Issue
TLDR:
A simple (single hiddenlayer) feedforward Pytorch model trained to predict the function y = sin(X1) + sin(X2) + ... sin(X10)
substantially underperforms an identical model built/trained with Keras. Why is this so and what can be done to mitigate the difference in performance?
In training a regression model, I noticed that PyTorch drastically underperforms an identical model built with Keras.
This phenomenon has been observed and reported previously:

The same model produces worse results on pytorch than on tensorflow

CNN model in pytorch giving 30% less accuracy to Tensoflowflow model:

PyTorch comparable but worse than keras on a simple feed forward network

Why Keras behave better than Pytorch under the same network configuration?
The following explanations and suggestions have been made previously as well:

Change
retain_graph=True
tocreate_graph=True
in computing the 2nd derivative withautograd.grad
: 1 
Check if keras is using a regularizer, constraint, bias, or loss function in a different way from pytorch: 1,2

Ensure you are computing the validation loss in the same way: 1

Training the pytorch model for longer epochs: 1

Trying several random seeds: 1

Ensure that
model.eval()
is called in validation step when training pytorch model: 1 
The main issue is with the Adam optimizer, not the initialization: 1
To understand this issue, I trained a simple twolayer neural network (much simpler than my original model) in Keras and PyTorch, using the same hyperparameters and initialization routines, and following all the recommendations listed above. However, the PyTorch model results in a mean squared error (MSE) that is 400% higher than the MSE of the Keras model.
Here is my code:
0. Imports
import numpy as np
from scipy.stats import pearsonr
from sklearn.preprocessing import MinMaxScaler
from sklearn import metrics
from torch.utils.data import Dataset, DataLoader
import tensorflow as tf
from tensorflow.keras import layers
from tensorflow.keras.regularizers import L2
from tensorflow.keras.models import Model
from tensorflow.keras.optimizers import Adam
1. Generate a reproducible dataset
def get_data():
np.random.seed(0)
Xtrain = np.random.normal(0, 1, size=(7000,10))
Xval = np.random.normal(0, 1, size=(700,10))
ytrain = np.sum(np.sin(Xtrain), axis=1)
yval = np.sum(np.sin(Xval), axis=1)
scaler = MinMaxScaler()
ytrain = scaler.fit_transform(ytrain.reshape(1,1)).reshape(1)
yval = scaler.transform(yval.reshape(1,1)).reshape(1)
return Xtrain, Xval, ytrain, yval
class XYData(Dataset):
def __init__(self, X, y):
super(XYData, self).__init__()
self.X = torch.tensor(X, dtype=torch.float32)
self.y = torch.tensor(y, dtype=torch.float32)
self.len = len(y)
def __getitem__(self, index):
return (self.X[index], self.y[index])
def __len__(self):
return self.len
# Data, dataset, and dataloader
Xtrain, Xval, ytrain, yval = get_data()
traindata = XYData(Xtrain, ytrain)
valdata = XYData(Xval, yval)
trainloader = DataLoader(dataset=traindata, shuffle=True, batch_size=32, drop_last=False)
valloader = DataLoader(dataset=valdata, shuffle=True, batch_size=32, drop_last=False)
2. Build Keras and PyTorch models with identical hyperparameters and initialization methods
class TorchLinearModel(nn.Module):
def __init__(self, input_dim=10, random_seed=0):
super(TorchLinearModel, self).__init__()
_ = torch.manual_seed(random_seed)
self.hidden_layer = nn.Linear(input_dim,100)
self.initialize_layer(self.hidden_layer)
self.output_layer = nn.Linear(100, 1)
self.initialize_layer(self.output_layer)
def initialize_layer(self, layer):
_ = torch.nn.init.xavier_normal_(layer.weight)
#_ = torch.nn.init.xavier_uniform_(layer.weight)
_ = torch.nn.init.constant(layer.bias,0)
def forward(self, x):
x = self.hidden_layer(x)
x = self.output_layer(x)
return x
def mean_squared_error(ytrue, ypred):
return torch.mean(((ytrue  ypred) ** 2))
def build_torch_model():
torch_model = TorchLinearModel()
optimizer = optim.Adam(torch_model.parameters(),
betas=(0.9,0.9999),
eps=1e7,
lr=1e3,
weight_decay=0)
return torch_model, optimizer
def build_keras_model():
x = layers.Input(shape=10)
z = layers.Dense(units=100, activation=None, use_bias=True, kernel_regularizer=None,
bias_regularizer=None)(x)
y = layers.Dense(units=1, activation=None, use_bias=True, kernel_regularizer=None,
bias_regularizer=None)(z)
keras_model = Model(x, y, name='linear')
optimizer = Adam(learning_rate=1e3, beta_1=0.9, beta_2=0.9999, epsilon=1e7,
amsgrad=False)
keras_model.compile(optimizer=optimizer, loss='mean_squared_error')
return keras_model
# Instantiate models
torch_model, optimizer = build_torch_model()
keras_model = build_keras_model()
3. Train PyTorch model for 100 epochs:
torch_trainlosses, torch_vallosses = [], []
for epoch in range(100):
# Training
losses = []
_ = torch_model.train()
for i, (x,y) in enumerate(trainloader):
optimizer.zero_grad()
ypred = torch_model(x)
loss = mean_squared_error(y, ypred)
_ = loss.backward()
_ = optimizer.step()
losses.append(loss.item())
torch_trainlosses.append(np.mean(losses))
# Validation
losses = []
_ = torch_model.eval()
with torch.no_grad():
for i, (x, y) in enumerate(valloader):
ypred = torch_model(x)
loss = mean_squared_error(y, ypred)
losses.append(loss.item())
torch_vallosses.append(np.mean(losses))
print(f"epoch={epoch+1}, train_loss={torch_trainlosses[1]:.4f}, val_loss={torch_vallosses[1]:.4f}")
4. Train Keras model for 100 epochs:
history = keras_model.fit(Xtrain, ytrain, sample_weight=None, batch_size=32, epochs=100,
validation_data=(Xval, yval))
5. Loss in training history
plt.plot(torch_trainlosses, color='blue', label='PyTorch Train')
plt.plot(torch_vallosses, color='blue', linestyle='', label='PyTorch Val')
plt.plot(history.history['loss'], color='brown', label='Keras Train')
plt.plot(history.history['val_loss'], color='brown', linestyle='', label='Keras Val')
plt.legend()
Keras records a much lower error in the training. Since this may be due to a difference in how Keras computes the loss, I calculated the prediction error on the validation set with sklearn.metrics.mean_squared_error
6. Validation error after training
ypred_keras = keras_model.predict(Xval).reshape(1)
ypred_torch = torch_model(torch.tensor(Xval, dtype=torch.float32))
ypred_torch = ypred_torch.detach().numpy().reshape(1)
mse_keras = metrics.mean_squared_error(yval, ypred_keras)
mse_torch = metrics.mean_squared_error(yval, ypred_torch)
print('Percent error difference:', (mse_torch / mse_keras  1) * 100)
r_keras = pearsonr(yval, ypred_keras)[0]
r_pytorch = pearsonr(yval, ypred_torch)[0]
print("r_keras:", r_keras)
print("r_pytorch:", r_pytorch)
plt.scatter(ypred_keras, yval); plt.title('Keras'); plt.show(); plt.close()
plt.scatter(ypred_torch, yval); plt.title('Pytorch'); plt.show(); plt.close()
Percent error difference: 479.1312469426776
r_keras: 0.9115184443702814
r_pytorch: 0.21728812737220082
The correlation of predicted values with ground truth is 0.912 for Keras but 0.217 for Pytorch, and the error for Pytorch is 479% higher!
7. Other trials
I also tried:
 Lowering the learning rate for Pytorch (lr=1e4), R increases from 0.217 to 0.576, but it’s still much worse than Keras (r=0.912).
 Increasing the learning rate for Pytorch (lr=1e2), R is worse at 0.095
 Training numerous times with different random seeds. The performance is roughly the same, regardless.
 Trained for longer than 100 epochs. No improvement was observed!
 Used
torch.nn.init.xavier_uniform_
instead oftorch.nn.init.xavier_normal_
in the initialization of the weights. R improves from 0.217 to 0.639, but it’s still worse than Keras (0.912).
What can be done to ensure that the PyTorch model converges to a reasonable error comparable with the Keras model?
Solution
The problem here is unintentional broadcasting in the PyTorch training loop.
The result of a nn.Linear
operation always has shape [B,D]
, where B
is the batch size and D
is the output dimension. Therefore, in your mean_squared_error
function ypred
has shape [32,1]
and ytrue
has shape [32]
. By the broadcasting rules used by NumPy and PyTorch this means that ytrue  ypred
has shape [32,32]
. What you almost certainly meant is for ypred
to have shape [32]
. This can be accomplished in many ways; probably the most readable is to use Tensor.flatten
class TorchLinearModel(nn.Module):
...
def forward(self, x):
x = self.hidden_layer(x)
x = self.output_layer(x)
return x.flatten()
which produces the following train/val curves
Answered By – jodag
This Answer collected from stackoverflow, is licensed under cc bysa 2.5 , cc bysa 3.0 and cc bysa 4.0