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Ignore problematic batch 8590 #39

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Merged
ravwojdyla merged 1 commit into from
Jul 16, 2025
Merged

Ignore problematic batch 8590 #39

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12 changes: 10 additions & 2 deletions caduceus_distill/distill.py
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Original file line number Diff line number Diff line change
Expand Up @@ -139,9 +139,11 @@ class DistillationDataset(Dataset[EXAMPLE_T]):
def __init__(
self,
zarr_path: str,
skip_batches: set[int] | None = None,
) -> None:
self.zarr_path = zarr_path
self.ds: xr.Dataset | None = None
self.skip_batches = skip_batches if skip_batches is not None else set()

with self.__maybe_open_zarr() as temp_ds:
total_samples = len(temp_ds.sample)
Expand Down Expand Up @@ -177,6 +179,12 @@ def __len__(self) -> int:
return self._len

def __getitem__(self, idx: int) -> EXAMPLE_T:
# TODO: better doc, is there an idiomatic way to skip a batch?
if idx in self.skip_batches:
new_idx = np.random.randint(0, len(self))
logger.debug(f"Using batch {new_idx} instead of {idx}")
idx = new_idx

self.ds = self.__maybe_open_zarr()
sample = self.ds.isel(sample=idx)
input_ids = torch.tensor(sample.input_ids.values, dtype=torch.long)
Expand Down Expand Up @@ -522,8 +530,8 @@ def main(
) -> None:
L.seed_everything(42, workers=True)

# Initialize datasets
train_dataset = DistillationDataset(zarr_path_train)
# NOTE: skip due to https://github.com/Open-Athena/caduceus-distill/issues/38
train_dataset = DistillationDataset(zarr_path_train, skip_batches={8590})
val_dataset = DistillationDataset(zarr_path_val)

# Create data loaders
Expand Down