a new paper claims there is a free lunch by setting model weights to …

…ema weights every epoch. allow researchers to experiment with this, conveniently already available in EMA-pytorch due to hare and tortoise paper

README.md

@@ -483,3 +483,14 @@ docker run -v .:/data --gpus all -it af3
     journal = {bioRxiv}
 }
 ```
+
+```bibtex
+@article{Li2024SwitchEA,
+    title   = {Switch EMA: A Free Lunch for Better Flatness and Sharpness},
+    author  = {Siyuan Li and Zicheng Liu and Juanxi Tian and Ge Wang and Zedong Wang and Weiyang Jin and Di Wu and Cheng Tan and Tao Lin and Yang Liu and Baigui Sun and Stan Z. Li},
+    journal = {ArXiv},
+    year    = {2024},
+    volume  = {abs/2402.09240},
+    url     = {https://api.semanticscholar.org/CorpusID:267657558}
+}
+```

alphafold3_pytorch/trainer.py

@@ -178,6 +178,7 @@ def __init__(
             use_foreach = True
         ),
         ema_on_cpu = False,
+        ema_update_model_with_ema_every: int | None = None,
         use_adam_atan2: bool = False,
         use_lion: bool = False,
         use_torch_compile: bool = False
@@ -220,6 +221,7 @@ def __init__(
                 include_online_model = False,
                 allow_different_devices = True,
                 coerce_dtype = True,
+                update_model_with_ema_every = ema_update_model_with_ema_every,
                 **ema_kwargs
             )
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "alphafold3-pytorch"
-version = "0.6.2"
+version = "0.6.3"
 description = "Alphafold 3 - Pytorch"
 authors = [
     { name = "Phil Wang", email = "[email protected]" },
@@ -33,7 +33,7 @@ dependencies = [
     "CoLT5-attention>=0.11.0",
     "einops>=0.8.0",
     "einx>=0.2.2",
-    "ema-pytorch>=0.6.4",
+    "ema-pytorch>=0.7.0",
     "environs",
     "lion-pytorch>=0.2.2",
     "joblib",