updated tutos

Author: ori-kron-wis

multimodal/totalVI.ipynb

@@ -448,51 +448,6 @@
     ")"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(last_val_valid)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(last_val_train)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(global_min_loss)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(last_max_loss)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(global_max_loss)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 16,
@@ -510,42 +465,6 @@
     ")  # keep it under the 25% part of figure"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(min_loss)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(max_loss)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(ylim_min)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print(ylim_max)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 17,
@@ -588,9 +507,10 @@
     "fig, ax = plt.subplots(1, 1)\n",
     "model.history[\"elbo_train\"].plot(ax=ax, label=\"train\")\n",
     "model.history[\"elbo_validation\"].plot(ax=ax, label=\"validation\")\n",
-    "ax.set(\n",
-    "    title=\"Negative ELBO over training epochs\", ylim=(ylim_min, ylim_max)\n",
-    ")  # you can still plug in you numbers\n",
+    "if isinstance(ylim_min, (int, float)) and isinstance(ylim_max, (int, float)):\n",
+    "    ax.set(title=\"Negative ELBO over training epochs\", ylim=(ylim_min, ylim_max))\n",
+    "else:\n",
+    "    ax.set(title=\"Negative ELBO over training epochs\")\n",
     "ax.legend()"
    ]
   },
@@ -1334,28 +1254,6 @@
     "sc.tl.dendrogram(protein, groupby=TOTALVI_CLUSTERS_KEY, use_rep=TOTALVI_LATENT_KEY)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 34,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "'1.11.1'"
-      ]
-     },
-     "execution_count": 34,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "import scipy\n",
-    "scipy.__version__ \n",
-    "sc.__version__"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {