comments

netam/dasm.py

@@ -204,7 +204,8 @@ def loss_of_batch(self, batch):
 
     def build_selection_matrix_from_parent(self, parent: str):
         # This is simpler than the equivalent in dnsm.py because we get the selection
-        # matrix directly.
+        # matrix directly. Note that selection_factors_of_aa_str does the exponentiation
+        # so this indeed gives us the selection factors, not the log selection factors.
         parent = translate_sequence(parent)
         selection_factors = self.model.selection_factors_of_aa_str(parent)
         parent_idxs = sequences.aa_idx_array_of_str(parent)

netam/models.py

@@ -537,7 +537,8 @@ def __init__(self):
         super().__init__()
 
     def selection_factors_of_aa_str(self, aa_str: str) -> Tensor:
-        """Do the forward method without gradients from an amino acid string.
+        """Do the forward method then exponentiation without gradients from an amino
+        acid string.
 
         Args:
             aa_str: A string of amino acids.