train_ar_conditioned.sh

#!/usr/bin/env bash
set -euo pipefail

SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
source "${SCRIPT_DIR}/../00_setup/env.sh"

cd "${GENERATOR_DIR}"
python3 src/tasks/downstream/fine_tuning.py \
  --model_name "${GENERATOR_BASE_MODEL}" \
  --parquet_path "${CONDITIONED_DEEPSTARR_DIR}/train.parquet" \
  --sequence_col conditioned_sequence \
  --conditioned_input \
  --output_dir "${RESULT_ROOT}/checkpoints/deepstarr_sft_conditioned" \
  --saved_model_dir "${AR_COND_MODEL}" \
  --tmp_dir "${RUN_ROOT}/tmp/deepstarr_sft_conditioned" \
  --epochs "${AR_EPOCHS:-3}" \
  --batch_size "${AR_BATCH_SIZE:-4}" \
  --gradient_accumulation "${AR_GRAD_ACCUM:-1}" \
  --lr "${AR_LR:-5e-5}" \
  --max_token_length "${AR_MAX_TOKEN_LENGTH:-256}" \
  --attn_implementation "${ATTN_IMPLEMENTATION:-sdpa}" \
  --bf16 \
  --report_to none \
  --run_name deepstarr_sft_conditioned

for filename in modeling_generator.py tokenizer.py; do
  if [[ -f "${GENERATOR_BASE_MODEL}/${filename}" && ! -f "${AR_COND_MODEL}/${filename}" ]]; then
    cp "${GENERATOR_BASE_MODEL}/${filename}" "${AR_COND_MODEL}/${filename}"
  fi
done