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Updated to run hg38 experiment on newer pytorch lightning version. #33

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Updated to run hg38 experiment on newer pytorch lightning version. #33

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4 changes: 2 additions & 2 deletions requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ scikit-learn
matplotlib
tqdm
rich
pytorch-lightning==1.8.6
pytorch-lightning==2.1.2
hydra-core
omegaconf
wandb
Expand All @@ -29,4 +29,4 @@ pyfaidx
polars
genomic-benchmarks
loguru
liftover
liftover
3 changes: 3 additions & 0 deletions src/dataloaders/datasets/hg38_char_tokenizer.py
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Expand Up @@ -71,6 +71,9 @@ def __init__(self, characters: Sequence[str], model_max_length: int, padding_sid
def vocab_size(self) -> int:
return len(self._vocab_str_to_int)

def get_vocab(self) -> dict[str, int]:
return self.get_added_vocab()

def _tokenize(self, text: str) -> List[str]:
return list(text)

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8 changes: 0 additions & 8 deletions train.py
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Expand Up @@ -364,19 +364,11 @@ def on_train_epoch_start(self):
# Reset training torchmetrics
self.task._reset_torchmetrics("train")

def training_epoch_end(self, outputs):
# Log training torchmetrics
super().training_epoch_end(outputs)

def on_validation_epoch_start(self):
# Reset all validation torchmetrics
for name in self.val_loader_names:
self.task._reset_torchmetrics(name)

def validation_epoch_end(self, outputs):
# Log all validation torchmetrics
super().validation_epoch_end(outputs)

def on_test_epoch_start(self):
# Reset all test torchmetrics
for name in self.test_loader_names:
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