Merge pull request #285 from twrightsman/fix-aparent

Fix APARENT/site_probabilities output labels
kipoi · Jan 3, 2022 · d8c5bec · d8c5bec
2 parents 9ec83ce + 068ca78
commit d8c5bec
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diff --git a/APARENT/site_probabilities/model.py b/APARENT/site_probabilities/model.py
@@ -18,14 +18,14 @@ def _predict(self, inputs):
 
         _, pred = self.model.predict_on_batch([input_1, input_2, input_3])
 
-        site_probs = pred[:, 1:]
-        polya_prob = pred[:, 0]
-        return site_probs, polya_prob
+        site_props = pred[:, :-1]
+        distal_prop = pred[:, -1]
+        return site_props, distal_prop
 
     def predict_on_batch(self, inputs):
-        site_probs, polya_prob = self._predict(inputs)
+        site_props, distal_prop = self._predict(inputs)
 
         return {
-            "logit_polya_prob": polya_prob,
-            "logit_site_probs": site_probs,
+            "distal_prop": distal_prop,
+            "site_props": site_props,
         }
diff --git a/APARENT/site_probabilities/model.yaml b/APARENT/site_probabilities/model.yaml
@@ -53,19 +53,19 @@ schema:
   targets:
     doc: >
       Predicts 206 features:
-      1 prediction for % proximal isoform + 205 predictions for % cleavage at each position
+      1 prediction for % distal cleavage + 205 predictions for % cleavage at each position
     shape: (206, )
-    logit_polya_prob:
+    distal_prop:
       shape: (1, )
       doc: >
-        Predicts logit probability of having a PolyA cut site in the specified DNA range
-    logit_site_probs:
+        Predicts proportion of cleavage occuring outside of the specified DNA range
+    site_props:
       shape: (205, )
       doc: >
-        Predicts logit probability of having a PolyA cut site for each position in the specified DNA range
+        Predicts proportion of cleavage occuring at each position in the specified DNA range
 
 test:
   expect:
     url: https://zenodo.org/record/5511940/files/APARENT.site_probabilities.predictions.hdf5?download=1
     md5: 1adb12be84240ffb7d7ca556eeb19e01
-        
+