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train_peptides_func.py
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import argparse
import os
import torch_geometric
from torch_geometric.loader import DataLoader
import pickle
from torch_geometric.transforms import AddRandomWalkPE, AddLaplacianEigenvectorPE
from utils import *
from metrics import eval_ap
from network.model import *
from dataset.peptides_dataset import PeptidesFunctionalDataset
from network.wave_pe import WaveletPE, Learnable_Equiv_WaveletPE
parser = argparse.ArgumentParser(description="MGT on Peptides Functional Prediction")
parser.add_argument("--out_dir", type = str, default = "./results")
parser.add_argument("--seed", type = int, default=123456)
parser.add_argument("--pe_name", type = str, default = "spectral")
parser.add_argument("--device", type=str, default="cuda:0", help = "cuda device")
parser.add_argument("--batch_size", type = int, default = 128)
parser.add_argument("--num_layer", type = int, default = 2)
parser.add_argument("--num_epoch", type = int, default = 200)
parser.add_argument("--num_head", type = int, default = 4)
parser.add_argument("--norm", type = str, default = "batch")
parser.add_argument('--emb_dim', type = int, default = 84)
parser.add_argument("--num_task", type = int, default = 10)
parser.add_argument("--dropout", type = float, default=0.25)
parser.add_argument("--residual", type = int, default = 1)
parser.add_argument("--num_cluster", type = int, default = 10)
parser.add_argument("--attn_dropout", type = float, default = 0.5)
parser.add_argument("--local_gnn_type", type = str, default = "CustomGatedGCN")
parser.add_argument("--global_model_type", type = str, default = "Transformer")
parser.add_argument("--pos_dim", type = int, default = 8)
parser.add_argument("--version", type = str, default = "custom")
parser.add_argument("--gnn_type", type = str, default = "gine")
args = parser.parse_args()
torch_geometric.seed_everything(1235)
if args.pe_name == "wave":
### Wavelet should be preprocessed to reduce loading time in dataloader during the optimization phase ###
pre_transform = WaveletPE(args.pos_dim, is_undirected = True)
dataset = PeptidesFunctionalDataset(pre_transform=pre_transform)
elif args.pe_name == "learnable_equiv_wave":
pre_transform = Learnable_Equiv_WaveletPE(args.pos_dim, is_undirected=True)
dataset = PeptidesFunctionalDataset(pre_transform = pre_transform)
elif args.pe_name == "laplacian":
transform = AddLaplacianEigenvectorPE(args.pos_dim, attr_name = "pos", is_undirected=True)
dataset = PeptidesFunctionalDataset(transform = transform)
elif args.pe_name == "random_walk":
transform = AddRandomWalkPE(args.pos_dim, attr_name = "pos")
dataset = PeptidesFunctionalDataset(transform=transform)
else:
raise NotImplementedError
split = dataset.get_idx_split()
train_data = dataset[split['train']]
valid_data = dataset[split["val"]]
test_data = dataset[split["test"]]
print("Num train: ", len(train_data))
print("Num valid: ", len(valid_data))
print("Num test: ", len(test_data))
train_loader = DataLoader(train_data, batch_size = args.batch_size, shuffle = True, num_workers = 6, pin_memory = False)
valid_loader = DataLoader(valid_data, batch_size = args.batch_size, shuffle = False, num_workers = 6, pin_memory = False)
test_loader = DataLoader(test_data, batch_size = args.batch_size, shuffle = False, num_workers = 6, pin_memory = False)
device = args.device
num_layer = args.num_layer
num_head = args.num_head
for batch in train_loader:
print(batch)
break
if args.version == "custom":
model = CustomMGT(args).to(args.device)
else:
model = MGT(args.num_layer, args.emb_dim, args.pos_dim, args.num_task, args.num_head, args.dropout,
args.attn_dropout, args.norm, args.num_cluster, args.gnn_type, args.pe_name, args.device).to(args.device)
print("Number of parameters: ", model.num_parameters)
optimizer = torch.optim.AdamW(model.parameters(), lr = 0.001)
scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer, 'max', min_lr = 1e-6, verbose=True, factor = 0.5)
evaluator = eval_ap
best_val_loss = 1e9
best_val_ap = 0
test_ap_at_best_val_ap = -1
valid_loss = None
for epoch in range(1, args.num_epoch + 1):
print("=====Epoch {}".format(epoch))
print('Training...')
train_loss = train_with_cluster(model, args.device, train_loader, optimizer, ["classification"])
print('Evaluating...')
valid_ap = eval_with_cluster(model, args.device, valid_loader, evaluator, "classification")
test_ap = eval_with_cluster(model, args.device, test_loader, evaluator, "classification")
scheduler.step(valid_ap)
if best_val_ap < valid_ap:
best_val_ap = valid_ap
test_ap_at_best_val_ap = test_ap
print('| Train Loss: {:5.5f} | Validation AP: {:5.5f} | Test AP: {:5.5f}'.format(train_loss, valid_ap, test_ap))
print()
print()
print(args)
print()
print("Seed: ", args.seed)
print("Best validation ap: ", best_val_ap)
print("Test ap: ", test_ap_at_best_val_ap)