add hyper connections to diffusion transformer

README.md

@@ -523,3 +523,14 @@ docker run -v .:/data --gpus all -it af3
     url     = {https://api.semanticscholar.org/CorpusID:273849947}
 }
 ```
+
+```bibtex
+@article{Zhu2024HyperConnections,
+    title   = {Hyper-Connections},
+    author  = {Defa Zhu and Hongzhi Huang and Zihao Huang and Yutao Zeng and Yunyao Mao and Banggu Wu and Qiyang Min and Xun Zhou},
+    journal = {ArXiv},
+    year    = {2024},
+    volume  = {abs/2409.19606},
+    url     = {https://api.semanticscholar.org/CorpusID:272987528}
+}
+```

alphafold3_pytorch/alphafold3.py

@@ -111,18 +111,19 @@
 
 from alphafold3_pytorch.utils.model_utils import distance_to_dgram
 
+# personal libraries
+
 from frame_averaging_pytorch import FrameAverage
 
 from taylor_series_linear_attention import TaylorSeriesLinearAttn
 
 from colt5_attention import ConditionalRoutedAttention
 
-import einx
-from einops import rearrange, repeat, reduce, einsum, pack, unpack
-from einops.layers.torch import Rearrange
+from hyper_connections import HyperConnections
 
-from tqdm import tqdm
+# other external libs
 
+from tqdm import tqdm
 from loguru import logger
 
 from importlib.metadata import version
@@ -132,6 +133,12 @@
 from Bio.PDB.Structure import Structure
 from Bio.PDB.StructureBuilder import StructureBuilder
 
+# einstein notation related
+
+import einx
+from einops import rearrange, repeat, reduce, einsum, pack, unpack
+from einops.layers.torch import Rearrange
+
 """
 global ein notation:
 
@@ -2008,6 +2015,7 @@ def __init__(
         use_linear_attn = False,
         checkpoint = False,
         add_value_residual = False,
+        num_residual_streams = 1,
         linear_attn_kwargs = dict(
             heads = 8,
             dim_head = 16
@@ -2026,6 +2034,12 @@ def __init__(
 
         dim_single_cond = default(dim_single_cond, dim)
 
+        # hyper connections
+
+        init_hyper_conn, self.expand_streams, self.reduce_streams = HyperConnections.get_init_and_expand_reduce_stream_functions(num_residual_streams, disable = num_residual_streams == 1)
+
+        # layers
+
         layers = ModuleList([])
 
         for i in range(depth):
@@ -2042,6 +2056,8 @@ def __init__(
                     **linear_attn_kwargs
                 )
 
+                linear_attn = init_hyper_conn(dim = dim, branch = linear_attn)
+
             colt5_attn = None
 
             if use_colt5_attn:
@@ -2051,6 +2067,8 @@ def __init__(
                     **colt5_attn_kwargs
                 )
 
+                colt5_attn = init_hyper_conn(dim = dim, branch = colt5_attn)
+
             accept_value_residual = add_value_residual and not is_first
 
             pair_bias_attn = AttentionPairBias(
@@ -2083,8 +2101,8 @@ def __init__(
             layers.append(ModuleList([
                 linear_attn,
                 colt5_attn,
-                conditionable_pair_bias,
-                conditionable_transition
+                init_hyper_conn(dim = dim, branch = conditionable_pair_bias),
+                init_hyper_conn(dim = dim, branch = conditionable_transition)
             ]))
 
         self.checkpoint = checkpoint
@@ -2112,24 +2130,21 @@ def to_checkpointed_serial_layers(
         windowed_mask: Bool['b nw w (w*2)'] | None = None
     ):
 
-        inputs = (noised_repr, single_repr, pairwise_repr, mask, windowed_mask, None)
-
         wrapped_layers = []
 
         def efficient_attn_wrapper(fn):
             @wraps(fn)
             def inner(inputs):
                 noised_repr, single_repr, pairwise_repr, mask, windowed_mask, maybe_value_residual = inputs
-                noised_repr = fn(noised_repr, mask = mask) + noised_repr
+                noised_repr = fn(noised_repr, mask = mask)
                 return noised_repr, single_repr, pairwise_repr, mask, windowed_mask, maybe_value_residual
             return inner
 
         def attn_wrapper(fn):
             @wraps(fn)
             def inner(inputs):
                 noised_repr, single_repr, pairwise_repr, mask, windowed_mask, maybe_value_residual = inputs
-                attn_out, attn_values = fn(noised_repr, cond = single_repr, pairwise_repr = pairwise_repr, mask = mask, windowed_mask = windowed_mask, value_residual = maybe_value_residual, return_values = True)
-                noised_repr = attn_out + noised_repr
+                noised_repr, attn_values = fn(noised_repr, cond = single_repr, pairwise_repr = pairwise_repr, mask = mask, windowed_mask = windowed_mask, value_residual = maybe_value_residual, return_values = True)
 
                 if self.add_value_residual:
                     maybe_value_residual = default(maybe_value_residual, attn_values)
@@ -2141,10 +2156,12 @@ def transition_wrapper(fn):
             @wraps(fn)
             def inner(inputs):
                 noised_repr, single_repr, pairwise_repr, mask, windowed_mask, maybe_value_residual = inputs
-                noised_repr = fn(noised_repr, cond = single_repr) + noised_repr
+                noised_repr = fn(noised_repr, cond = single_repr)
                 return noised_repr, single_repr, pairwise_repr, mask, windowed_mask, maybe_value_residual
             return inner
 
+        # wrap layers
+
         for linear_attn, colt5_attn, attn, transition in self.layers:
 
             if exists(linear_attn):
@@ -2156,10 +2173,19 @@ def inner(inputs):
             wrapped_layers.append(attn_wrapper(attn))
             wrapped_layers.append(transition_wrapper(transition))
 
+        # forward
+
+        noised_repr = self.expand_streams(noised_repr)
+
+        inputs = (noised_repr, single_repr, pairwise_repr, mask, windowed_mask, None)
+
         for layer in wrapped_layers:
             inputs = checkpoint(layer, inputs)
 
         noised_repr, *_ = inputs
+
+        noised_repr = self.reduce_streams(noised_repr)
+
         return noised_repr
 
     @typecheck
@@ -2175,15 +2201,17 @@ def to_serial_layers(
 
         value_residual = None
 
+        noised_repr = self.expand_streams(noised_repr)
+
         for linear_attn, colt5_attn, attn, transition in self.layers:
 
             if exists(linear_attn):
-                noised_repr = linear_attn(noised_repr, mask = mask) + noised_repr
+                noised_repr = linear_attn(noised_repr, mask = mask)
 
             if exists(colt5_attn):
-                noised_repr = colt5_attn(noised_repr, mask = mask) + noised_repr
+                noised_repr = colt5_attn(noised_repr, mask = mask)
 
-            attn_out, attn_values = attn(
+            noised_repr, attn_values = attn(
                 noised_repr,
                 cond = single_repr,
                 pairwise_repr = pairwise_repr,
@@ -2193,15 +2221,15 @@ def to_serial_layers(
                 value_residual = value_residual
             )
 
-            noised_repr = noised_repr + attn_out
-
             if self.add_value_residual:
                 value_residual = default(value_residual, attn_values)
 
             noised_repr = transition(
                 noised_repr,
                 cond = single_repr
-            ) + noised_repr
+            )
+
+        noised_repr = self.reduce_streams(noised_repr)
 
         return noised_repr
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "alphafold3-pytorch"
-version = "0.7.2"
+version = "0.7.3"
 description = "Alphafold 3 - Pytorch"
 authors = [
     { name = "Phil Wang", email = "[email protected]" },
@@ -41,6 +41,7 @@ dependencies = [
     "fair-esm",
     "fastapi",
     "frame-averaging-pytorch>=0.0.18",
+    "hyper-connections>=0.0.14",
     "gradio",
     "gradio_molecule3d",
     "huggingface_hub>=0.21.4",

tests/test_af3.py

@@ -372,11 +372,13 @@ def test_msa_module(
 @pytest.mark.parametrize('use_linear_attn', (False, True))
 @pytest.mark.parametrize('use_colt5_attn', (False, True))
 @pytest.mark.parametrize('add_value_residual', (False, True))
+@pytest.mark.parametrize('num_residual_streams', (1, 4))
 def test_diffusion_transformer(
     checkpoint,
     use_linear_attn,
     use_colt5_attn,
-    add_value_residual
+    add_value_residual,
+    num_residual_streams
 ):
 
     single = torch.randn(2, 16, 384).requires_grad_()
@@ -389,7 +391,8 @@ def test_diffusion_transformer(
         checkpoint = checkpoint,
         use_linear_attn = use_linear_attn,
         use_colt5_attn = use_colt5_attn,
-        add_value_residual = add_value_residual
+        add_value_residual = add_value_residual,
+        num_residual_streams = num_residual_streams
     )
 
     single_out = diffusion_transformer(