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new_optimization_frag.py
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new_optimization_frag.py
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# -*- coding: utf-8 -*-
# @Time : 2022/4/10 11:36
# @Author : FAN FAN
# @Site :
# @File : optimization.py
# @Software: PyCharm
from src.feature.atom_featurizer import classic_atom_featurizer
from src.feature.bond_featurizer import classic_bond_featurizer
from src.feature.mol_featurizer import classic_mol_featurizer
from utils.mol2graph import smiles_2_bigraph
from utils.junctiontree_encoder import JT_SubGraph
from utils.splitter import Splitter
from utils.metrics import Metrics
from utils.Earlystopping import EarlyStopping
from data.csv_dataset import MoleculeCSVDataset
from src.dgltools import collate_molgraphs, collate_fraggraphs
from data.dataloading import import_dataset
import torch
from torch.utils.data import DataLoader
import os
import time
import numpy as np
import pandas as pd
from tqdm import tqdm
from utils.count_parameters import count_parameters
from networks.DMPNN import DMPNNNet
from networks.MPNN import MPNNNet
from networks.AttentiveFP import AttentiveFPNet
from networks.AGC import AGCNet
from networks.FraGAT import NewFraGATNet
from utils.Set_Seed_Reproducibility import set_seed
from utils.piplines import train_epoch, evaluate, train_epoch_frag, evaluate_frag, PreFetch
from bayes_opt import BayesianOptimization, SequentialDomainReductionTransformer
params = {}
net_params = {}
#params['Dataset'] = 'HFUS'
params['init_lr'] = 1e-3
params['min_lr'] = 1e-9
params['weight_decay'] = 0
params['lr_reduce_factor'] = 0.8
params['lr_schedule_patience'] = 30
params['earlystopping_patience'] = 50
params['max_epoch'] = 300
net_params['num_atom_type'] = 39
net_params['num_bond_type'] = 12
net_params['hidden_dim'] = 16
net_params['num_heads'] = 1
net_params['dropout'] = 0
net_params['depth'] = 2
net_params['layers'] = 2
net_params['residual'] = False
net_params['batch_norm'] = False
net_params['layer_norm'] = False
net_params['device'] = 'cuda'
dataset_list = ['BMP']
#splitting_list = [3807, 146, 1945, 3560] DMPNN
#splitting_list = [27, 1538, 848, 4113] MPNN
#splitting_list = [1453, 2450, 777, 1748] #AGC
splitting_list = [2450]
def main(params, net_params):
#set_seed(seed=1000)
model = NewFraGATNet(net_params).to(device='cuda')
optimizer = torch.optim.Adam(model.parameters(), lr=params['init_lr'], weight_decay=params['weight_decay'])
scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer, mode='min', factor=params['lr_reduce_factor'],
patience=params['lr_schedule_patience'], verbose=False)
t0 = time.time()
per_epoch_time = []
early_stopping = EarlyStopping(patience=params['earlystopping_patience'], path='checkpoint1' + params['Dataset'] + 'FraGAT' + '.pt')
n_param = count_parameters(model)
for epoch in range(params['max_epoch']):
#t.set_description('Epoch %d' % epoch)
start = time.time()
model, epoch_train_loss, epoch_train_metrics = train_epoch_frag(model, optimizer, scaling,
fetched_data.train_iter, fetched_data.train_batched_origin_graph_list,
fetched_data.train_batched_frag_graph_list,
fetched_data.train_batched_motif_graph_list,
fetched_data.train_targets_list,
fetched_data.train_smiles_list,
fetched_data.train_names_list, n_param)
epoch_val_loss, epoch_val_metrics = evaluate_frag(model, scaling, fetched_data.val_iter, fetched_data.val_batched_origin_graph_list,
fetched_data.val_batched_frag_graph_list, fetched_data.val_batched_motif_graph_list,
fetched_data.val_targets_list, fetched_data.val_smiles_list, fetched_data.val_names_list, n_param)
#t.set_postfix({'time': time.time() - start, 'lr': optimizer.param_groups[0]['lr'],
# 'train_loss': epoch_train_loss, 'val_loss': epoch_val_loss,
# 'train_R2': epoch_train_metrics.R2, 'val_R2': epoch_val_metrics.R2})
#per_epoch_time.append(time.time() - start)
scheduler.step(epoch_val_loss)
if optimizer.param_groups[0]['lr'] < params['min_lr']:
print('\n! LR equal to min LR set.')
break
early_stopping(epoch_val_loss, model)
if early_stopping.early_stop:
break
model = early_stopping.load_checkpoint(model)
_, epoch_train_metrics = evaluate_frag(model, scaling, fetched_data.train_iter, fetched_data.train_batched_origin_graph_list,
fetched_data.train_batched_frag_graph_list, fetched_data.train_batched_motif_graph_list,
fetched_data.train_targets_list, fetched_data.train_smiles_list, fetched_data.train_names_list, n_param)
_, epoch_val_metrics = evaluate_frag(model, scaling, fetched_data.val_iter, fetched_data.val_batched_origin_graph_list,
fetched_data.val_batched_frag_graph_list, fetched_data.val_batched_motif_graph_list,
fetched_data.val_targets_list, fetched_data.val_smiles_list, fetched_data.val_names_list, n_param)
_, epoch_test_metrics = evaluate_frag(model, scaling, fetched_data.test_iter, fetched_data.test_batched_origin_graph_list,
fetched_data.test_batched_frag_graph_list, fetched_data.test_batched_motif_graph_list,
fetched_data.test_targets_list, fetched_data.test_smiles_list, fetched_data.test_names_list, n_param)
_, epoch_raw_metrics = evaluate_frag(model, scaling, fetched_data.all_iter, fetched_data.all_batched_origin_graph_list,
fetched_data.all_batched_frag_graph_list, fetched_data.all_batched_motif_graph_list,
fetched_data.all_targets_list, fetched_data.all_smiles_list, fetched_data.all_names_list, n_param)
return epoch_train_metrics, epoch_val_metrics, epoch_test_metrics, epoch_raw_metrics
def Splitting_Main_MO(params, net_params):
"""Built-in function. Use the basic block of implementation in Multi-objective Bayesian Optimization.
Parameters
----------
params : dict
Set of parameters for workflow.
net_params : dict
Set of parameters for architectures of models.
Returns
----------
-train_metrics.RMSE : float
Optimization Objective-1, negative number of RMSE metric in training
-val_metrics.RMSE : float
Optimization Objective-2, negative number of RMSE metric in validation
"""
train_metrics, val_metrics, test_metrics, all_metrics = main(params, net_params)
return -val_metrics.RMSE
def func_to_be_opt_MO(hidden_dim, depth, layers, decay, dropout, init_lr, lr_reduce_factor):
"""Built-in function. Objective function in Single-objective Bayesian Optimization.
Parameters
----------
Returns
----------
"""
net_params['hidden_dim'] = int(hidden_dim)
net_params['layers'] = int(layers)
net_params['depth'] = int(depth)
#net_params['num_heads'] = int(num_heads)
params['weight_decay'] = 10 ** (-int(decay))
params['init_lr'] = 10 ** (-init_lr)
params['lr_reduce_factor'] = 0.4 + 0.05 * int(lr_reduce_factor)
net_params['dropout'] = dropout
return Splitting_Main_MO(params, net_params)
set_seed(seed=1000)
torch.manual_seed(327)
for i in range(len(dataset_list)):
params['Dataset'] = dataset_list[i]
df, scaling = import_dataset(params)
cache_file_path = os.path.realpath('./cache')
if not os.path.exists(cache_file_path):
os.mkdir(cache_file_path)
cache_file = os.path.join(cache_file_path, params['Dataset'] + '_CCC')
error_path = os.path.realpath('./error_log')
if not os.path.exists(error_path):
os.mkdir(error_path)
error_log_path = os.path.join(error_path, '{}_{}'.format(params['Dataset'], time.strftime('%Y-%m-%d-%H-%M')) + '.csv')
fragmentation = JT_SubGraph(scheme='MG_plus_reference')
net_params['frag_dim'] = fragmentation.frag_dim
dataset = MoleculeCSVDataset(df, smiles_2_bigraph, classic_atom_featurizer, classic_bond_featurizer, classic_mol_featurizer, cache_file, load=False
, error_log=error_log_path, fragmentation=fragmentation)
splitter = Splitter(dataset)
rows = []
file_path = os.path.realpath('./output')
if not os.path.exists(file_path):
os.mkdir(file_path)
save_file_path = os.path.join(file_path, '{}_{}_{}_{}_{}'.format('SOPT_UCB_5', params['Dataset'], 'FraGAT', splitting_list[i], time.strftime('%Y-%m-%d-%H-%M')) + '.csv')
#df = pd.DataFrame(columns=['seed', 'train_R2', 'val_R2', 'test_R2', 'all_R2', 'train_MAE', 'val_MAE', 'test_MAE', 'all_MAE',
# 'train_RMSE', 'val_RMSE', 'test_RMSE', 'all_RMSE'])
train_set, val_set, test_set, raw_set = splitter.Random_Splitter(seed=splitting_list[i], frac_train=0.8, frac_val=0.1)
train_loader = DataLoader(train_set, collate_fn=collate_fraggraphs, batch_size=len(train_set), shuffle=False, num_workers=0, worker_init_fn=np.random.seed(1000))
val_loader = DataLoader(val_set, collate_fn=collate_fraggraphs, batch_size=len(val_set), shuffle=False, num_workers=0, worker_init_fn=np.random.seed(1000))
test_loader = DataLoader(test_set, collate_fn=collate_fraggraphs, batch_size=len(test_set), shuffle=False, num_workers=0, worker_init_fn=np.random.seed(1000))
raw_loader = DataLoader(raw_set, collate_fn=collate_fraggraphs, batch_size=len(raw_set), shuffle=False, num_workers=0, worker_init_fn=np.random.seed(1000))
fetched_data = PreFetch(train_loader, val_loader, test_loader, raw_loader, frag=True)
hpbounds = {'hidden_dim': (16, 256.99), 'depth': (1, 5.99), 'layers': (1, 5.99), 'decay': (0, 6.99), 'dropout': (0, 0.5), 'init_lr': (2, 5), 'lr_reduce_factor': (0, 10.99)}
#bounds_transformer = SequentialDomainReductionTransformer()
mutating_optimizer = BayesianOptimization(f=func_to_be_opt_MO, pbounds=hpbounds, verbose=1, random_state=250)
mutating_optimizer.maximize(init_points=5, n_iter=50, acq='ucb', kappa=5)
lst = mutating_optimizer.space.keys
lst.append('target')
df = pd.DataFrame(columns=lst)
for i, res in enumerate(mutating_optimizer.res):
_dict = res['params']
_dict['target'] = res['target']
row = pd.DataFrame(_dict, index=[0])
df = pd.concat([df, row], axis=0, ignore_index=True, sort=False)
df.to_csv(save_file_path, index=False)