International_Deer27 OP t1_j6rxjtd wrote on February 1, 2023 at 1:54 PM

import torch

import torch.nn as nn

from torch.utils.data import Dataset, DataLoader

from sklearn.model_selection import train_test_split

import numpy as np

df_Y_MACE = np.array(df_Y_MACE)

df_X_MACE = np.array(df_X_MACE)

X = torch.from_numpy(df_X_MACE).float()

Y = torch.from_numpy(df_Y_MACE).float()

# Define the dataset

class ECGDataset(Dataset):

def __init__(self, data, labels):

self.data = data

self.labels = labels

def __len__(self):

return len(self.data)

def __getitem__(self, idx):

return self.data[idx], self.labels[idx]

# Split the data into training and testing sets

train_data, test_data, train_labels, test_labels = train_test_split(X, Y, test_size=0.2)

# Create the dataset and data loader

train_dataset = ECGDataset(train_data, train_labels)

test_dataset = ECGDataset(test_data, test_labels)

train_loader = DataLoader(train_dataset, batch_size=32, shuffle=True)

test_loader = DataLoader(test_dataset, batch_size=32, shuffle=False)

# Define the CNN

class ECGClassifier(nn.Module):

def __init__(self):

super(ECGClassifier, self).__init__()

self.fc = nn.Linear(128*5, 1)

self.act = nn.ReLU()

self.sigmoid = nn.Sigmoid()

self.dropout = nn.Dropout(0.5)

self.layers = [[],[],[],[],[]]

for i in range(5):

self.layers[i].append(nn.Conv1d(1, 32, kernel_size=20, stride=5))

self.layers[i].append(nn.BatchNorm1d(32))

self.layers[i].append(nn.MaxPool1d(7,2))

self.layers[i].append(nn.Conv1d(32, 64, kernel_size=16, stride=5))

self.layers[i].append(nn.BatchNorm1d(64))

self.layers[i].append(nn.MaxPool1d(7,3))

self.layers[i].append(nn.Conv1d(64, 128, kernel_size=2, stride=3))

self.layers[i].append(nn.BatchNorm1d(128))

self.layers[i].append(nn.Linear(4, 1))

self.layers[i].append(nn.BatchNorm1d(128))

self.layers[i].append(nn.Dropout(0.5))

def forward(self, x):

x_cols = [[], [], [], [], []]

for i in range(5):

x_cols[i] = x[:,:,i].unsqueeze(1)

x_cols[i] = self.layers[i][0](x_cols[i])

x_cols[i] = self.layers[i][1](x_cols[i])

x_cols[i] = self.act(x_cols[i])

x_cols[i] = self.layers[i][2](x_cols[i])

x_cols[i] = self.layers[i][3](x_cols[i])

x_cols[i] = self.layers[i][4](x_cols[i])

x_cols[i] = self.act(x_cols[i])

x_cols[i] = self.layers[i][5](x_cols[i])

x_cols[i] = self.layers[i][6](x_cols[i])

x_cols[i] = self.layers[i][7](x_cols[i])

x_cols[i] = self.act(x_cols[i])

x_cols[i] = self.layers[i][8](x_cols[i])

x_cols[i] = self.layers[i][9](x_cols[i])

x_cols[i] = self.layers[i][10](x_cols[i])

x = torch.cat((*x_cols, ), 1)

x = x.view(-1, 128*5)

x = self.fc(x)

x = self.sigmoid(x)

return x

# Define the model and move it to the device

device = torch.device('cpu')

model = ECGClassifier()

model = model.to(device)

model = model.float()

# Define the loss function and optimizer

criterion = nn.BCELoss()

optimizer = torch.optim.Adam(model.parameters(), lr=0.001, weight_decay=0.001)

# Train the model

for epoch in range(5):

for i, (data, labels) in enumerate(train_loader):

data, labels = data.to(device), labels.to(device)

# Forward pass

with torch.set_grad_enabled(True):

outputs = model(data)

labels = labels.unsqueeze(1)

loss = criterion(outputs, labels)

# Backward and optimize

optimizer.zero_grad()

loss.backward()

optimizer.step()

print ('Epoch [{}/{}], Loss: {:.4f}'.format(epoch+1, 5, loss.item()))

BlacksmithNo4415 t1_j6tfpkg wrote on February 1, 2023 at 7:39 PM

try using markdowns:

        plotter = DLPlotter()     # add this line
        model = MyModel()
        ...
        total_loss = 0
        for epoch in range(5):
            for step, (x, y) in enumerate(loader):
                ...
                output = model(x)
                loss = loss_func(output, y)
                total_loss += loss.item()
                ...
        config = dict(lr=0.001, batch_size=64, ...)
        plotter.collect_parameter("exp001"", config, total_loss / (5 * len(loader))     # add this line
        plotter.construct()     # add this line

International_Deer27 OP t1_j6usb0i wrote on February 2, 2023 at 12:57 AM

I’m not sure about the DLPlotter, which library did you get it from, I can’t seem to find it? I’m using Python 3

BlacksmithNo4415 t1_j6usty4 wrote on February 2, 2023 at 1:01 AM

no, that was an example code to show you how much better the code is readable when you use markdowns..

DLPlotter is a library i am building in the moment.. :)

International_Deer27 OP t1_j6uufti wrote on February 2, 2023 at 1:13 AM

Ah alright, thanks, I’ll try and see how else I can modify the code and get it working. Good luck with the library!

International_Deer27 OP t1_j6x0tpy wrote on February 2, 2023 at 2:27 PM

I've simplified my model a lot to only take into account 2000x1 tensors as input for X and the prediction is either 0 or 1 as before. I've made it using nn.Sequential with only a few layers to be easier to follow:

import torch

import torch.nn as nn

from torch.utils.data import Dataset, DataLoader

import torch.nn.functional as F

from sklearn.model_selection import train_test_split

import numpy as np

import matplotlib as plt

df_Y_MACE = np.array(df_Y_MACE)

df_X_MACE1 = []

for i in range(len(df_X_MACE)):

df_X_MACE1.append(df_X_MACE[i][0])

df_X_MACE1 = np.array(df_X_MACE1)

X = torch.from_numpy(df_X_MACE1).float()

Y = torch.from_numpy(df_Y_MACE).float()

# Define the dataset

class ECGDataset(Dataset):

def __init__(self, data, labels):

self.data = data

self.labels = labels

def __len__(self):

return len(self.data)

def __getitem__(self, idx):

return self.data[idx], self.labels[idx]

# Split the data into training and testing sets

train_data, test_data, train_labels, test_labels = train_test_split(X, Y, test_size=0.8)

# Create the dataset and data loader

train_dataset = ECGDataset(train_data, train_labels)

test_dataset = ECGDataset(test_data, test_labels)

train_loader = DataLoader(train_dataset, batch_size=32, shuffle=True)

test_loader = DataLoader(test_dataset, batch_size=32, shuffle=False)

# Define the CNN

class ECGClassifier(nn.Module):

def __init__(self):

super(ECGClassifier, self).__init__()

self.ECG_seq = nn.Sequential(nn.Conv1d(1, 32, kernel_size = 50, stride = 5), nn.ReLU(), nn.MaxPool1d(7,2), nn.Linear(193,1))

self.fc = nn.Linear(32, 1)

self.sigmoid = nn.Sigmoid()

def forward(self, x):

x = x.unsqueeze(1)

out = self.ECG_seq(x)

out = self.fc(out.view(-1,32))

out = self.sigmoid(out)

return out

# Define the model and move it to the device

device = torch.device('cpu')

model = ECGClassifier()

model = model.to(device)

model = model.float()

# Define the loss function and optimizer

criterion = nn.BCELoss()

optimizer = torch.optim.Adam(model.parameters(), lr=0.001, weight_decay=0.01)

total_loss = []

# Train the model

for epoch in range(5):

for i, (data, labels) in enumerate(train_loader):

data, labels = data.to(device), labels.to(device)

# Forward pass

with torch.set_grad_enabled(True):

outputs = model(data)

labels = labels.unsqueeze(1)

loss = criterion(outputs, labels)

total_loss.append(loss)

# Backward and optimize

optimizer.zero_grad()

loss.backward()

optimizer.step()

print ('Epoch [{}/{}], Loss: {:.4f}'.format(epoch+1, 5, loss.item()))

BlacksmithNo4415 t1_j6x1ugb wrote on February 2, 2023 at 2:34 PM

https://www.freecodecamp.org/news/how-to-format-code-in-markdown/

International_Deer27 OP t1_j6x0yff wrote on February 2, 2023 at 2:28 PM

For this new model the loss function looks pretty much the same:

Epoch [1/5], Loss: 0.8073

Epoch [2/5], Loss: 0.8680

Epoch [3/5], Loss: 0.5826

Epoch [4/5], Loss: 0.7626

Epoch [5/5], Loss: 0.6099

BlacksmithNo4415 t1_j6x2xia wrote on February 2, 2023 at 2:42 PM

i've checked for papers that do exactly what you want.

so as I assumed this data is time sensitive and therefor you need an additional temporal dimension.

this model needs to be more complex in order to solve this problem.

i suggest reading this:

https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-021-01736-y

BTW: have you tried grid search for finding the right hyperparametrs?

oh and your model does improve..

have you increased the data set size??

Loss function fluctuating

sulpha1 t1_j6qyygr wrote on February 1, 2023 at 7:06 AM

International_Deer27 OP t1_j6rxjtd wrote on February 1, 2023 at 1:54 PM

BlacksmithNo4415 t1_j6tfpkg wrote on February 1, 2023 at 7:39 PM

International_Deer27 OP t1_j6usb0i wrote on February 2, 2023 at 12:57 AM

BlacksmithNo4415 t1_j6usty4 wrote on February 2, 2023 at 1:01 AM

International_Deer27 OP t1_j6uufti wrote on February 2, 2023 at 1:13 AM

International_Deer27 OP t1_j6x0tpy wrote on February 2, 2023 at 2:27 PM

BlacksmithNo4415 t1_j6x1ugb wrote on February 2, 2023 at 2:34 PM

International_Deer27 OP t1_j6x0yff wrote on February 2, 2023 at 2:28 PM

BlacksmithNo4415 t1_j6x2xia wrote on February 2, 2023 at 2:42 PM