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kegg_distmult.py
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kegg_distmult.py
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import openke
from openke.config import Trainer, Tester
from openke.module.model import DistMult
from openke.module.loss import SoftplusLoss
from openke.module.strategy import NegativeSampling
from openke.data import TrainDataLoader, TestDataLoader
import os
os.environ['CUDA_VISIBLE_DEVICES'] = '0'
# True表示加入分子结构信息，False表示不加入
add_mol = True # False or True
# 数据集名字
dataset = "KEGG"
# 药物表示的路径
entity_description_path = './gin_infomax_'+dataset+'.npy'
# dataloader for training
train_dataloader = TrainDataLoader(
in_path = "./benchmarks/%s/"%dataset,
nbatches = 10,
threads = 8,
sampling_mode = "normal",
bern_flag = 1,
filter_flag = 1,
neg_ent = 25,
neg_rel = 0
)
# define the model
distmult = DistMult(
add_mol = add_mol,
entity_description_path = entity_description_path,
ent_tot = train_dataloader.get_ent_tot(),
rel_tot = train_dataloader.get_rel_tot(),
dim = 300
)
# define the loss function
model = NegativeSampling(
model = distmult,
loss = SoftplusLoss(),
batch_size = train_dataloader.get_batch_size(),
regul_rate = 1.0
)
# ----------------------------------------------训练----------------------------------------
""""""
trainer = Trainer(model = model, data_loader = train_dataloader, train_times = 500, alpha = 0.1, use_gpu = True, opt_method = "adagrad")
trainer.run()
if add_mol:
distmult.save_checkpoint('./checkpoint_'+dataset+'/distmult_my.ckpt')
else:
distmult.save_checkpoint('./checkpoint_'+dataset+'/distmult.ckpt')
# ----------------------------------------------测试----------------------------------------
# 读取模型
if add_mol:
distmult.load_checkpoint('./checkpoint_'+dataset+'/distmult_my.ckpt')
else:
distmult.load_checkpoint('./checkpoint_'+dataset+'/distmult.ckpt')
""""""
# 1、链接预测
test_dataloader = TestDataLoader("./benchmarks/%s/"%dataset, "test2id.txt", "link")
tester = Tester(model = distmult, data_loader = test_dataloader, use_gpu = True)
tester.run_link_prediction(type_constrain = False)
"""
# 2、三元组分类
# 2.1先用验证集找到最好的threshold
print("---------------------------------------三元组分类验证--------------------=--------------")
valid_dataloader = TestDataLoader("./benchmarks/DeepDDI/", "valid2id.txt", "classification")
valider = Tester(model = complEx, data_loader = valid_dataloader, use_gpu = True)
acc, precision, recall, F1, roc_auc, pr_auc, threshlod = valider.run_triple_classification()
# 2.2拿得到的threshold去测试
print("---------------------------------------三元组分类测试--------------------=--------------")
test_dataloader = TestDataLoader("./benchmarks/DeepDDI/", "test2id.txt", "classification")
tester = Tester(model = complEx, data_loader = test_dataloader, use_gpu = True)
acc, precision, recall, F1, roc_auc, pr_auc, threshlod = tester.run_triple_classification(threshlod = threshlod)
print("准确率为：%.4f;精确率为：%.4f;召回率为：%.4f;F1值为：%.4f;roc_auc值为：%.4f;pr_auc为：%.4f" % (acc, precision, recall, F1, roc_auc, pr_auc))
"""
# 3、关系预测
test_dataloader = TestDataLoader("./benchmarks/%s/"%dataset, "test2id.txt", "relation")
tester = Tester(model = distmult, data_loader = test_dataloader, use_gpu = True)
tester.run_relation_prediction()
""" 4、DDI分类"""
tester = Tester(model = distmult, data_loader = None, use_gpu = True)
tester.run_ddi_classification("./benchmarks/%s/"%dataset, "test2id.txt")