fix AssertionError: First token is not <cls> token value in extract_and_plot_cell_embeddings.ipynb

examples/extract_and_plot_cell_embeddings.ipynb

@@ -22,6 +22,7 @@
     "# (otherwise the EmbExtractor will use the current default model dictionary)\n",
     "embex = EmbExtractor(model_type=\"CellClassifier\",\n",
     "                     num_classes=3,\n",
+    "                     emb_mode=\"cell\",\n",
     "                     filter_data={\"cell_type\":[\"Cardiomyocyte1\",\"Cardiomyocyte2\",\"Cardiomyocyte3\"]},\n",
     "                     max_ncells=1000,\n",
     "                     emb_layer=0,\n",

examples/in_silico_perturbation.ipynb

@@ -44,6 +44,7 @@
     "# 30M token dictionary: https://huggingface.co/ctheodoris/Geneformer/blob/main/geneformer/gene_dictionaries_30m/token_dictionary_gc30M.pkl\n",
     "embex = EmbExtractor(model_type=\"CellClassifier\", # if using previously fine-tuned cell classifier model\n",
     "                     num_classes=3,\n",
+    "                     emb_mode=\"cell\",\n",
     "                     filter_data=filter_data_dict,\n",
     "                     max_ncells=1000,\n",
     "                     emb_layer=0,\n",