hook up the smooth lddt loss end2end, thanks to @joseph-c-kim

README.md

@@ -8,7 +8,7 @@ Getting a fair number of emails. You can chat with me about this work <a href="h
 
 ## Appreciation
 
-- <a href="https://github.com/joseph-c-kim">Joseph</a> for contributing the relative positional encoding module!
+- <a href="https://github.com/joseph-c-kim">Joseph</a> for contributing the Relative Positional Encoding and the Smooth LDDT Loss!
 
 ## Install
 

alphafold3_pytorch/alphafold3.py

@@ -23,7 +23,7 @@
 from collections import namedtuple
 
 import torch
-from torch import nn
+from torch import nn, sigmoid
 from torch import Tensor
 import torch.nn.functional as F
 
@@ -80,15 +80,15 @@ def unpack_one(t, ps, pattern):
 
 # Loss functions
 
-def smoothlddtloss(
+@typecheck
+def calc_smooth_lddt_loss(
     denoised: Float['b m 3'], 
     ground_truth: Float['b m 3'], 
     is_rna_per_atom: Float['b m'],
     is_dna_per_atom: Float['b m']
-) -> Float['b']:
-    from torch import sigmoid
+) -> Float[' b']:
 
-    m = is_rna_per_atom.shape[-1]
+    m, device = is_rna_per_atom.shape[-1], denoised.device
 
     dx_denoised = torch.cdist(denoised, denoised)
     dx_gt = torch.cdist(ground_truth, ground_truth)
@@ -102,10 +102,11 @@ def smoothlddtloss(
     mask = einx.multiply('b i, b j -> b i j', is_nuc, is_nuc)
     c = (dx_gt < 30) * mask + (dx_gt < 15) * (1 - mask)
 
-    num = einx.sum('b [...]', c * eps * (1 - torch.eye(m))) / (m**2 - m)
-    den = einx.sum('b [...]', c * (1 - torch.eye(m))) / (m**2 - m)
-
-    return 1 - num/den
+    eye = torch.eye(m, device = device)
+    num = einx.sum('b [...]', c * eps * (1 - eye)) / (m**2 - m)
+    den = einx.sum('b [...]', c * (1 - eye)) / (m**2 - m)
+
+    return 1. - num/den
 
 # linear and outer sum
 # for single repr -> pairwise pattern throughout this architecture
@@ -1699,6 +1700,8 @@ def forward(
         normalized_atom_pos: Float['b m 3'],
         atom_mask: Bool['b m'],
         return_denoised_pos = False,
+        additional_residue_feats: Float['b n rf'] | None = None,
+        add_smooth_lddt_loss = False,
         **network_condition_kwargs
     ) -> Float[''] | Tuple[Float[''], Float['b m 3']]:
 
@@ -1726,6 +1729,22 @@ def forward(
 
         loss = losses.mean()
 
+        if add_smooth_lddt_loss:
+            assert exists(additional_residue_feats)
+            w = self.net.atoms_per_window
+
+            is_dna, is_rna = additional_residue_feats[..., 7], additional_residue_feats[..., 8]
+            atom_is_dna, atom_is_rna = tuple(repeat(t, 'b n -> b (n w)', w = w) for t in (is_dna, is_rna))
+
+            smooth_lddt_loss = calc_smooth_lddt_loss(
+                denoised,
+                normalized_atom_pos,
+                atom_is_dna,
+                atom_is_rna
+            ).mean()
+
+            loss = loss + smooth_lddt_loss
+
         if not return_denoised_pos:
             return loss
 
@@ -2354,7 +2373,13 @@ def forward(
         # otherwise, noise and make it learn to denoise
 
         if exists(atom_pos):
-            diffusion_loss, denoised_atom_pos = self.edm(atom_pos, return_denoised_pos = True, **diffusion_cond)
+            diffusion_loss, denoised_atom_pos = self.edm(
+                atom_pos,
+                additional_residue_feats = additional_residue_feats,
+                add_smooth_lddt_loss = True,
+                return_denoised_pos = True,
+                **diffusion_cond
+            )
 
         # calculate all logits and losses
 

tests/test_af3.py

@@ -19,21 +19,23 @@
     Alphafold3,
 )
 
-from alphafold3_pytorch.alphafold3 import smoothlddtloss
+from alphafold3_pytorch.alphafold3 import (
+    calc_smooth_lddt_loss
+)
 
-def test_smoothlddtloss():
+def test_calc_smooth_lddt_loss():
     denoised = torch.randn(8, 100, 3)
     ground_truth = torch.randn(8, 100, 3)
-    is_rna_per_atom = torch.randint(0, 2, (8, 100))
-    is_dna_per_atom = torch.randint(0, 2, (8, 100))
+    is_rna_per_atom = torch.randint(0, 2, (8, 100)).float()
+    is_dna_per_atom = torch.randint(0, 2, (8, 100)).float()
 
-    loss = smoothlddtloss(
+    loss = calc_smooth_lddt_loss(
         denoised, 
         ground_truth, 
         is_rna_per_atom, 
         is_dna_per_atom
     )
-    
+
     assert torch.all(loss <= 1) and torch.all(loss >= 0)
 
 def test_pairformer():