From c1667fdedff18cbe168a7ae0c167b91ae4863f68 Mon Sep 17 00:00:00 2001
From: Pablo E Garcia-Nieto <paedugar@gmail.com>
Date: Fri, 16 Jun 2023 16:18:27 -0600
Subject: [PATCH] run full notebook

---
 .../notebooks/experimental/pytorch.ipynb      | 188 ++++++++++++++++--
 1 file changed, 175 insertions(+), 13 deletions(-)

diff --git a/api/python/notebooks/experimental/pytorch.ipynb b/api/python/notebooks/experimental/pytorch.ipynb
index 5af72e253..54b0fd873 100644
--- a/api/python/notebooks/experimental/pytorch.ipynb
+++ b/api/python/notebooks/experimental/pytorch.ipynb
@@ -347,7 +347,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "id": "733ec2fb",
    "metadata": {},
    "outputs": [
@@ -355,10 +355,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Epoch 1: Train Loss: 0.1156352 Accuracy 0.4472\n",
-      "Epoch 2: Train Loss: 0.1096967 Accuracy 0.7261\n",
-      "Epoch 3: Train Loss: 0.1082206 Accuracy 0.7729\n",
-      "Epoch 4: Train Loss: 0.1071653 Accuracy 0.8268\n"
+      "Epoch 1: Train Loss: 0.1156322 Accuracy 0.4494\n",
+      "Epoch 2: Train Loss: 0.1095988 Accuracy 0.7357\n",
+      "Epoch 3: Train Loss: 0.1089615 Accuracy 0.7300\n",
+      "Epoch 4: Train Loss: 0.1080885 Accuracy 0.7275\n",
+      "Epoch 5: Train Loss: 0.1101440 Accuracy 0.4220\n"
      ]
     }
    ],
@@ -397,7 +398,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 10,
    "id": "d3e33edc",
    "metadata": {},
    "outputs": [],
@@ -417,10 +418,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 11,
    "id": "00e12182",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "tensor([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "model.eval()\n",
     "\n",
@@ -444,10 +456,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 12,
    "id": "1cfff865",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "array(['basal cell', 'basal cell', 'basal cell', 'basal cell',\n",
+       "       'basal cell', 'basal cell', 'basal cell', 'basal cell',\n",
+       "       'basal cell', 'basal cell', 'basal cell', 'basal cell',\n",
+       "       'basal cell', 'basal cell', 'basal cell', 'basal cell'],\n",
+       "      dtype=object)"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "cell_type_encoder = experiment_datapipe.obs_encoders()[\"cell_type\"]\n",
     "\n",
@@ -466,10 +493,145 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 13,
    "id": "f4ac8087",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>actual cell type</th>\n",
+       "      <th>predicted cell type</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>5</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>6</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>8</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>9</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>10</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>11</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>12</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>13</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>14</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>15</th>\n",
+       "      <td>epithelial cell</td>\n",
+       "      <td>basal cell</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "   actual cell type predicted cell type\n",
+       "0   epithelial cell          basal cell\n",
+       "1   epithelial cell          basal cell\n",
+       "2   epithelial cell          basal cell\n",
+       "3   epithelial cell          basal cell\n",
+       "4   epithelial cell          basal cell\n",
+       "5   epithelial cell          basal cell\n",
+       "6   epithelial cell          basal cell\n",
+       "7   epithelial cell          basal cell\n",
+       "8   epithelial cell          basal cell\n",
+       "9   epithelial cell          basal cell\n",
+       "10  epithelial cell          basal cell\n",
+       "11  epithelial cell          basal cell\n",
+       "12  epithelial cell          basal cell\n",
+       "13  epithelial cell          basal cell\n",
+       "14  epithelial cell          basal cell\n",
+       "15  epithelial cell          basal cell"
+      ]
+     },
+     "execution_count": 13,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "import pandas as pd\n",
     "\n",
@@ -506,7 +668,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.10.10"
   }
  },
  "nbformat": 4,