Make the faster option for bias fusions the default

sub-packages/bionemo-geneformer/src/bionemo/geneformer/scripts/train_geneformer.py

@@ -93,7 +93,7 @@ def main(
     gc_interval: int = 0,
     aligned_megatron_ddp: bool = False,
     recompilation_check: bool = False,
-    bias_fusions: bool = False,
+    skip_bias_fusions: bool = False,
     # TODO add datamodule class, and ability to change data step to get full support for pretraining workflows
 ) -> None:
     """Train a Geneformer model on single cell data.
@@ -148,10 +148,11 @@ def main(
             good for clusters. This will likely slow down single node runs though.
         recompilation_check (bool): enable a recompilation check (only do on a small run) to verify that fused gpu
             kernels are not being regularly recompiled, which is very expensive, with a particular model/settings.
-        bias_fusions (bool): enable two bias fusions (dropout and activation) which improve performance but should be
-            evaluated for impacting training stability. At the very least they trigger recompilations.
+        skip_bias_fusions (bool): Disable the two bias fusions (dropout and activation) which improve performance but
+            cause recompilations. In testing they still seem to result in higher performance despite the recompilations.
     """
     # Create the result directory if it does not exist.
+    bias_fusions = not skip_bias_fusions
     if wandb_tags is None:
         wandb_tags = []
     result_dir.mkdir(parents=True, exist_ok=True)
@@ -624,10 +625,10 @@ def config_class_type(desc: str) -> Type[BioBertConfig]:
         "triggering regular recompilations which can be very expensive for fused gpu kernels.",
     )
     parser.add_argument(
-        "--bias-fusions",
+        "--skip-bias-fusions",
         action="store_true",
         default=False,
-        help="Activate bias fusions which seem to reduce precision but are slightly faster.",
+        help="Deactivate bias fusions which seem to reduce precision but are slightly faster.",
     )
 
     return parser
@@ -679,7 +680,7 @@ def entrypoint():
         gc_interval=args.gc_interval,
         aligned_megatron_ddp=args.aligned_megatron_ddp,
         recompilation_check=args.recompilation_check,
-        bias_fusions=args.bias_fusions,
+        skip_bias_fusions=args.skip_bias_fusions,
     )