smi-ted/finetune/args.py

import argparse


def get_parser(parser=None):
    if parser is None:
        parser = argparse.ArgumentParser()

    # Model
    # model_arg = parser.add_argument_group('Model')
    parser.add_argument("--n_head", type=int, default=8, help="GPT number of heads")
    parser.add_argument("--n_layer", type=int, default=12, help="GPT number of layers")
    parser.add_argument(
        "--q_dropout", type=float, default=0.5, help="Encoder layers dropout"
    )
    parser.add_argument(
        "--d_dropout", type=float, default=0.1, help="Decoder layers dropout"
    )
    parser.add_argument(
        "--n_embd", type=int, default=768, help="Latent vector dimensionality"
    )
    parser.add_argument(
        "--fc_h", type=int, default=512, help="Fully connected hidden dimensionality"
    )
    parser.add_argument("--n_output", type=int, default=1)

    # Train
    # train_arg = parser.add_argument_group('Train')
    parser.add_argument("--n_batch", type=int, default=512, help="Batch size")
    parser.add_argument(
        "--unlike_alpha", type=float, default=1.0, help="unlikelihood loss alpha weight"
    )
    parser.add_argument(
        "--from_scratch",
        action="store_true",
        default=False,
        help="train on qm9 from scratch",
    )
    parser.add_argument(
        "--unlikelihood",
        action="store_true",
        default=False,
        help="use unlikelihood loss with gpt pretrain",
    )
    parser.add_argument(
        "--grad_acc",
        type=int,
        default=1,
        help="number of batches to accumulate gradients",
    )
    parser.add_argument(
        "--checkpoint_every",
        type=int,
        default=1000,
        help="save checkpoint every x iterations",
    )
    parser.add_argument(
        "--clip_grad", type=int, default=50, help="Clip gradients to this value"
    )
    parser.add_argument(
        "--lr_start", type=float, default=3 * 1e-4, help="Initial lr value"
    )
    parser.add_argument(
        "--lr_end", type=float, default=3 * 1e-4, help="Maximum lr weight value"
    )
    parser.add_argument(
        "--lr_multiplier", type=int, default=1, help="lr weight multiplier"
    )
    parser.add_argument(
        "--n_last", type=int, default=1000, help="Number of iters to smooth loss calc"
    )
    parser.add_argument("--n_jobs", type=int, default=1, help="Number of threads")
    parser.add_argument(
        "--accelerator",
        type=str,
        default="ddp",
        help="The accelerator backend to use (previously known as distributed_backend)",
    )
    parser.add_argument(
        "--num_nodes",
        type=int,
        default=1,
        help="number of GPU nodes for distributed training",
    )
    parser.add_argument(
        "--device",
        type=str,
        default="cuda",
        help='Device to run: "cpu" or "cuda:<device number>"',
    )
    parser.add_argument("--seed", type=int, default=12345, help="Seed")
    parser.add_argument(
        "--init_params_from",
        type=str,
        default="",
        help="Path to a ckpt used to initialize the parameters if no restart_path is provided",
    )
    parser.add_argument(
        "--train_decoder_every",
        type=int,
        default=10,
        help="Optimize decoder params every n batches",
    )
    parser.add_argument(
        "--lr_decoder", type=float, default=1e-4, help="Learning rate for decoder part"
    )
    parser.add_argument(
        "--local_rank",
        type=int,
        default=-1,
        help="local_rank for distributed training on gpus",
    )
    parser.add_argument("--gpu", default=None, type=int, help="GPU id to use.")
    parser.add_argument(
        "--dist-backend", default="nccl", type=str, help="distributed backend"
    )
    parser.add_argument(
        "--tensorboard_path", default="./runs/deepspeed", help="tensorboard log dir"
    )

    # common_arg = parser.add_argument_group('Common')
    parser.add_argument(
        "--vocab_load", type=str, required=False, help="Where to load the vocab"
    )
    parser.add_argument(
        "--n_samples", type=int, required=False, help="Number of samples to sample"
    )
    parser.add_argument(
        "--gen_save", type=str, required=False, help="Where to save the gen molecules"
    )
    parser.add_argument(
        "--max_len", type=int, default=100, help="Max of length of SMILES"
    )
    parser.add_argument(
        "--train_load", type=str, required=False, help="Where to load the model"
    )
    parser.add_argument(
        "--val_load", type=str, required=False, help="Where to load the model"
    )
    parser.add_argument(
        "--n_workers",
        type=int,
        required=False,
        default=1,
        help="Where to load the model",
    )
    # beam search hyper parameters
    parser.add_argument(
        "--beam_size", type=int, default=0, help="Number of beams to generate"
    )
    parser.add_argument(
        "--num_seq_returned",
        type=int,
        default=0,
        help="number of beams to be returned (must be <= beam_size",
    )
    parser.add_argument(
        "--min_len", type=int, default=1, help="minimum length to be generated"
    )
    parser.add_argument(
        "--nucleus_thresh", type=float, default=0.9, help="nucleus sampling threshold"
    )
    parser.add_argument(
        "--finetune_path",
        type=str,
        default="",
        help="path to  trainer file to continue training",
    )
    parser.add_argument(
        "--restart_path",
        type=str,
        default="",
        help="path to  trainer file to continue training",
    )
    parser.add_argument(
        "--data_path", type=str, default="", help="path to pubchem file"
    )
    parser.add_argument(
        "--pretext_size", type=int, default=0, help="number of k-mers to pretext"
    )
    parser.add_argument(
        "--model_save_dir",
        type=str,
        required=False,
        default="./models_dump/",
        help="Where to save the models/log/config/vocab",
    )
    parser.add_argument(
        "--model_save",
        type=str,
        required=False,
        default="model.pt",
        help="Where to save the model",
    )
    # parser.add_argument('--save_frequency',
    #                        type=int, default=20,
    #                        help='How often to save the model')
    parser.add_argument(
        "--num_epoch", type=int, default=1, help="number of epochs to train"
    )
    # parser.add_argument('--num_iter',
    #                        type=int, default=-1,
    #                        help='how many itersations per epoch (for unlikelihood tuning)')
    parser.add_argument(
        "--log_file", type=str, required=False, help="Where to save the log"
    )
    parser.add_argument(
        "--tb_loc",
        type=str,
        required=False,
        help="Where to save the tensorflow location",
    )
    parser.add_argument(
        "--config_save", type=str, required=False, help="Where to save the config"
    )
    parser.add_argument("--vocab_save", type=str, help="Where to save the vocab")

    # resume_arg = parser.add_argument_group('Resume')
    parser.add_argument(
        "--debug",
        default=False,
        action="store_true",
        help="do not erase cache at end of program",
    )
    parser.add_argument(
        "--fast_dev_run",
        default=False,
        help="This flag runs a “unit test” by running n if set to n (int) else 1 if set to True training and validation batch(es).",
    )
    parser.add_argument(
        "--freeze_model",
        default=False,
        action="store_true",
        help="freeze weights of bert model during fine tuning",
    )
    parser.add_argument(
        "--resume", default=False, action="store_true", help="Resume from a saved model"
    )
    parser.add_argument(
        "--rotate",
        default=False,
        action="store_true",
        help="use rotational relative embedding",
    )
    parser.add_argument(
        "--model_load", type=str, required=False, help="Where to load the model"
    )
    parser.add_argument(
        "--root_dir", type=str, required=False, default=".", help="location of root dir"
    )
    parser.add_argument(
        "--config_load", type=str, required=False, help="Where to load the config"
    )
    parser.add_argument(
        "--gpus", type=int, required=False, default=1, help="number of gpus to use"
    )
    # parser.add_argument('--start_epoch',
    #                        type=int, required=False, default=0,
    #                        help='Where to load the config')

    parser.add_argument(
        "--model_arch",
        type=str,
        required=False,
        help="used to teack model arch in params",
    )
    parser.add_argument(
        "--eval_every",
        type=int,
        default=50000,
        help="run evaluation every x iterations",
    )
    parser.add_argument(
        "--num_feats",
        type=int,
        required=False,
        default=32,
        help="number of random reatures for FAVOR+",
    )
    parser.add_argument(
        "--max_epochs", type=int, required=False, default=1, help="max number of epochs"
    )

    # debug() FINE TUNEING
    # parser.add_argument('--save_dir', type=str, required=True)
    parser.add_argument(
        "--mode", type=str, default="cls", help="type of pooling to use"
    )
    parser.add_argument("--dataset_length", type=int, default=None, required=False)
    parser.add_argument("--num_workers", type=int, default=0, required=False)
    parser.add_argument("--dropout", type=float, default=0.1, required=False)
    # parser.add_argument("--dims", type=int, nargs="*", default="", required=False)
    parser.add_argument(
        "--smiles_embedding",
        type=str,
        default="/dccstor/medscan7/smallmolecule/runs/ba-predictor/small-data/embeddings/protein/ba_embeddings_tanh_512_2986138_2.pt",
    )
    # parser.add_argument("--train_pct", type=str, required=False, default="95")
    # parser.add_argument("--aug", type=int, required=True)
    parser.add_argument("--dataset_name", type=str, required=False, default="sol")
    parser.add_argument("--measure_name", type=str, required=False, default="measure")
    # parser.add_argument("--emb_type", type=str, required=True)
    parser.add_argument("--checkpoints_folder", type=str, required=True)
    # parser.add_argument("--results_dir", type=str, required=True)
    # parser.add_argument("--patience_epochs", type=int, required=True)
    parser.add_argument("--model_path", type=str, default="./smi_ted/")
    parser.add_argument("--ckpt_filename", type=str, default="smi_ted_Light_40.pt")
    # parser.add_argument('--n_output', type=int, default=1)
    parser.add_argument("--save_every_epoch", type=int, default=0)
    parser.add_argument("--save_ckpt", type=int, default=1)
    parser.add_argument("--start_seed", type=int, default=0)
    parser.add_argument("--smi_ted_version", type=str, default="v1")
    parser.add_argument("--train_decoder", type=int, default=1)
    parser.add_argument("--target_metric", type=str, default="rmse")
    parser.add_argument("--loss_fn", type=str, default="mae")

    parser.add_argument(
        "--data_root",
        type=str,
        required=False,
        default="/dccstor/medscan7/smallmolecule/runs/ba-predictor/small-data/affinity",
    )
    # parser.add_argument("--use_bn", type=int, default=0)
    parser.add_argument("--use_linear", type=int, default=0)

    parser.add_argument("--lr", type=float, default=0.001)
    # parser.add_argument("--weight_decay", type=float, default=5e-4)
    # parser.add_argument("--val_check_interval", type=float, default=1.0)
    parser.add_argument("--batch_size", type=int, default=64)

    return parser


def parse_args():
    parser = get_parser()
    args = parser.parse_args()
    return args