Merge pull request #1 from aqlaboratory/main

Fix batched finetuning bugs

openfold/utils/loss.py

@@ -1353,7 +1353,10 @@ def violation_loss(
         + l_clash
     )
 
-    return loss
+    # Average over the batch dimension
+    mean = torch.mean(loss)
+
+    return mean
 
 
 def compute_renamed_ground_truth(
@@ -1476,7 +1479,7 @@ def experimentally_resolved_loss(
 ) -> torch.Tensor:
     errors = sigmoid_cross_entropy(logits, all_atom_mask)
     loss = torch.sum(errors * atom37_atom_exists, dim=-1)
-    loss = loss / (eps + torch.sum(atom37_atom_exists, dim=(-1, -2)))
+    loss = loss / (eps + torch.sum(atom37_atom_exists, dim=(-1, -2)).unsqueeze(-1))
     loss = torch.sum(loss, dim=-1)
     
     loss = loss * (

openfold/utils/validation_metrics.py

@@ -29,7 +29,7 @@ def drmsd(structure_1, structure_2, mask=None):
     if(mask is not None):
         drmsd = drmsd * (mask[..., None] * mask[..., None, :])
     drmsd = torch.sum(drmsd, dim=(-1, -2))
-    n = d1.shape[-1] if mask is None else torch.sum(mask, dim=-1)
+    n = d1.shape[-1] if mask is None else torch.min(torch.sum(mask, dim=-1))
     drmsd = drmsd * (1 / (n * (n - 1))) if n > 1 else (drmsd * 0.)
     drmsd = torch.sqrt(drmsd)
 

train_openfold.py

@@ -88,9 +88,10 @@ class OpenFoldWrapper(pl.LightningModule):
             )
 
         for k,v in other_metrics.items():
+            assert(len(v.shape) == 1)
             self.log(
-                f"{phase}/{k}", 
-                v, 
+                f"{phase}/{k}",
+                torch.mean(v),
                 on_step=False, on_epoch=True, logger=True
             )