git clone https://github.com/HySonLab/Directed_Evolution.git 
cd Directed_Evolution 

conda create -n mlde python=3.10 -y 
conda activate mlde

pip install -e .

python train_decoder.py \
    --data_file /path/to/AAV.csv \
    --dataset_name AAV \
    --pretrained_encoder facebook/esm_t12_35M_UR5D \
    --dec_hidden_dim 1280 \
    --batch_size 256 \
    --ckpt_path /path/to/ckpt_to_continue_from \
    --devices 0 \
    --grad_accum_steps 1 \
    --lr 5e-5 \
    --num_epochs 50 \
    --num_ckpts 2 \

WANDB_DISABLED=True python train_decoder.py ...

options:
  -h, --help            show this help message and exit
  --data_file DATA_FILE
                        Path to data directory.
  --dataset_name DATASET_NAME
                        Name of trained dataset.
  --pretrained_encoder PRETRAINED_ENCODER
                        Path to pretrained encoder.
  --dec_hidden_dim DEC_HIDDEN_DIM
                        Hidden dim of decoder.
  --batch_size BATCH_SIZE
                        Batch size.
  --ckpt_path CKPT_PATH
                        Checkpoint of model.
  --devices DEVICES     Training devices separated by comma.
  --output_dir OUTPUT_DIR
                        Path to output directory.
  --grad_accum_steps GRAD_ACCUM_STEPS
                        No. updates steps to accumulate the gradient.
  --lr LR               Learning rate.
  --num_epochs NUM_EPOCHS
                        Number of epochs.
  --wandb_project WANDB_PROJECT
                        WandB project's name.
  --seed SEED           Random seed for reproducibility.
  --set_seed_only       Whether to not set deterministic flag.
  --num_workers NUM_WORKERS
                        No. workers.
  --num_ckpts NUM_CKPTS
                        Maximum no. checkpoints can be saved.
  --log_interval LOG_INTERVAL
                        How often to log within steps.
  --precision {highest,high,medium}
                        Internal precision of float32 matrix multiplications.

python run_discrete_de.py \
    --wt DEEEIRTTNPVATEQYGSVSTNLQRGNR
    --wt_fitness -100 \
    --n_steps 60 \
    --population 128 \
    --num_proposes_per_var 4 \
    --k 1 \
    --rm_dups \
    --population_ratio_per_mask 0.6 0.4 \
    --pretrained_mutation_name facebook/esm2_t12_35M_UR50D \
    --dec_hidden_size 1280 \
    --predictor_ckpt_path /path/to/ckpt \
    --verbose \
    --devices 0 \

options:
  -h, --help            show this help message and exit
  --data_file DATA_FILE
                        Path to data file.
  --wt WT               Amino acid sequence.
  --wt_fitness WT_FITNESS
                        Wild-type sequence's fitness.
  --n_steps N_STEPS     No. steps to run directed evolution.
  --population POPULATION
                        No. population per step.
  --num_proposes_per_var NUM_PROPOSES_PER_VAR
                        Number of proposed mutations for each variant in the pool.
  --k K                 Split sequence into multiple tokens with length `k`.
  --rm_dups             Whether to remove duplications in the proposed candidate pool.
  --population_ratio_per_mask POPULATION_RATIO_PER_MASK [POPULATION_RATIO_PER_MASK ...]
                        Population ratio to run per masker.
  --pretrained_mutation_name PRETRAINED_MUTATION_NAME
                        Pretrained model name or path for mutation checkpoint.
  --dec_hidden_size DEC_HIDDEN_SIZE
                        Decoder hidden size (for conditional task).
  --predictor_ckpt_path PREDICTOR_CKPT_PATH
                        Path to fitness predictor checkpoints.
  --num_masked_tokens NUM_MASKED_TOKENS
                        No. masked tokens to predict.
  --mask_high_importance
                        Whether to mask high-importance token in the sequence.
  --verbose             Whether to display output.
  --seed SEED           Random seed.
  --set_seed_only       Whether to enable full determinism or set random seed only.
  --result_dir RESULT_DIR
                        Directory to save result csv file.
  --save_name SAVE_NAME
                        Filename of the result csv file.
  --devices DEVICES     Devices, separated by commas.