我正在尝试将下面的3layer CNN架构从keras翻译为pytorch。该模型的用途是从DNA序列(input_shape_hot)预测表达值(input_shape_val)。序列是一个热编码。该架构最初旨在连续训练模型CNN(3层)-FC(2层),在所有层之后应用批量归一化和权重丢弃,并在CNN层之后应用最大池化(参考论文,ref-code)。
def POC_model2(input_shape_hot,input_shape_val,DR):
X_input1 = Input(shape = input_shape_hot)
X_input2 = Input(shape = input_shape_val)
# L 1: CONV
X1 = Conv1D(filters=32, kernel_size=10, strides=1, activation='relu')(X_input1)
X1 = BatchNormalization()(X1)
X1 = Dropout(DR)(X1)
X1 = MaxPooling1D(pool_size=4, strides=4)(X1)
# L 3: CONV
X1 = Conv1D(filters=64, kernel_size=10, strides=1, activation='relu')(X_input1)
X1 = BatchNormalization()(X1)
X1 = Dropout(DR)(X1)
X1 = MaxPooling1D(pool_size=4, strides=4)(X1)
# L 2: CONV
X1 = Conv1D(filters=128, kernel_size=10, strides=1, activation='relu')(X_input1)
X1 = BatchNormalization()(X1)
X1 = Dropout(DR)(X1)
X1 = MaxPooling1D(pool_size=4, strides=4)(X1)
X1 = Flatten()(X1)
X1 = Concatenate(axis=1)([X1,X_input2])
# fully connected
X = Dense(64, activation='relu')(X1)
X = BatchNormalization()(X)
X = Dropout(DR)(X)
X = Dense(1)(X)
model = Model(inputs = [X_input1,X_input2], outputs = X)
return model
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我试着用这个代码:
from typing import List
class DNA_CNN_test2(nn.Module):
def __init__(self,
seq_len: int,
num_filters: List[int] = [32, 64,128],
kernel_size: int = 3,
p = 0.2):
super().__init__()
self.seq_len = seq_len
# CNN module
self.conv_net = nn.Sequential()
num_filters = [4] + num_filters
for idx in range(len(num_filters) - 1):
self.conv_net.add_module(
f"conv_{idx}",
nn.Conv1d(num_filters[idx], num_filters[idx + 1],
kernel_size=kernel_size, padding='same')
)
self.conv_net.add_module(f"relu_{idx}", nn.ReLU(inplace=True))
self.conv_net.add_module(f"batchNor_{idx}",nn.BatchNorm1d(num_filters[idx + 1]))
self.conv_net.add_module(f"dropout_{idx}",nn.Dropout(0.2))
self.conv_net.add_module(f"MaxP_{idx}",nn.MaxPool1d(4,stride= 4))
self.conv_net.add_module("flatten", nn.Flatten())
self.conv_net.add_module("linear",nn.Linear(num_filters[-1]*seq_len, 1))
def forward(self, xb: torch.Tensor):
"""Forward pass."""
xb = xb.permute(0, 2, 1)
out = self.conv_net(xb)
return out
型
并收到错误消息:
mat1 and mat2 shapes cannot be multiplied (2048x1920 and 128000x1)
型
1条答案
按热度按时间ztmd8pv51#
您忘记了BN和dropout的
add_module
函数:字符串