Improved notebook formatting

demo/HF_TCM+P3GPT_sceening.ipynb

@@ -200,106 +200,7 @@
       "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",
-      "Running generations for muscle-methylation\n",
-      "[BOS]<age_group2diff2age_group><tissue>muscle </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>methylation </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>muscle </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>methylation </dataset_type><gender></gender><species>human </species>\n",
-      "This is token index where gene should be predicted:  260\n",
-      "Running generations for muscle-proteomics\n",
-      "[BOS]<age_group2diff2age_group><tissue>muscle </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><up>\n",
-      "This is token index where gene should be predicted:  1\n",
-      "[BOS]<age_group2diff2age_group><tissue>muscle </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 muscle-expression\n",
-      "[BOS]<age_group2diff2age_group><tissue>muscle </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>muscle </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:  259\n",
-      "Running generations for whole blood-methylation\n",
-      "[BOS]<age_group2diff2age_group><tissue>whole blood </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>methylation </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>whole blood </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>methylation </dataset_type><gender></gender><species>human </species>\n",
-      "This is token index where gene should be predicted:  259\n",
-      "Running generations for whole blood-proteomics\n",
-      "[BOS]<age_group2diff2age_group><tissue>whole blood </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><up>\n",
-      "This is token index where gene should be predicted:  1\n",
-      "[BOS]<age_group2diff2age_group><tissue>whole blood </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:  120\n",
-      "Running generations for whole blood-expression\n",
-      "[BOS]<age_group2diff2age_group><tissue>whole blood </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>whole blood </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:  13\n",
-      "Running generations for epithelium-methylation\n",
-      "[BOS]<age_group2diff2age_group><tissue>epithelium </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>methylation </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>epithelium </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>methylation </dataset_type><gender></gender><species>human </species>\n",
-      "This is token index where gene should be predicted:  120\n",
-      "Running generations for epithelium-proteomics\n",
-      "[BOS]<age_group2diff2age_group><tissue>epithelium </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><up>\n",
-      "This is token index where gene should be predicted:  1\n",
-      "[BOS]<age_group2diff2age_group><tissue>epithelium </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:  11\n",
-      "Running generations for epithelium-expression\n",
-      "[BOS]<age_group2diff2age_group><tissue>epithelium </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>epithelium </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:  11\n",
-      "Running generations for artery-methylation\n",
-      "[BOS]<age_group2diff2age_group><tissue>artery </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>methylation </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>artery </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>methylation </dataset_type><gender></gender><species>human </species>\n",
-      "This is token index where gene should be predicted:  13\n",
-      "Running generations for artery-proteomics\n",
-      "[BOS]<age_group2diff2age_group><tissue>artery </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><up>\n",
-      "This is token index where gene should be predicted:  1\n",
-      "[BOS]<age_group2diff2age_group><tissue>artery </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:  261\n",
-      "Running generations for artery-expression\n",
-      "[BOS]<age_group2diff2age_group><tissue>artery </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>artery </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:  261\n",
-      "Running generations for fat tissue-methylation\n",
-      "[BOS]<age_group2diff2age_group><tissue>fat tissue </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>methylation </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>fat tissue </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>methylation </dataset_type><gender></gender><species>human </species>\n",
-      "This is token index where gene should be predicted:  261\n",
-      "Running generations for fat tissue-proteomics\n",
-      "[BOS]<age_group2diff2age_group><tissue>fat tissue </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><up>\n",
-      "This is token index where gene should be predicted:  1\n",
-      "[BOS]<age_group2diff2age_group><tissue>fat tissue </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 fat tissue-expression\n",
-      "[BOS]<age_group2diff2age_group><tissue>fat tissue </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>fat tissue </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:  260\n",
-      "Running generations for brain-methylation\n",
-      "[BOS]<age_group2diff2age_group><tissue>brain </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>methylation </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>brain </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>methylation </dataset_type><gender></gender><species>human </species>\n",
-      "This is token index where gene should be predicted:  261\n",
-      "Running generations for brain-proteomics\n",
-      "[BOS]<age_group2diff2age_group><tissue>brain </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><up>\n",
-      "This is token index where gene should be predicted:  1\n",
-      "[BOS]<age_group2diff2age_group><tissue>brain </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:  260\n",
-      "Running generations for brain-expression\n",
-      "[BOS]<age_group2diff2age_group><tissue>brain </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>brain </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:  260\n",
-      "Running generations for liver-methylation\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>methylation </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>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>methylation </dataset_type><gender></gender><species>human </species>\n",
-      "This is token index where gene should be predicted:  125\n",
-      "Running generations for liver-proteomics\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>proteomics </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>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>proteomics </dataset_type><gender></gender><species>human </species>\n",
-      "This is token index where gene should be predicted:  261\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",
       "This is token index where gene should be predicted:  1\n",
@@ -401,54 +302,18 @@
       "text/plain": [
        "(5281792,\n",
        " {'title': 'rosmarinic-acid',\n",
-       "  'known_targets': {'symbols': ['C5',\n",
-       "    'CCR3',\n",
-       "    'CCL2',\n",
-       "    'PREP',\n",
-       "    'NFKB1',\n",
-       "    'IKBKB',\n",
-       "    'CASP3',\n",
-       "    'C3',\n",
-       "    'OLIG2',\n",
-       "    'CCL11',\n",
-       "    'CD86',\n",
-       "    'AURKA',\n",
-       "    'IL2',\n",
-       "    'F2',\n",
-       "    'IDO1',\n",
-       "    'IL4',\n",
-       "    'RPS6KB1',\n",
-       "    'ABAT',\n",
-       "    'CCL3',\n",
-       "    'STAT1',\n",
-       "    'CD80',\n",
-       "    'IL5',\n",
-       "    'IL6'],\n",
-       "   'entrez_ids': [18,\n",
-       "    3565,\n",
-       "    4790,\n",
-       "    836,\n",
-       "    3551,\n",
-       "    3620,\n",
-       "    6772,\n",
-       "    718,\n",
-       "    2147,\n",
-       "    3558,\n",
-       "    3569,\n",
-       "    6347,\n",
-       "    6356,\n",
-       "    727,\n",
-       "    6790,\n",
-       "    3567,\n",
-       "    942,\n",
-       "    6348,\n",
-       "    10215,\n",
-       "    6198,\n",
-       "    5550,\n",
-       "    1232,\n",
-       "    941]},\n",
+       "  'known_targets': {'symbols': ['C5', 'CCR3', 'CCL2', 'PREP', 'NFKB1',\n",
+       "                                'IKBKB', 'CASP3', 'C3', 'OLIG2', 'CCL11', \n",
+       "                                'CD86', 'AURKA', 'IL2', 'F2', 'IDO1',\n",
+       "                                'IL4', 'RPS6KB1','ABAT', 'CCL3','STAT1',\n",
+       "                                'CD80', 'IL5', 'IL6'],\n",
+       "   'entrez_ids': [18, 3565, 4790, 836, 3551,\n",
+       "                  3620, 6772, 718, 2147, 3558,\n",
+       "                  3569, 6347, 6356, 727, 6790,\n",
+       "                  3567, 942, 6348, 10215, 6198,\n",
+       "                  5550, 1232, 941]},\n",
        "  'predicted_targets': {'symbols': ['IFNG', 'PTGS1', 'PTGS2', 'TPMT'],\n",
-       "   'entrez_ids': [3458, 5742, 5743, 7172]}})"
+       "  'entrez_ids': [3458, 5742, 5743, 7172]}})"
       ]
      },
      "execution_count": 10,