\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mconstraint\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcheck\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     54\u001b[0m                 \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mvalid\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mall\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 55\u001b[0;31m                     raise ValueError(\n\u001b[0m\u001b[1;32m     56\u001b[0m                         \u001b[0;34mf\"Expected parameter {param} \"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     57\u001b[0m                         \u001b[0;34mf\"({type(value).__name__} of shape {tuple(value.shape)}) \"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mValueError\u001b[0m: Expected parameter loc (Tensor of shape (128, 10)) of distribution Normal(loc: torch.Size([128, 10]), scale: torch.Size([128, 10])) to satisfy the constraint Real(), but found invalid values:\ntensor([[nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        ...,\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan],\n        [nan, nan, nan, nan, nan, nan, nan, nan, nan, nan]],\n       grad_fn=<AddmmBackward0>)"
     ]
    }
   ],
   "source": [
    "vae.train()\n",
    "#array_sum = np.sum(hnc.X)\n",
    "#array_has_nan = np.isnan(array_sum)\n",
    "#print(array_sum)"
   ]
  }
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