scripts/compute_fitness.sh

# zero-shot with aa sequence alignment
export HF_ENDPOINT=https://hf-mirror.com
protein_dir=proteingym_v1
CUDA_VISIBLE_DEVICES=0 python scripts/compute_fitness.py \
    --model_name weight/ProSST-2048 \
    --base_dir conf/data/$protein_dir \
    --out_scores_dir output/$protein_dir

# zero-shot without alignment (ProSST-2048)
export HF_ENDPOINT=https://hf-mirror.com
alpha=0
protein_dir=proteingym_v1
CUDA_VISIBLE_DEVICES=0 python scripts/compute_fitness.py \
    --model_name weight/ProSST-2048 \
    --base_dir conf/data/$protein_dir \
    --out_scores_dir output/$protein_dir \
    --alpha $alpha \
    --model_out_name ProSST-2048

# zero-shot with structure sequence alignment
export HF_ENDPOINT=https://hf-mirror.com
alpha=0.8
protein_dir=proteingym_v1
CUDA_VISIBLE_DEVICES=0 python scripts/compute_fitness.py \
    --model_name weight/ProSST-2048 \
    --logit_mode struc_seq_aln \
    --alpha $alpha \
    --model_out_name ProtREM-struc \
    --base_dir conf/data/$protein_dir \
    --out_scores_dir output/$protein_dir