赛事背景
赛题地址:https://challenge.xfyun.cn/topic/info?type=abstract-of-the-paper&option=ssgy&ch=ZuoaKcY
医学领域的文献库中蕴含了丰富的疾病诊断和治疗信息，如何高效地从海量文献中提取关键信息，进行疾病诊断和治疗推荐，对于临床医生和研究人员具有重要意义。
赛事任务
本任务分为两个子任务：
- 机器通过对论文摘要等信息的理解，判断该论文是否属于医学领域的文献。
- 提取出该论文关键词。
实践思路
基于任务一：使用BERT模型预训练进行建模预测。
学习文档：https://datawhaler.feishu.cn/docx/EVoodR6WroWZxXxa3a0cukIanRO
任务1示例：
输入：
论文信息，格式如下：
Inflammatory Breast Cancer: What to Know About This Unique, Aggressive Breast Cancer.，
[Arjun Menta, Tamer M Fouad, Anthony Lucci, Huong Le-Petross, Michael C Stauder, Wendy A Woodward, Naoto T Ueno, Bora Lim]，
Inflammatory breast cancer (IBC) is a rare form of breast cancer that accounts for only 2% to 4% of all breast cancer cases. Despite its low incidence, IBC contributes to 7% to 10% of breast cancer caused mortality. Despite ongoing international efforts to formulate better diagnosis, treatment, and research, the survival of patients with IBC has not been significantly improved, and there are no therapeutic agents that specifically target IBC to date. The authors present a comprehensive overview that aims to assess the present and new management strategies of IBC.，
Breast changes; Clinical trials; Inflammatory breast cancer; Trimodality care.
输出：
是
#导入前置依赖
import os
import pandas as pd
import torch
from torch import nn
from torch.utils.data import Dataset, DataLoader
# 用于加载bert模型的分词器
from transformers import AutoTokenizer
# 用于加载bert模型
from transformers import BertModel, BertTokenizer
from pathlib import Path
batch_size = 16
# 文本的最大长度
text_max_length = 256
# 总训练的epochs数，我只是随便定义了个数
epochs = 50
# 学习率
lr = 3e-5
# 取多少训练集的数据作为验证集
validation_ratio = 0.1
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
# 每多少步，打印一次loss
log_per_step = 50
# # 数据集所在位置
# dataset_dir = Path("./基于论文摘要的文本分类与关键词抽取挑战赛公开数据")
# os.makedirs(dataset_dir) if not os.path.exists(dataset_dir) else ''
# 模型存储路径
model_dir = Path("./model/bert_checkpoints")
# 如果模型目录不存在，则创建一个
os.makedirs(model_dir) if not os.path.exists(model_dir) else ''
print("Device:", device)
# 读取数据集，进行数据处理
pd_train_data = pd.read_csv('./train.csv')
pd_train_data['title'] = pd_train_data['title'].fillna('')
pd_train_data['abstract'] = pd_train_data['abstract'].fillna('')
test_data = pd.read_csv('./test.csv')
test_data['title'] = test_data['title'].fillna('')
test_data['abstract'] = test_data['abstract'].fillna('')
pd_train_data['text'] = pd_train_data['title'].fillna('') + '[SEP]' + pd_train_data['author'].fillna('') + '[SEP]' + pd_train_data['abstract'].fillna('')+ '[SEP]' + pd_train_data['Keywords'].fillna('')
test_data['text'] = test_data['title'].fillna('') + '[SEP]' + test_data['author'].fillna('') + '[SEP]' + test_data['abstract'].fillna('')+ ' ' + pd_train_data['Keywords'].fillna('')
# 从训练集中随机采样测试集
validation_data = pd_train_data.sample(frac=validation_ratio)
train_data = pd_train_data[~pd_train_data.index.isin(validation_data.index)]
# 构建Dataset
class MyDataset(Dataset):
def __init__(self, mode='train'):
super(MyDataset, self).__init__()
self.mode = mode
# 拿到对应的数据
if mode == 'train':
self.dataset = train_data
elif mode == 'validation':
self.dataset = validation_data
elif mode == 'test':
# 如果是测试模式，则返回内容和uuid。拿uuid做target主要是方便后面写入结果。
self.dataset = test_data
else:
raise Exception("Unknown mode {}".format(mode))
def __getitem__(self, index):
# 取第index条
data = self.dataset.iloc[index]
# 取其内容
text = data['text']
# 根据状态返回内容
if self.mode == 'test':
# 如果是test，将uuid做为target
label = data['uuid']
else:
label = data['label']
# 返回内容和label
return text, label
def __len__(self):
return len(self.dataset)
train_dataset = MyDataset('train')
validation_dataset = MyDataset('validation')
#获取Bert预训练模型
tokenizer = AutoTokenizer.from_pretrained("./bert-base-uncased")
#接着构造我们的Dataloader。
#我们需要定义一下collate_fn，在其中完成对句子进行编码、填充、组装batch等动作：
def collate_fn(batch):
"""
将一个batch的文本句子转成tensor，并组成batch。
:param batch: 一个batch的句子，例如: [('推文', target), ('推文', target), ...]
:return: 处理后的结果，例如：
src: {'input_ids': tensor([[ 101, ..., 102, 0, 0, ...], ...]), 'attention_mask': tensor([[1, ..., 1, 0, ...], ...])}
target：[1, 1, 0, ...]
"""
text, label = zip(*batch)
text, label = list(text), list(label)
# src是要送给bert的，所以不需要特殊处理，直接用tokenizer的结果即可
# padding='max_length' 不够长度的进行填充
# truncation=True 长度过长的进行裁剪
src = tokenizer(text, padding='max_length', max_length=text_max_length, return_tensors='pt', truncation=True)
return src, torch.LongTensor(label)
train_loader = DataLoader(train_dataset, batch_size=batch_size, shuffle=True, collate_fn=collate_fn)
validation_loader = DataLoader(validation_dataset, batch_size=batch_size, shuffle=False, collate_fn=collate_fn)
#定义预测模型，该模型由bert模型加上最后的预测层组成
class MyModel(nn.Module):
def __init__(self):
super(MyModel, self).__init__()
# 加载bert模型
self.bert = BertModel.from_pretrained('bert-base-uncased')
# 最后的预测层
self.predictor = nn.Sequential(
nn.Linear(768, 256),
nn.ReLU(),
nn.Linear(256, 1),
nn.Sigmoid()
)
def forward(self, src):
"""
:param src: 分词后的推文数据
"""
# 将src直接序列解包传入bert，因为bert和tokenizer是一套的，所以可以这么做。
# 得到encoder的输出，用最前面[CLS]的输出作为最终线性层的输入
outputs = self.bert(**src)[0][:, 0, :]
# 使用线性层来做最终的预测
return self.predictor(outputs)
model = MyModel()
model = model.to(device)
#定义出损失函数和优化器。这里使用Binary Cross Entropy：
criteria = nn.BCELoss()
optimizer = torch.optim.Adam(model.parameters(), lr=lr)
# 由于inputs是字典类型的，定义一个辅助函数帮助to(device)
def to_device(dict_tensors):
result_tensors = {}
for key, value in dict_tensors.items():
result_tensors[key] = value.to(device)
return result_tensors
#定义一个验证方法，获取到验证集的精准率和loss
def validate():
model.eval()
total_loss = 0.
total_correct = 0
for inputs, targets in validation_loader:
inputs, targets = to_device(inputs), targets.to(device)
outputs = model(inputs)
loss = criteria(outputs.view(-1), targets.float())
total_loss += float(loss)
correct_num = (((outputs >= 0.5).float() * 1).flatten() == targets).sum()
total_correct += correct_num
return total_correct / len(validation_dataset), total_loss / len(validation_dataset)
# 首先将模型调成训练模式
model.train()
# 清空一下cuda缓存
if torch.cuda.is_available():
torch.cuda.empty_cache()
# 定义几个变量，帮助打印loss
total_loss = 0.
# 记录步数
step = 0
# 记录在验证集上最好的准确率
best_accuracy = 0
# 开始训练
for epoch in range(epochs):
model.train()
for i, (inputs, targets) in enumerate(train_loader):
# 从batch中拿到训练数据
inputs, targets = to_device(inputs), targets.to(device)
# 传入模型进行前向传递
outputs = model(inputs)
# 计算损失
loss = criteria(outputs.view(-1), targets.float())
loss.backward()
optimizer.step()
optimizer.zero_grad()
total_loss += float(loss)
step += 1
if step % log_per_step == 0:
print("Epoch {}/{}, Step: {}/{}, total loss:{:.4f}".format(epoch+1, epochs, i, len(train_loader), total_loss))
total_loss = 0
del inputs, targets
# 一个epoch后，使用过验证集进行验证
accuracy, validation_loss = validate()
print("Epoch {}, accuracy: {:.4f}, validation loss: {:.4f}".format(epoch+1, accuracy, validation_loss))
# 保存最好的模型
if accuracy > best_accuracy:
torch.save(model, model_dir / f"attention_model_best.pt")
best_accuracy = accuracy
model = torch.load(model_dir / f"attention_model_best.pt")
model = model.eval()
test_dataset = MyDataset('test')
test_loader = DataLoader(test_dataset, batch_size=batch_size, shuffle=False, collate_fn=collate_fn)
results = []
for inputs, ids in test_loader:
outputs = model(inputs.to(device))
outputs = (outputs >= 0.5).int().flatten().tolist()
ids = ids.tolist()
results = results + [(id, result) for result, id in zip(outputs, ids)]
test_label = [pair[1] for pair in results]
test_data['label'] = test_label
test_data[['uuid', 'Keywords', 'label']].to_csv('submit_task1.csv', index=None)
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