使用python编写DNN神经网络根据基因的表达量来预测患者是否患病并且满足以下要求:1读入Excel表格第一行为患者状态标志state1为患病0为正常和16个基因名称第0列为患者是否患病的真值其余列为基因的表达量2路径为CUserslenovoDesktopHIVDNN神经网络测试data1xlsx3使用贝叶斯优化对神经网络模型进行优化4模型为二分类有三个隐藏层5加入注意力机制6给出详细注释7数
import numpy as np import pandas as pd from sklearn.model_selection import train_test_split from sklearn.preprocessing import StandardScaler from bayes_opt import BayesianOptimization import torch from torch import nn, optim from torch.utils.data import Dataset, DataLoader
读取数据
data = pd.read_excel(r'C:\Users\lenovo\Desktop\HIV\DNN神经网络测试\data1.xlsx', header=0) X = data.iloc[:, 1:].values y = data.iloc[:, 0].values
数据标准化
sc = StandardScaler() X = sc.fit_transform(X)
定义数据集类
class HIVDataset(Dataset): def init(self, X, y): self.X = torch.tensor(X, dtype=torch.float32) self.y = torch.tensor(y, dtype=torch.float32)
def __getitem__(self, index):
return self.X[index], self.y[index]
def __len__(self):
return len(self.X)
定义模型
class DNN(nn.Module): def init(self, input_dim, output_dim, hidden_dim1, hidden_dim2, hidden_dim3): super(DNN, self).init() self.fc1 = nn.Linear(input_dim, hidden_dim1) self.fc2 = nn.Linear(hidden_dim1, hidden_dim2) self.fc3 = nn.Linear(hidden_dim2, hidden_dim3) self.fc4 = nn.Linear(hidden_dim3, output_dim) self.relu = nn.ReLU() self.softmax = nn.Softmax(dim=1) self.attention = nn.Sequential( nn.Linear(hidden_dim3, 1), nn.Softmax(dim=0) )
def forward(self, x):
x = self.relu(self.fc1(x))
x = self.relu(self.fc2(x))
x = self.relu(self.fc3(x))
attn_weight = self.attention(x)
x = x * attn_weight
x = self.fc4(x)
x = self.softmax(x)
return x
定义训练函数
def train(hidden_dim1, hidden_dim2, hidden_dim3, lr, weight_decay): # 定义模型 model = DNN(input_dim=X.shape[1], output_dim=2, hidden_dim1=int(hidden_dim1), hidden_dim2=int(hidden_dim2), hidden_dim3=int(hidden_dim3)) # 定义损失函数和优化器 criterion = nn.CrossEntropyLoss() optimizer = optim.Adam(model.parameters(), lr=lr, weight_decay=weight_decay) # 定义数据集和数据加载器 dataset = HIVDataset(X, y) loader = DataLoader(dataset, batch_size=32, shuffle=True) # 开始训练 for epoch in range(50): running_loss = 0.0 correct = 0 total = 0 for batch_x, batch_y in loader: optimizer.zero_grad() outputs = model(batch_x) loss = criterion(outputs, batch_y.long()) loss.backward() optimizer.step() _, predicted = torch.max(outputs.data, 1) total += batch_y.size(0) correct += (predicted == batch_y).sum().item() running_loss += loss.item() * batch_y.size(0) epoch_loss = running_loss / total epoch_acc = correct / total print('Epoch [{}/{}], Loss: {:.4f}, Accuracy: {:.4f}'.format(epoch+1, 50, epoch_loss, epoch_acc)) return epoch_acc
使用贝叶斯优化寻找最优参数
pbounds = {'hidden_dim1': (10, 100), 'hidden_dim2': (10, 100), 'hidden_dim3': (10, 100), 'lr': (0.0001, 0.1), 'weight_decay': (0, 0.1)} optimizer = BayesianOptimization(f=train, pbounds=pbounds) optimizer.maximize(init_points=5, n_iter=10)
输出最优参数和最优结果
print('Maximum accuracy value: {:.4f}'.format(optimizer.max['target'])) print('Best parameters: ', optimizer.max['params'])
原文地址: https://www.cveoy.top/t/topic/bK0W 著作权归作者所有。请勿转载和采集!