VAE (Ecoder as well) is outputting nan

I am working with VAE and I don’t know why but during the training process, I am getting the output of VAE as well as that of the encoder as nan. I am reading a CSV file with rows as my data. Here’s my code:

My data loader:

class data_gen(
    def __init__(self, files):
        = files
    def __getitem__(self, i):

        tmp =[i]
        tmp = np.reshape(tmp,(1025))
        tmp = torch.from_numpy(tmp).float()

        return tmp

    def __len__(self): 
        return len(

Here’s how I am normalising it:

def norm(data):
    norm_data = []
    for j in data:
        temp = float(2.0*(j-np.amin(data))/(np.amax(data)-np.amin(data)) - 1.0)
    return norm_data


class Encoder(nn.Module):
    def __init__(self):
        super(Encoder, self).__init__()
        self.lin1 = nn.Linear(in_features = 1025, out_features = 500)
        self.lin2 = nn.Linear(in_features=500, out_features=100)
        self.lin3 = nn.Linear(in_features=100, out_features=10) 
        self.fc_mu = nn.Linear(in_features=10, out_features=latent_dims)
        self.fc_logvar = nn.Linear(in_features=10, out_features=latent_dims)
    def forward(self, x):

        x = F.relu(self.lin1(x))
        x = F.relu(self.lin2(x))
        x = torch.tanh(self.lin3(x))
        x_mu = self.fc_mu(x)
        x_logvar = self.fc_logvar(x)
        return x_mu, x_logvar

class Decoder(nn.Module):
    def __init__(self):
        super(Decoder, self).__init__()
        c = capacity
        self.fc = nn.Linear(in_features=latent_dims, out_features=10)
        self.lin3 = nn.Linear(in_features=10, out_features=100)
        self.lin2 = nn.Linear(in_features=100, out_features=500)
        self.lin1 = nn.Linear(in_features=500, out_features=1025)

    def forward(self, x):
        x = self.fc(x)
        x = F.relu(self.lin3(x))
        x = torch.tanh(self.lin2(x))
        x = torch.tanh(self.lin1(x)) # last layer before output is sigmoid, since we are using BCE as reconstruction loss
        return x

I am using tanh because I have some negative values. The weird thing is, it sometimes gives proper values. I have normalized by input data, my libraries are up to date and I have tried almost all the solutions provided. Even if I just run the inference, I still get nan. So I don’t know if the learning rate is the issue. What should I do?

Could you check, if your normalization is creating invalid values via torch.isfinite(input).all()?

I get this as well when I run the normalizing code on my data

  0%|          | 10/63100 [00:00<10:32, 99.74it/s]<ipython-input-17-a47b51071277>:4: RuntimeWarning: invalid value encountered in double_scalars
  temp = float(2.0*(j-np.amin(data))/(np.amax(data)-np.amin(data)) - 1.0)

However, it ends normalizing the data though.

And you pointed to something here. Some of the output for

are false. What am I doing wrong in norm?

I guess you might encounter specific data arrays with constant values, so that amin and amax would return the same value and divide by 0:

data = np.array([0.1, 0.1])
print(np.amin(data) == np.amax(data))
> True
1 / (np.amin(data) - np.amax(data))
> inf

Yup, I was getting true for that. What a catch. WOW!