improved formatting

demo/HF_TCM+P3GPT_sceening.ipynb

@@ -30,20 +30,17 @@
     "```\n",
     "> In the end, your directory structure should look as follows:\n",
     "```\n",
-    "└─ P3GPT+TCM_Demo\n",
-    "    ├── HF_TCM+P3GPT_sceening.ipynb\n",
-    "    │   └── P3LIB\n",
-    "    │       ├── mpt_7b\n",
-    "    │       │   ├── ...\n",
-    "    │       │   └── ...\n",
-    "    │       ├─ endpoints.py\n",
-    "    │       ├─ formula_picker.py\n",
-    "    │       └─ precious3_gpt_multi_modal.py\n",
-    "    ├── imgs\n",
-    "    │   ├── cpds_affecting_tissue_aging.svg\n",
-    "    │   └── experiment_scheme.png\n",
+    "└── demo\n",
     "    ├── 1Aug2024_aging_signatures.pckl [optional]\n",
-    "    └── P3GPT_compound_targets.pckl\n",
+    "    ├── HF_TCM+P3GPT_sceening.ipynb\n",
+    "    ├── P3GPT_compound_targets.pckl\n",
+    "    └── P3LIB\n",
+    "        ├── mpt_7b\n",
+    "        │   ├── ...\n",
+    "        │   └── ...\n",
+    "        ├─ endpoints.py\n",
+    "        ├─ formula_picker.py\n",
+    "        └─ precious3_gpt_multi_modal.py\n",
     "```"
    ]
   },
@@ -196,10 +193,6 @@
       "[BOS]<age_group2diff2age_group><tissue>skin </tissue><cell></cell><efo></efo><datatype></datatype><drug></drug><dose></dose><time></time><case>70.0-80.0 </case><control>19.95-25.0 </control><dataset_type>proteomics </dataset_type><gender></gender><species>human </species>\n",
       "This is token index where gene should be predicted:  259\n",
       "Running generations for skin-expression\n",
-      "[BOS]<age_group2diff2age_group><tissue>skin </tissue><cell></cell><efo></efo><datatype></datatype><drug></drug><dose></dose><time></time><case>70.0-80.0 </case><control>19.95-25.0 </control><dataset_type>expression </dataset_type><gender></gender><species>human </species><up>\n",
-      "This is token index where gene should be predicted:  1\n",
-      "[BOS]<age_group2diff2age_group><tissue>skin </tissue><cell></cell><efo></efo><datatype></datatype><drug></drug><dose></dose><time></time><case>70.0-80.0 </case><control>19.95-25.0 </control><dataset_type>expression </dataset_type><gender></gender><species>human </species>\n",
-      "This is token index where gene should be predicted:  251\n",
       "...\n",
       "Running generations for liver-expression\n",
       "[BOS]<age_group2diff2age_group><tissue>liver </tissue><cell></cell><efo></efo><datatype></datatype><drug></drug><dose></dose><time></time><case>70.0-80.0 </case><control>19.95-25.0 </control><dataset_type>expression </dataset_type><gender></gender><species>human </species><up>\n",