utils/args.py

import argparse
import uuid
import logging
import time
import os
import sys
from utils.logger import create_exp_dir
import glob


class ArgsInit(object):
    def __init__(self):
        parser = argparse.ArgumentParser(description="DeeperGCN")
        # ===================== DATASET =====================
        parser.add_argument(
            "--seed", type=int,
            default=1, help="Seed for numpy and torch"
        )
        parser.add_argument(
            "--num_workers", type=int, 
            default=0, help="number of workers (default: 0)"
        )
        parser.add_argument(
            "--batch_size", type=int, 
            default=5120, help="input batch size for training (default: 5120)",
        )
        parser.add_argument(
            "--feature", type=str,
            default="full", help="two options: full or simple"
        )
        parser.add_argument(
            "--add_virtual_node",
            action="store_true"
        )
        
        # ===================== TRAIN & EVAL =====================
        parser.add_argument(
            "--use_gpu", action="store_true"
        )
        parser.add_argument(
            "--device", type=int,
            default=0, help="which gpu to use if any (default: 0)"
        )
        parser.add_argument(
            "--epochs", type=int,
            default=20, help="number of epochs to train (default: 300)",
        )
        parser.add_argument(
            "--lr", type=float,
            default=5e-5, help="learning rate set for optimizer (default: 5e-5)"
        )
        parser.add_argument(
            "--dropout", type=float,
            default=0.2, help="Dropout rate layer (default: 0.2)"
        )
        # model
        parser.add_argument(
            "--num_layers",
            type=int,
            default=20,
            help="the number of layers of the networks",
        )
        parser.add_argument(
            "--mlp_layers",
            type=int,
            default=3,
            help="the number of layers of mlp in conv",
        )
        parser.add_argument(
            "--hidden_channels",
            type=int,
            default=128,
            help="the dimension of embeddings of nodes and edges",
        )
        parser.add_argument(
            "--block",
            default="res+",
            type=str,
            help="graph backbone block type {res+, res, dense, plain}",
        )
        parser.add_argument("--conv", type=str, default="gen", help="the type of GCNs")
        parser.add_argument(
            "--gcn_aggr",
            type=str,
            default="softmax",
            help="the aggregator of GENConv [mean, max, add, softmax, softmax_sg, power]",
        )
        parser.add_argument(
            "--norm", type=str, default="batch", help="the type of normalization layer"
        )
        parser.add_argument(
            "--num_tasks", type=int, default=1, help="the number of prediction tasks"
        )
        # learnable parameters
        parser.add_argument(
            "--t", type=float, default=1.0, help="the temperature of SoftMax"
        )
        parser.add_argument(
            "--p", type=float, default=1.0, help="the power of PowerMean"
        )
        parser.add_argument("--learn_t", action="store_true")
        parser.add_argument("--learn_p", action="store_true")
        # message norm
        parser.add_argument("--msg_norm", action="store_true")
        parser.add_argument("--learn_msg_scale", action="store_true")
        # encode edge in conv
        parser.add_argument("--conv_encode_edge", action="store_true")
        # graph pooling type
        parser.add_argument(
            "--graph_pooling", type=str, default="mean", help="graph pooling method"
        )
        # save model
        parser.add_argument(
            "--model_save_path",
            type=str,
            default="model_ckpt",
            help="the directory used to save models",
        )
        parser.add_argument("--save", type=str, default="EXP", help="experiment name")
        # load pre-trained model
        parser.add_argument(
            "--model_load_init_path",
            type=str,
            default="/media/SSD5/pruiz/home/Best_Models",
            help="the directory to load adversarial weights",
        )
        parser.add_argument(
            "--model_load_prot_init_path",
            type=str,
            default="/media/SSD5/pruiz/home/Best_Models",
            help="the directory to load protein weights",
        )
        parser.add_argument(
            "--model_load_path",
            type=str,
            default="Checkpoint_Last_model.pth",
            help="the path of pre-trained model",
        )
        parser.add_argument(
            "--resume",
            action="store_true",
            default=False,
            help="resume training from a previous model",
        )
        # data partition
        parser.add_argument("--cross_val", type=int, default=0, help="Data partition")
        # Task
        parser.add_argument(
            "--task_type", type=str, default="classification", help="Choose task type"
        )
        parser.add_argument(
            "--binary",
            action="store_true",
            default=False,
            help="Performed de binary task",
        )
        parser.add_argument(
            "--balanced_loader",
            action="store_true",
            default=False,
            help="Balance the dataloader",
        )
        parser.add_argument(
            "--target", type=str, default=None, help="Target for the binary task"
        )
        parser.add_argument(
            "--nclasses", type=int, default=102, help="number of target classes"
        )
        parser.add_argument(
            "--num_features",
            type=int,
            default=2,
            help="Num of features used for simple classification",
        )
        # PROTEIN MODEL
        parser.add_argument(
            "--LMPM",
            action="store_true",
            default=False,
            help="Initialize training the LM and PM jointly.",
        )
        parser.add_argument(
            "--PLANET",
            action="store_true",
            default=False,
            help="Initialize training PLANET.",
        )
        parser.add_argument(
            "--use_prot", action="store_true", default=False, help="Use protein info"
        )
        parser.add_argument(
            "--freeze_molecule",
            action="store_true",
            default=False,
            help="Whether to freeze molecule network",
        )
        parser.add_argument(
            "--num_layers_prot",
            type=int,
            default=20,
            help="the number of layers of the networks",
        )
        parser.add_argument(
            "--mlp_layers_prot",
            type=int,
            default=3,
            help="the number of layers of mlp in conv",
        )
        parser.add_argument(
            "--hidden_channels_prot",
            type=int,
            default=128,
            help="the dimension of embeddings of nodes and edges",
        )
        parser.add_argument("--msg_norm_prot", action="store_true", default=False)
        parser.add_argument(
            "--learn_msg_scale_prot", action="store_true", default=False
        )
        parser.add_argument(
            "--conv_encode_edge_prot", action="store_true", default=False
        )
        parser.add_argument("--use_prot_metadata", action="store_true", default=False)
        parser.add_argument(
            "--num_metadata",
            type=int,
            default=240,
            help="Number of metadata of the protein.",
        )
        parser.add_argument(
            "--scalar",
            action="store_true",
            default=False,
            help="Use same multiplier factor for all metadata",
        )
        # CONCATENATION MULTIPLIER
        parser.add_argument(
            "--multi_concat",
            action="store_true",
            default=False,
            help="Use a multiplier to concant info",
        )
        # CONCATENATION MLP
        parser.add_argument(
            "--MLP",
            action="store_true",
            default=False,
            help="Use a multiplier to concant info",
        )
        # ADVERSARIAL AUGMENTATION TRAINING
        parser.add_argument(
            "--init_adv_training",
            action="store_true",
            default=False,
            help="Initialize training with adversarial molecules",
        )
        parser.add_argument(
            "--advs",
            action="store_true",
            default=False,
            help="Training with adversarial molecules",
        )
        parser.add_argument(
            "--saliency",
            action="store_true",
            default=False,
            help="Allow backpropagation through atom features.",
        )
        parser.add_argument(
            "--inference_path",
            type=str,
            help='path model for inference',
            default=None
        )
        parser.add_argument(
            "--target_checkpoint_path",
            type=str,
            help='path to the target checkpoints',
            default=None
        )
        parser.add_argument(
            "--target_list",
            type=str,
            help='path to the target list mappings',
            default=None
        )
        parser.add_argument(
            "--input_file_smiles",
            type=str,
            help='path input file with smiles for inference',
            default=None
        )
        parser.add_argument(
            "--output_file",
            type=str,
            help='path output file with predictions',
            default=None
        )

        self.args = parser.parse_args()

    def save_exp(self):
        self.args.save = "{}/Fold{}".format(self.args.save, str(self.args.cross_val))
        self.args.save = "log/{}".format(self.args.save)
        self.args.model_save_path = os.path.join(
            self.args.save, self.args.model_save_path
        )
        create_exp_dir(self.args.save, scripts_to_save=glob.glob("*.py"))
        log_format = "%(asctime)s %(message)s"
        logging.basicConfig(
            stream=sys.stdout,
            level=logging.INFO,
            format=log_format,
            datefmt="%m/%d %I:%M:%S %p",
        )
        fh = logging.FileHandler(os.path.join(self.args.save, "log.txt"))
        fh.setFormatter(logging.Formatter(log_format))
        logging.getLogger().addHandler(fh)

        return self.args