def create_dataset(X, y, seq_len=7): features = [] targets = [] for i in range(0, len(X) - seq_len, 1): data = X.iloc[i:i+seq_len] # 序列数据 label = y.iloc[i+seq_len] # 标签数据 # 保存到features和labels features.append(data) targets.append(label) # 返回 return np.array(features), np.array(targets)

这是一个用于创建数据集的函数。函数的输入是X（特征数据）和y（目标数据），以及一个可选的参数seq_len（序列长度，默认为7）。函数的目标是将数据集划分为一组特征和对应的标签。

在函数内部，首先定义了两个空列表features和targets，用于保存特征和标签数据。

然后，通过一个for循环遍历数据集，从索引0开始，每次移动1个步长，直到len(X) - seq_len的位置。在每次迭代中，根据序列长度seq_len，从特征数据X中获取一段连续的子序列data，从目标数据y中获取对应的标签值label。

接下来，将每个子序列data添加到features列表中，将对应的标签值label添加到targets列表中。

最后，将features和targets转换为NumPy数组，并作为函数的输出返回。

这个函数的作用是将时间序列数据转换为可用于训练模型的特征和标签组合。通常用于构建适用于序列模型（如循环神经网络）的输入数据。

相关问题

帮我为下面的代码加上注释：class SimpleDeepForest: def __init__(self, n_layers): self.n_layers = n_layers self.forest_layers = [] def fit(self, X, y): X_train = X for _ in range(self.n_layers): clf = RandomForestClassifier() clf.fit(X_train, y) self.forest_layers.append(clf) X_train = np.concatenate((X_train, clf.predict_proba(X_train)), axis=1) return self def predict(self, X): X_test = X for i in range(self.n_layers): X_test = np.concatenate((X_test, self.forest_layers[i].predict_proba(X_test)), axis=1) return self.forest_layers[-1].predict(X_test[:, :-2]) # 1. 提取序列特征（如：GC-content、序列长度等） def extract_features(fasta_file): features = [] for record in SeqIO.parse(fasta_file, "fasta"): seq = record.seq gc_content = (seq.count("G") + seq.count("C")) / len(seq) seq_len = len(seq) features.append([gc_content, seq_len]) return np.array(features) # 2. 读取相互作用数据并创建数据集 def create_dataset(rna_features, protein_features, label_file): labels = pd.read_csv(label_file, index_col=0) X = [] y = [] for i in range(labels.shape[0]): for j in range(labels.shape[1]): X.append(np.concatenate([rna_features[i], protein_features[j]])) y.append(labels.iloc[i, j]) return np.array(X), np.array(y) # 3. 调用SimpleDeepForest分类器 def optimize_deepforest(X, y): X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2) model = SimpleDeepForest(n_layers=3) model.fit(X_train, y_train) y_pred = model.predict(X_test) print(classification_report(y_test, y_pred)) # 4. 主函数 def main(): rna_fasta = "RNA.fasta" protein_fasta = "pro.fasta" label_file = "label.csv" rna_features = extract_features(rna_fasta) protein_features = extract_features(protein_fasta) X, y = create_dataset(rna_features, protein_features, label_file) optimize_deepforest(X, y) if __name__ == "__main__": main()

# Define a class named 'SimpleDeepForest'
class SimpleDeepForest:

# Initialize the class with 'n_layers' parameter
def __init__(self, n_layers):
self.n_layers = n_layers
self.forest_layers = []

# Define a method named 'fit' to fit the dataset into the classifier
def fit(self, X, y):
X_train = X

# Use the forest classifier to fit the dataset for 'n_layers' times
for _ in range(self.n_layers):
clf = RandomForestClassifier()
clf.fit(X_train, y)

# Append the classifier to the list of forest layers
self.forest_layers.append(clf)

# Concatenate the training data with the predicted probability of the last layer
X_train = np.concatenate((X_train, clf.predict_proba(X_train)), axis=1)

# Return the classifier
return self

# Define a method named 'predict' to make predictions on the test set
def predict(self, X):
X_test = X

# Concatenate the test data with the predicted probability of each layer
for i in range(self.n_layers):
X_test = np.concatenate((X_test, self.forest_layers[i].predict_proba(X_test)), axis=1)

# Return the predictions of the last layer
return self.forest_layers[-1].predict(X_test[:, :-2])

# Define a function named 'extract_features' to extract sequence features
def extract_features(fasta_file):
features = []

# Parse the fasta file to extract sequence features
for record in SeqIO.parse(fasta_file, "fasta"):
seq = record.seq
gc_content = (seq.count("G") + seq.count("C")) / len(seq)
seq_len = len(seq)
features.append([gc_content, seq_len])

# Return the array of features
return np.array(features)

# Define a function named 'create_dataset' to create the dataset
def create_dataset(rna_features, protein_features, label_file):
labels = pd.read_csv(label_file, index_col=0)
X = []
y = []

# Create the dataset by concatenating the RNA and protein features
for i in range(labels.shape[0]):
for j in range(labels.shape[1]):
X.append(np.concatenate([rna_features[i], protein_features[j]]))
y.append(labels.iloc[i, j])

# Return the array of features and the array of labels
return np.array(X), np.array(y)

# Define a function named 'optimize_deepforest' to optimize the deep forest classifier
def optimize_deepforest(X, y):
# Split the dataset into training set and testing set
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2)

# Create an instance of the SimpleDeepForest classifier with 3 layers
model = SimpleDeepForest(n_layers=3)

# Fit the training set into the classifier
model.fit(X_train, y_train)

# Make predictions on the testing set
y_pred = model.predict(X_test)

# Print the classification report
print(classification_report(y_test, y_pred))

# Define the main function to run the program
def main():
rna_fasta = "RNA.fasta"
protein_fasta = "pro.fasta"
label_file = "label.csv"

# Extract the RNA and protein features
rna_features = extract_features(rna_fasta)
protein_features = extract_features(protein_fasta)

# Create the dataset
X, y = create_dataset(rna_features, protein_features, label_file)

# Optimize the DeepForest classifier
optimize_deepforest(X, y)

# Check if the program is being run as the main program
if __name__ == "__main__":
main()

def load_data(file_name): df = pd.read_csv('data/new_data/' + file_name, encoding='gbk') columns = df.columns df.fillna(df.mean(), inplace=True) return df class MyDataset(Dataset): def __init__(self, data): self.data = data def __getitem__(self, item): return self.data[item] def __len__(self): return len(self.data) def nn_seq_us(B): print('data processing...') dataset = load_data() # split train = dataset[:int(len(dataset) * 0.6)] val = dataset[int(len(dataset) * 0.6):int(len(dataset) * 0.8)] test = dataset[int(len(dataset) * 0.8):len(dataset)] m, n = np.max(train[train.columns[1]]), np.min(train[train.columns[1]]) def process(data, batch_size): load = data[data.columns[1]] load = load.tolist() data = data.values.tolist() load = (load - n) / (m - n) seq = [] for i in range(len(data) - 24): train_seq = [] train_label = [] for j in range(i, i + 24): x = [load[j]] train_seq.append(x) # for c in range(2, 8): # train_seq.append(data[i + 24][c]) train_label.append(load[i + 24]) train_seq = torch.FloatTensor(train_seq) train_label = torch.FloatTensor(train_label).view(-1) seq.append((train_seq, train_label)) # print(seq[-1]) seq = MyDataset(seq) seq = DataLoader(dataset=seq, batch_size=batch_size, shuffle=False, num_workers=0, drop_last=True) return seq Dtr = process(train, B) Val = process(val, B) Dte = process(test, B) return Dtr, Val, Dte, m, n这是关于什么的代码

这是一个关于神经网络序列预测的代码，它将数据集加载并进行预处理，然后将其分为训练、验证和测试集。代码中的 load_data 函数用于加载数据文件，MyDataset 类用于创建数据集对象，nn_seq_us 函数则用于对数据进行预处理并将其转换为 PyTorch 数据加载器对象。最后，该函数返回训练、验证和测试数据集对象，以及数据的最大值和最小值。