diff --git a/seqio/metrics.py b/seqio/metrics.py
index dee1dfce..94d80c24 100644
--- a/seqio/metrics.py
+++ b/seqio/metrics.py
@@ -184,9 +184,9 @@ def from_model_output(  # pylint:disable=missing-function-docstring
       )
     return cls(
         values={  # pyrefly: ignore[bad-argument-type]
-            "model_output": model_output,
-            "indices_2d": indices_2d,
-            "mask": mask,
+            "model_output": model_output,  # pyrefly: ignore[bad-assignment]
+            "indices_2d": indices_2d,  # pyrefly: ignore[bad-assignment]
+            "mask": mask,  # pyrefly: ignore[bad-assignment]
         }
     )