small changes to config files

Author: janursa

common

@@ -4,8 +4,8 @@
 # 
 # set -e
 # Default parameters
-RUN_CONSENSUS=false
-RUN_METRICS=false
+RUN_CONSENSUS=true
+RUN_METRICS=true
 PROCESS_RESULTS=false
 TEMP_DIR="output/evaluation"
 RESULTS_FILE="resources/results/all_scores.csv"

docs/source/images/summary_figure.png

@@ -67,7 +67,7 @@ printf '%s\n' "${predictions[@]}"
 echo "Running consensus for Regression"
 datasets=(${DATASET})
 for dataset in "${datasets[@]}"; do
-    echo "Running reg2 consensus for dataset: $dataset"
+    echo "Running regression consensus for dataset: $dataset"
 
     python src/metrics/regression/consensus/script.py \
         --dataset "$dataset" \

scripts/local_workflows/run_grn_evaluation.sh

@@ -4,7 +4,7 @@
 
 subsamples=(-2 -3 -4)
 
-RUN_ID="robust_analy_reg2_$1"
+RUN_ID="robust_analy_regression_$1"
 # resources_dir="resources"
 resources_dir="s3://openproblems-data/resources/grn"
 

scripts/prior/run_consensus.sh

@@ -22,8 +22,8 @@ resources:
     dest: tf_recovery_helper.py
   - path: /src/metrics/tf_binding/helper.py
     dest: tf_binding_helper.py
-  - path: /src/metrics/replica_consistency/helper.py
-    dest: replica_consistency_helper.py
+  - path: /src/metrics/replicate_consistency/helper.py
+    dest: replicate_consistency_helper.py
   - path: /src/utils/config.py
     dest: config.py
 

scripts/repo/run_pc_vs_nc.sh

@@ -13,7 +13,7 @@
 # from anchor_regression.helper import main as anchor_regression
 from tf_recovery.helper import main as tf_recovery
 from tf_binding.helper import main as tf_binding
-from rc_tf_act.helper import main as rc_tf_act
+from replicate_consistency.helper import main as replicate_consistency
 from vc.helper import main as vc
 from gs_recovery.helper import main as gs_recovery
 
@@ -26,7 +26,7 @@
     # 'anchor_regression': anchor_regression,
     'tf_recovery': tf_recovery,
     'tf_binding': tf_binding,
-    'rc_tf_act': rc_tf_act,
+    'replicate_consistency': replicate_consistency,
     'vc': vc,
     'gs_recovery': gs_recovery,
 }

src/metrics/all_metrics/config.novsh.yaml

@@ -1,9 +1,9 @@
 __merge__: ../../api/comp_metric.yaml
 
-name: replica_consistency
+name: replicate_consistency
 namespace: "metrics"
 info:
-  label: Replica consistency
+  label: Replicate consistency
   summary: Calculates replica consistency scores
 
 

src/metrics/all_metrics/helper.py

@@ -305,20 +305,20 @@ def main(par):
     tgtg_score_lift = np.mean([score_lift for score_lift, score in tgtg_results])
     # final_score = (tftg_score + tgtg_score + tftg_tgtg_score) / 3.0
     if True:
-        replica_consistency_precision = np.mean([tftg_score_lift, tgtg_score_lift])
-        replica_consistency_balanced = np.mean([tftg_score, tgtg_score])
+        replicate_consistency_precision = np.mean([tftg_score_lift, tgtg_score_lift])
+        replicate_consistency_balanced = np.mean([tftg_score, tgtg_score])
     else:
-        replica_consistency_precision = tgtg_score_lift
-        replica_consistency_balanced = tgtg_score
+        replicate_consistency_precision = tgtg_score_lift
+        replicate_consistency_balanced = tgtg_score
 
     # Create results DataFrame with all three scores
     results = pd.DataFrame({
         # 'tftg': [tftg_score],
         # 'tftg_score_lift': [tftg_score_lift],
         # 'tgtg': [tgtg_score],
         # 'tgtg_score_lift': [tgtg_score_lift],
-        'rc_precision': [replica_consistency_precision],
-        'rc_balanced': [replica_consistency_balanced],
+        'rc_precision': [replicate_consistency_precision],
+        'rc_balanced': [replicate_consistency_balanced],
     })
     print(results)