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run.py
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run.py
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# -*- coding: utf-8 -*-
import sys
import random
import os
import numpy as np
from collections import defaultdict
sys.path.append(os.getcwd()) #add the env path
from sklearn.model_selection import train_test_split,StratifiedKFold
from main import train
from config import DRUG_EXAMPLE, RESULT_LOG, PROCESSED_DATA_DIR, LOG_DIR, MODEL_SAVED_DIR, ENTITY2ID_FILE, KG_FILE, \
EXAMPLE_FILE, DRUG_VOCAB_TEMPLATE, ENTITY_VOCAB_TEMPLATE, \
RELATION_VOCAB_TEMPLATE, SEPARATOR, THRESHOLD, TRAIN_DATA_TEMPLATE, DEV_DATA_TEMPLATE, \
TEST_DATA_TEMPLATE, ADJ_ENTITY_TEMPLATE, ADJ_RELATION_TEMPLATE, ModelConfig, NEIGHBOR_SIZE
from utils import pickle_dump, format_filename,write_log,pickle_load
def read_entity2id_file(file_path: str, drug_vocab: dict, entity_vocab: dict):
print(f'Logging Info - Reading entity2id file: {file_path}' )
assert len(drug_vocab) == 0 and len(entity_vocab) == 0
with open(file_path, encoding='utf8') as reader:
count=0
for line in reader:
if(count==0):
count+=1
continue
drug, entity = line.strip().split('\t')
drug_vocab[entity]=len(drug_vocab)
entity_vocab[entity] = len(entity_vocab)
def read_example_file(file_path:str,separator:str,drug_vocab:dict):
print(f'Logging Info - Reading example file: {file_path}')
assert len(drug_vocab)>0
examples=[]
with open(file_path,encoding='utf8') as reader:
for idx,line in enumerate(reader):
d1,d2,flag=line.strip().split(separator)[:3]
if d1 not in drug_vocab or d2 not in drug_vocab:
continue
if d1 in drug_vocab and d2 in drug_vocab:
examples.append([drug_vocab[d1],drug_vocab[d2],int(flag)])
examples_matrix=np.array(examples)
print(f'size of example: {examples_matrix.shape}')
X=examples_matrix[:,:2]
y=examples_matrix[:,2:3]
train_data_X, valid_data_X,train_y,val_y = train_test_split(X,y, test_size=0.2,stratify=y)
train_data=np.c_[train_data_X,train_y]
valid_data_X, test_data_X,val_y,test_y = train_test_split(valid_data_X,val_y, test_size=0.5)
valid_data=np.c_[valid_data_X,val_y]
test_data=np.c_[test_data_X,test_y]
return examples_matrix
def read_kg(file_path: str, entity_vocab: dict, relation_vocab: dict, neighbor_sample_size: int):
print(f'Logging Info - Reading kg file: {file_path}')
kg = defaultdict(list)
with open(file_path, encoding='utf8') as reader:
count=0
for line in reader:
if count==0:
count+=1
continue
head, tail, relation = line.strip().split(' ')
if head not in entity_vocab:
entity_vocab[head] = len(entity_vocab)
if tail not in entity_vocab:
entity_vocab[tail] = len(entity_vocab)
if relation not in relation_vocab:
relation_vocab[relation] = len(relation_vocab)
# undirected graph
kg[entity_vocab[head]].append((entity_vocab[tail], relation_vocab[relation]))
kg[entity_vocab[tail]].append((entity_vocab[head], relation_vocab[relation]))
print(f'Logging Info - num of entities: {len(entity_vocab)}, '
f'num of relations: {len(relation_vocab)}')
print('Logging Info - Constructing adjacency matrix...')
n_entity = len(entity_vocab)
adj_entity = np.zeros(shape=(n_entity, neighbor_sample_size), dtype=np.int64)
adj_relation = np.zeros(shape=(n_entity, neighbor_sample_size), dtype=np.int64)
for entity_id in range(n_entity):
all_neighbors = kg[entity_id]
n_neighbor = len(all_neighbors)
sample_indices = np.random.choice(
n_neighbor,
neighbor_sample_size,
replace=False if n_neighbor >= neighbor_sample_size else True
)
adj_entity[entity_id] = np.array([all_neighbors[i][0] for i in sample_indices])
adj_relation[entity_id] = np.array([all_neighbors[i][1] for i in sample_indices])
return adj_entity, adj_relation
def process_data(dataset: str, neighbor_sample_size: int,K:int):
drug_vocab = {}
entity_vocab = {}
relation_vocab = {}
read_entity2id_file(ENTITY2ID_FILE[dataset], drug_vocab, entity_vocab)
pickle_dump(format_filename(PROCESSED_DATA_DIR, DRUG_VOCAB_TEMPLATE, dataset=dataset),drug_vocab)
pickle_dump(format_filename(PROCESSED_DATA_DIR, ENTITY_VOCAB_TEMPLATE, dataset=dataset),entity_vocab)
examples_file=format_filename(PROCESSED_DATA_DIR, DRUG_EXAMPLE, dataset=dataset)
examples = read_example_file(EXAMPLE_FILE[dataset], SEPARATOR[dataset],drug_vocab)
np.save(examples_file,examples)
adj_entity_file = format_filename(PROCESSED_DATA_DIR, ADJ_ENTITY_TEMPLATE, dataset=dataset)
adj_relation_file = format_filename(PROCESSED_DATA_DIR, ADJ_RELATION_TEMPLATE, dataset=dataset)
adj_entity, adj_relation = read_kg(KG_FILE[dataset], entity_vocab, relation_vocab,
neighbor_sample_size)
pickle_dump(format_filename(PROCESSED_DATA_DIR, DRUG_VOCAB_TEMPLATE, dataset=dataset),
drug_vocab)
pickle_dump(format_filename(PROCESSED_DATA_DIR, ENTITY_VOCAB_TEMPLATE, dataset=dataset),
entity_vocab)
pickle_dump(format_filename(PROCESSED_DATA_DIR, RELATION_VOCAB_TEMPLATE, dataset=dataset),
relation_vocab)
adj_entity_file = format_filename(PROCESSED_DATA_DIR, ADJ_ENTITY_TEMPLATE, dataset=dataset)
np.save(adj_entity_file, adj_entity)
print('Logging Info - Saved:', adj_entity_file)
adj_relation_file = format_filename(PROCESSED_DATA_DIR, ADJ_RELATION_TEMPLATE, dataset=dataset)
np.save(adj_relation_file, adj_relation)
print('Logging Info - Saved:', adj_entity_file)
cross_validation(K,examples,dataset,neighbor_sample_size)
def cross_validation(K_fold,examples,dataset,neighbor_sample_size):
subsets=dict()
n_subsets=int(len(examples)/K_fold)
remain=set(range(0,len(examples)-1))
for i in reversed(range(0,K_fold-1)):
subsets[i]=random.sample(remain,n_subsets)
remain=remain.difference(subsets[i])
subsets[K_fold-1]=remain
aggregator_types=['sum','concat','neigh']
for t in aggregator_types:
count=1
temp={'dataset':dataset,'aggregator_type':t,'avg_auc':0.0,'avg_acc':0.0,'avg_f1':0.0,'avg_aupr':0.0}
for i in reversed(range(0,K_fold)):
test_d=examples[list(subsets[i])]
val_d,test_data=train_test_split(test_d,test_size=0.5)
train_d=[]
for j in range(0,K_fold):
if i!=j:
train_d.extend(examples[list(subsets[j])])
train_data=np.array(train_d)
train_log=train(
kfold=count,
dataset=dataset,
train_d=train_data,
dev_d=val_d,
test_d=test_data,
neighbor_sample_size=neighbor_sample_size,
embed_dim=32,
n_depth=2,
l2_weight=1e-7,
lr=2e-2,
#lr=5e-3,
optimizer_type='adam',
batch_size=2048,
aggregator_type=t,
n_epoch=50,
callbacks_to_add=['modelcheckpoint', 'earlystopping']
)
count+=1
temp['avg_auc']=temp['avg_auc']+train_log['test_auc']
temp['avg_acc']=temp['avg_acc']+train_log['test_acc']
temp['avg_f1']=temp['avg_f1']+train_log['test_f1']
temp['avg_aupr']=temp['avg_aupr']+train_log['test_aupr']
for key in temp:
if key=='aggregator_type' or key=='dataset':
continue
temp[key]=temp[key]/K_fold
write_log(format_filename(LOG_DIR, RESULT_LOG[dataset]),temp,'a')
print(f'Logging Info - {K_fold} fold result: avg_auc: {temp["avg_auc"]}, avg_acc: {temp["avg_acc"]}, avg_f1: {temp["avg_f1"]}, avg_aupr: {temp["avg_aupr"]}')
if __name__ == '__main__':
if not os.path.exists(PROCESSED_DATA_DIR):
os.makedirs(PROCESSED_DATA_DIR)
if not os.path.exists(LOG_DIR):
os.makedirs(LOG_DIR)
if not os.path.exists(MODEL_SAVED_DIR):
os.makedirs(MODEL_SAVED_DIR)
model_config = ModelConfig()
process_data('kegg',NEIGHBOR_SIZE['kegg'],5)