fix bug in geneformer

Author: janursa

docs/source/images/raw_scores_300BCG.png

@@ -1,11 +1,11 @@
 set -e
 
-datasets=( 'op' 'replogle' '300BCG') #'replogle' 'op' 'nakatake' 'adamson' 'norman'  'xaira_HEK293T' 'xaira_HCT116'  'parsebioscience' 'ibd' '300BCG'
+datasets=( 'op') #'replogle' 'op' 'nakatake' 'adamson' 'norman'  'xaira_HEK293T' 'xaira_HCT116'  'parsebioscience' 'ibd' '300BCG'
 
 run_local=false # set to true to run locally, false to run on AWS
 
-run_grn_inference=false
-run_grn_evaluation=true
+run_grn_inference=true
+run_grn_evaluation=false
 run_download=false
 
 

docs/source/images/raw_scores_ibd.png

@@ -36,6 +36,7 @@
 par = parse_args(par)
 
 if __name__ == "__main__":
+    dataset_id = ad.read_h5ad(par['rna'], backed='r').uns['dataset_id']
     net = main(par)
     output = ad.AnnData(
         X=None,

docs/source/images/raw_scores_op.png

@@ -410,8 +410,6 @@ def main(par):
         print(f"Final score: {score}")
 
         results = {
-            # 'r2': [float(np.mean(scores))],
-            # 'r2_baseline': [float(np.mean(scores_baseline))],
             'sem_precision': [float(np.mean(scores)/( np.mean(scores_baseline) + 1e-6))],
             'sem_balanced': [float(score)]
         }