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Optimizer: cos annealing for eFold #40

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cb0283f
Optimizer: cos annealing for eFold
taillades Oct 23, 2025
033d810
remove kaggle logger
taillades Oct 23, 2025
c47395f
remove unused imports
taillades Oct 23, 2025
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20 changes: 1 addition & 19 deletions efold/core/callbacks.py
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Original file line number Diff line number Diff line change
@@ -1,27 +1,9 @@
import os
from lightning import LightningModule, Trainer
import lightning.pytorch as pl
import torch
import numpy as np
import pandas as pd
from lightning.pytorch import LightningModule, Trainer
from lightning.pytorch import Trainer
from lightning.pytorch.utilities import rank_zero_only
import wandb
from typing import Any

from .visualisation import plot_factory
from .metrics import metric_factory
from .datamodule import DataModule
from .loader import Loader
from .batch import Batch
from ..config import (
TEST_SETS_NAMES,
REF_METRIC_SIGN,
REFERENCE_METRIC,
DATA_TYPES_TEST_SETS,
POSSIBLE_METRICS,
)
from .logger import Logger, LocalLogger


class ModelCheckpoint(pl.Callback):
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4 changes: 3 additions & 1 deletion efold/core/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,9 @@ def configure_optimizers(self):
if not hasattr(self, "gamma") or self.gamma is None:
return optimizer

scheduler = torch.optim.lr_scheduler.ExponentialLR(optimizer, gamma=self.gamma)
scheduler = torch.optim.lr_scheduler.LinearWarmupCosineAnnealingLR(
optimizer, warmup_epochs=3, max_epochs=self.max_epochs
)
return [optimizer], [scheduler]

def _loss_signal(self, batch: Batch, data_type: str):
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6 changes: 4 additions & 2 deletions scripts/efold_training.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,8 +59,10 @@
trainer = Trainer(
accelerator=device,
devices=n_gpu if STRATEGY == "ddp" else 1,
strategy=DDPStrategy(find_unused_parameters=False) if STRATEGY == "ddp" else 'auto',
max_epochs=15,
strategy=DDPStrategy(find_unused_parameters=False)
if STRATEGY == "ddp"
else "auto",
max_epochs=30,
log_every_n_steps=1,
accumulate_grad_batches=32,
use_distributed_sampler=STRATEGY != "ddp",
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2 changes: 1 addition & 1 deletion scripts/ribonanza-template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@

sys.path.append(os.path.dirname(os.path.dirname(__file__)))
from lightning.pytorch import Trainer
from efold.core.callbacks import WandbFitLogger, KaggleLogger
from efold.core.callbacks import WandbFitLogger
from efold.config import device
from efold import DataModule, create_model
import torch
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