diff --git a/vizier/_src/algorithms/optimizers/vectorized_base.py b/vizier/_src/algorithms/optimizers/vectorized_base.py
index 2ecfe2329..0375b3601 100644
--- a/vizier/_src/algorithms/optimizers/vectorized_base.py
+++ b/vizier/_src/algorithms/optimizers/vectorized_base.py
@@ -480,7 +480,7 @@ def _optimization_one_step(_, args):
         self.strategy.init_state(
             init_seed,
             n_parallel=parallel_dim,
-            prior_features=prior_features,
+            prior_features=prior_features,  # pyrefly: ignore[bad-argument-type]
             prior_rewards=prior_rewards,
         ),
         init_best_results,
@@ -658,7 +658,7 @@ def trials_to_sorted_array(
 ) -> Optional[types.ModelInput]:
   """Sorts trials by the order they were created and converts to array."""
   if prior_trials:
-    prior_trials = sorted(prior_trials, key=lambda x: x.creation_time)
+    prior_trials = sorted(prior_trials, key=lambda x: x.creation_time)  # pyrefly: ignore[no-matching-overload]
     prior_features = converter.to_features(prior_trials)
   else:
     prior_features = None
diff --git a/vizier/_src/benchmarks/analyzers/convergence_curve.py b/vizier/_src/benchmarks/analyzers/convergence_curve.py
index 40f0e387c..eb50a0ee5 100644
--- a/vizier/_src/benchmarks/analyzers/convergence_curve.py
+++ b/vizier/_src/benchmarks/analyzers/convergence_curve.py
@@ -995,7 +995,7 @@ def curve(self) -> ConvergenceCurve:
 class OptimalityGapWinRateComparatorFactory(ConvergenceComparatorFactory):
   """Factory class for OptimalityGapWinRateComparator."""
 
-  def __call__(
+  def __call__(  # pyrefly: ignore[bad-override]
       self,
       baseline_curve: ConvergenceCurve,
       compared_curve: ConvergenceCurve,
@@ -1016,7 +1016,7 @@ def __call__(
 class OptimalityGapGainComparatorFactory(ConvergenceComparatorFactory):
   """Factory class for OptimalityGapGainComparator."""
 
-  def __call__(
+  def __call__(  # pyrefly: ignore[bad-override]
       self,
       baseline_curve: ConvergenceCurve,
       compared_curve: ConvergenceCurve,
@@ -1040,7 +1040,7 @@ class WinRateConvergenceCurveComparatorFactory(ConvergenceComparatorFactory):
 
   comparison_mode: Literal['pairwise', 'quantiles'] = 'pairwise'
 
-  def __call__(
+  def __call__(  # pyrefly: ignore[bad-override]
       self,
       baseline_curve: ConvergenceCurve,
       compared_curve: ConvergenceCurve,
@@ -1064,7 +1064,7 @@ class LogEfficiencyConvergenceCurveComparatorFactory(
 ):
   """Factory class for LogEfficiencyConvergenceCurveComparator."""
 
-  def __call__(
+  def __call__(  # pyrefly: ignore[bad-override]
       self,
       baseline_curve: ConvergenceCurve,
       compared_curve: ConvergenceCurve,
@@ -1087,7 +1087,7 @@ class PercentageBetterConvergenceCurveComparatorFactory(
 ):
   """Factory class for PercentageBetterConvergenceCurveComparator."""
 
-  def __call__(
+  def __call__(  # pyrefly: ignore[bad-override]
       self,
       baseline_curve: ConvergenceCurve,
       compared_curve: ConvergenceCurve,
diff --git a/vizier/_src/jax/models/gaussian_process_model.py b/vizier/_src/jax/models/gaussian_process_model.py
index 4555c70b0..473c652a6 100644
--- a/vizier/_src/jax/models/gaussian_process_model.py
+++ b/vizier/_src/jax/models/gaussian_process_model.py
@@ -97,7 +97,7 @@ def __init__(
           ' True) to your main'
       )
 
-  def __call__(
+  def __call__(  # pyrefly: ignore[bad-override]
       self, inputs: Optional[types.ModelInput] = None
   ) -> Generator[sp_model.ModelParameter, Array, tfd.GaussianProcess]:
     # TODO: Remove the following line when the linter bug is fixed.
diff --git a/vizier/_src/jax/models/hebo_gp_model.py b/vizier/_src/jax/models/hebo_gp_model.py
index 8bb5db8cb..fc4bfac48 100644
--- a/vizier/_src/jax/models/hebo_gp_model.py
+++ b/vizier/_src/jax/models/hebo_gp_model.py
@@ -51,7 +51,7 @@ def build_model(
     gp_coroutine = VizierHeboGaussianProcess()
     return sp.StochasticProcessModel(gp_coroutine)
 
-  def __call__(
+  def __call__(  # pyrefly: ignore[bad-override]
       self, inputs: Optional[types.ModelInput] = None
   ) -> Generator[sp.ModelParameter, jax.Array, tfd.GaussianProcess]:
     """Creates a generator.
diff --git a/vizier/_src/jax/models/multitask_tuned_gp_models.py b/vizier/_src/jax/models/multitask_tuned_gp_models.py
index d6b926753..7b3d84c6e 100644
--- a/vizier/_src/jax/models/multitask_tuned_gp_models.py
+++ b/vizier/_src/jax/models/multitask_tuned_gp_models.py
@@ -217,7 +217,7 @@ def sample(key: Any) -> jnp.ndarray:
 
     return sample  # pyrefly: ignore[bad-return]
 
-  def __call__(
+  def __call__(  # pyrefly: ignore[bad-override]
       self, inputs: Optional[types.ModelInput] = None
   ) -> Generator[
       sp.ModelParameter,
diff --git a/vizier/_src/jax/models/tuned_gp_models.py b/vizier/_src/jax/models/tuned_gp_models.py
index 99006ba9f..1e60c1db4 100644
--- a/vizier/_src/jax/models/tuned_gp_models.py
+++ b/vizier/_src/jax/models/tuned_gp_models.py
@@ -129,7 +129,7 @@ def build_model(
     )
     return sp.StochasticProcessModel(gp_coroutine)
 
-  def __call__(
+  def __call__(  # pyrefly: ignore[bad-override]
       self,
       inputs: Optional[types.ModelInput] = None,
   ) -> Generator[sp.ModelParameter, jax.Array, tfd.GaussianProcess]: