I am using breast cancer wisconsin data and working on it with ANN, in keras library.
I've added codes and a part of data below, I hope it's readable and understandable.
One row from dataset:1000025,5,1,1,1,2,1,3,1,1,2
Prediction results:
Test Loss: 0.05948319600096771 - Test Accuracy: 0.9809523820877075
As seen, confusion matrix looks fine.
Here, loss graphic looks okay but accuracy graphic made me confused. Why does training_accuracy starts with a high value and doesnt change much?
Here's the main part of code, after importing libraries:
data = pd.read_csv('breast-cancer-wisconsin.data')
data_new = data.drop(['1000025'],axis=1)
X = data_new.iloc[:,0:8].values
Y = data_new.iloc[:,9].values
labelencoder_= LabelEncoder()
Y = labelencoder_.fit_transform(Y)
X_train, X_test, y_train, y_test = train_test_split(X, Y, test_size = 0.15, random_state = 0)
#Feature Scaling
sc = StandardScaler()
X_train = sc.fit_transform(X_train)
X_test = sc.transform(X_test)
classifier = Sequential()
classifier.add(Dense(8, input_dim=8))
classifier.add(Activation("relu"))
classifier.add(Dropout(0.1))
classifier.add(Dense(32))
classifier.add(Activation("relu"))
classifier.add(Dropout(0.1))
classifier.add(Dense(16))
classifier.add(Activation("relu"))
classifier.add(Dropout(0.1))
classifier.add(Dense(1))
classifier.add(Activation("sigmoid"))
classifier.compile(optimizer='adam', loss='binary_crossentropy', metrics=['accuracy'])
history = classifier.fit(X_train, y_train, epochs=100, batch_size=10, validation_split=0.11)
test_loss, test_acc = classifier.evaluate(X_test, y_test)
print('\nTest Loss:', test_loss)
print('Test Accuracy:', test_acc)
y_pred = classifier.predict(X_test)
And plots of the graphics and confusion matrix:
#LOSS---
training_loss = history.history['loss']
test_loss = history.history['val_loss']
epoch_count = range(1, len(training_loss) + 1)
plt.plot(epoch_count, training_loss, 'r-')
plt.plot(epoch_count, test_loss, 'b-')
plt.legend(['Training Loss', 'Test Loss'])
plt.xlabel('Epoch')
plt.ylabel('Loss')
plt.show()
#ACCURACY---
training_acc = history.history['accuracy']
test_acc = history.history['val_accuracy']
epoch_count2 = range(1, len(training_acc) + 1)
plt.plot(epoch_count2, training_acc, 'r-')
plt.plot(epoch_count2, test_acc, 'b-')
plt.legend(['Training Accuracy','Test Accuracy'])
plt.xlabel('Epoch')
plt.ylabel('Accuracy')
plt.show()
ConfMatrix = confusion_matrix(y_test,pred)
ax = sns.heatmap(ConfMatrix, annot=True, cmap="gray", fmt="d", xticklabels = ['Benign', 'Malignant'], yticklabels = ['Benign', 'Malignant'])
bottom, top = ax.get_ylim()
ax.set_ylim(bottom + 0.5, top - 0.5)
plt.ylabel('True')
plt.xlabel('Prediction')
plt.title("Confusion Matrix");
plt.figure(figsize=(7,17))
Related
I have created a simple pytorch classification model with sample datasets generated using sklearns make_classification. Even after training for thousands of epochs the accuracy of the model hovers between 30 and 40 percentage. During training itself the loss value is fluctuating very far and wide. I am wondering why this model is not learning, whether it's due to some logical error in the code.
import torch
from torch.utils.data import Dataset, DataLoader
import torch.nn as nn
from sklearn.datasets import make_classification
from sklearn.model_selection import train_test_split
X,y = make_classification(n_features=15,n_classes=5,n_informative=4)
DEVICE = torch.device('cuda')
epochs = 5000
class CustomDataset(Dataset):
def __init__(self,X,y):
self.X = torch.from_numpy(X)
self.y = torch.from_numpy(y)
def __len__(self):
return len(self.X)
def __getitem__(self, index):
X = self.X[index]
y = self.y[index]
return (X,y)
class Model(nn.Module):
def __init__(self):
super().__init__()
self.l1 = nn.Linear(15,10)
self.l2 = nn.Linear(10,5)
self.relu = nn.ReLU()
def forward(self,x):
x = self.l1(x)
x = self.relu(x)
x = self.l2(x)
x = self.relu(x)
return x
model = Model().double().to(DEVICE)
optimizer = torch.optim.Adam(model.parameters(), lr=0.001)
loss_function = nn.CrossEntropyLoss()
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.33, random_state=42)
train_data = CustomDataset(X_train,y_train)
test_data = CustomDataset(X_test,y_test)
trainloader = DataLoader(train_data, batch_size=32, shuffle=True)
testloader = DataLoader(test_data, batch_size=32, shuffle=True)
for i in range(epochs):
for (x,y) in trainloader:
x = x.to(DEVICE)
y = y.to(DEVICE)
optimizer.zero_grad()
output = model(x)
loss = loss_function(output,y)
loss.backward()
optimizer.step()
if i%200==0:
print("epoch: ",i," Loss: ",loss.item())
correct = 0
total = 0
# since we're not training, we don't need to calculate the gradients for our outputs
with torch.no_grad():
for x, y in testloader:
# calculate outputs by running x through the network
outputs = model(x.to(DEVICE)).to(DEVICE)
# the class with the highest energy is what we choose as prediction
_, predicted = torch.max(outputs.data, 1)
total += y.size(0)
correct += (predicted == y.to(DEVICE)).sum().item()
print(f'Accuracy of the network on the test data: {100 * correct // total} %')
EDIT
I tried to over-fit my model with only 10 samples (batch_size=5) X,y = make_classification(n_samples=10,n_features=15,n_classes=5,n_informative=4) but now the accuracy decreased to 15-20%. I then normalize the input data between the values 0 and 1 which pushed the accuracy a bit higher but not over 50 percentage. Any idea why this might be happening?
You should not be using ReLU activation on your output layer. Usually softmax activation is used for multi class classification on the final layer, or the logits are fed to the loss function directly without explicitly adding a softmax activation layer.
Try removing the ReLU activation from the final layer.
I'm using a LSTM model to predict BABA stock price using this dataset: "/kaggle/input/price-volume-data-for-all-us-stocks-etfs/Data/Stocks/baba.us.txt".
I'm not sure why my model is not learning and the y_test_prediction is so different from the actual y_test. I really appreciate your help as I'm beginning to learn machine learning. Thank you!
I have scaled the data with minMaxScaler before splitting it. This is how I split the data:
x_train, y_train, x_test, y_test = [], [], [], []
lags = 3
for t in range(len(train_data)-lags-1):
x_train.append(train_data[t:(t+lags),:])
y_train.append(train_data[(t+lags),:])
for t in range(len(test_data)-lags-1):
x_test.append(test_data[t:(t+lags),:])
y_test.append(test_data[(t+lags),:])
x_train = torch.FloatTensor(np.array(x_train))
y_train = torch.FloatTensor(np.array(y_train))
x_test = torch.FloatTensor(np.array(x_test))
y_test = torch.FloatTensor(np.array(y_test))
x_train = np.reshape(x_train,(x_train.shape[0],x_train.shape[1],1))
x_test = np.reshape(x_test,(x_test.shape[0],x_test.shape[1],1))
print(x_train.shape)
print(y_train.shape)
print(x_test.shape)
print(y_test.shape)
This is my LSTM model:
input_dim = 1
hidden_layer_dim = 32
num_layers = 1
output_dim = 1
class LSTM(nn.Module):
def __init__(self, input_dim,hidden_layer_dim, num_layers, output_dim ):
super(LSTM, self).__init__()
self.input_dim = input_dim
self.hidden_layer_dim = hidden_layer_dim
self.num_layers = num_layers
self.output_dim = output_dim
self.lstm = nn.LSTM(input_dim, hidden_layer_dim,num_layers,batch_first = True)
self.fc = nn.Linear(hidden_layer_dim, output_dim)
def forward(self, x):
# initial hidden state & cell state as zeros
h0 = Variable(torch.zeros(self.num_layers, x.size(0), self.hidden_layer_dim))
c0 = Variable(torch.zeros(self.num_layers, x.size(0), self.hidden_layer_dim))
# lstm output with hidden and cell state
output, (hn, cn) = self.lstm(x, (h0,c0))
# get hidden state to be passed to dense layer
hn = hn.view(-1, self.hidden_layer_dim)
output = self.fc(hn)
return output
This is my training:
num_epochs = 100
learning_rate = 0.01
model = LSTM(input_dim,hidden_layer_dim, num_layers, output_dim)
loss = torch.nn.MSELoss() # mean-squared error for regression
optimizer = torch.optim.Adam(model.parameters(), lr=learning_rate)
hist = np.zeros(num_epochs)
# train model
for epoch in range(num_epochs):
outputs = model(x_train)
optimizer.zero_grad()
#get loss function
loss_fn = loss(outputs, y_train.view(1,-1))
hist[epoch] = loss_fn.item()
loss_fn.backward()
optimizer.step()
if epoch %10==0:
print("Epoch: %d, loss: %1.5f" % (epoch, hist[epoch]))
This is the training loss and prediction vs actual
training loss
prediction vs actual
You are initialising hidden layers every time forward is being called, which might cause errors with backprop. You do not even have to initialise them. PyTorch takes care of that for you. You can check this implementation for the details. Also, as a side note, you might want to take a look at PyTorch dataloaders(just an easier way to make splits).
I am trying to make a simple classification using Logistic Regression. I fit the model and scale the values using a standard scaler. how can I make a single prediction after that? I am getting the same result for different values. For every value, I am getting 0. the prediction I am getting from single inputs does not resemble with the result from the prediction made by the testing dataset. Can someone please give me a hand?
dataset = pd.read_csv("Social_Network_Ads.csv")
x = dataset.iloc[:, 2:4].values
y = dataset.iloc[:, 4].values
print(dataset)
x_train, x_test, y_train, y_test = train_test_split(x, y, test_size=0.25, random_state=0)
scaler = StandardScaler()
x_train = scaler.fit_transform(x_train)
x_test = scaler.transform(x_test)
classifier = LogisticRegression()
classifier.fit(x_train, y_train)
y_pred = classifier.predict(x_test)
x_values = [36, 36000]
x_values = np.array(x_values).reshape(1, -1)
x_values = scaler.transform(x_values)
pred = classifier.predict(x_values)
print("single prediction: ", pred)
I'm completely new to PyTorch and tried out some models. I wanted to make an easy prediction rnn of stock market prices and found the following code:
I load the data set with pandas then split it into training and test data and load it into a pytorch DataLoader for later usage in training process. The model is defined in the GRU class. But the actual problem seems to be the optimisation. I think the problem could be gradient explosion. I thought about adding gradient clipping but the GRU design should actually prevent gradient explosion or am I wrong? What could cause the loss to be instantly NaN (already in the first epoch)
from sklearn.preprocessing import MinMaxScaler
import time
import pandas as pd
import numpy as np
import torch
import torch.nn as nn
from torch.utils.data import TensorDataset, DataLoader
batch_size = 200
input_dim = 1
hidden_dim = 32
num_layers = 2
output_dim = 1
num_epochs = 10
nvda = pd.read_csv('dataset/stocks/NVDA.csv')
price = nvda[['Close']]
scaler = MinMaxScaler(feature_range=(-1, 1))
price['Close'] = scaler.fit_transform(price['Close'].values.reshape(-1, 1))
def split_data(stock, lookback):
data_raw = stock.to_numpy() # convert to numpy array
data = []
# create all possible sequences of length seq_len
for index in range(len(data_raw) - lookback):
data.append(data_raw[index: index + lookback])
data = np.array(data)
test_set_size = int(np.round(0.2 * data.shape[0]))
train_set_size = data.shape[0] - (test_set_size)
x_train = data[:train_set_size, :-1, :]
y_train = data[:train_set_size, -1, :]
x_test = data[train_set_size:, :-1]
y_test = data[train_set_size:, -1, :]
return [x_train, y_train, x_test, y_test]
lookback = 20 # choose sequence length
x_train, y_train, x_test, y_test = split_data(price, lookback)
train_data = TensorDataset(torch.from_numpy(x_train).float(), torch.from_numpy(y_train).float())
train_data = DataLoader(train_data, shuffle=True, batch_size=batch_size, drop_last=True)
test_data = TensorDataset(torch.from_numpy(x_test).float(), torch.from_numpy(y_test).float())
test_data = DataLoader(test_data, shuffle=True, batch_size=batch_size, drop_last=True)
class GRU(nn.Module):
def __init__(self, input_dim, hidden_dim, num_layers, output_dim):
super(GRU, self).__init__()
self.hidden_dim = hidden_dim
self.num_layers = num_layers
self.gru = nn.GRU(input_dim, hidden_dim, num_layers, batch_first=True, dropout=0.2)
self.fc = nn.Linear(hidden_dim, output_dim)
self.relu = nn.ReLU()
def forward(self, x, h):
out, h = self.gru(x, h)
out = self.fc(self.relu(out[:, -1]))
return out, h
def init_hidden(self, batch_size):
weight = next(self.parameters()).data
hidden = weight.new(self.num_layers, batch_size, self.hidden_dim).zero_()
return hidden
model = GRU(input_dim=input_dim, hidden_dim=hidden_dim, output_dim=output_dim, num_layers=num_layers)
criterion = nn.MSELoss()
optimizer = torch.optim.Adam(model.parameters(), lr=0.0000000001)
model.train()
start_time = time.time()
h = model.init_hidden(batch_size)
for epoch in range(1, num_epochs+1):
for x, y in train_data:
h = h.data
model.zero_grad()
y_train_pred, h = model(x, h)
loss = criterion(y_train_pred, y)
print("Epoch ", epoch, "MSE: ", loss.item())
loss.backward()
optimizer.step()
training_time = time.time() - start_time
print("Training time: {}".format(training_time))
This is the dataset which I used.
Not sure if it is the case, but did you preprocess and cleaned the data? I do not know it but maybe there are some values missing or it's something strange about it. I checked it here
https://ca.finance.yahoo.com/quote/NVDA/history?p=NVDA and it seems that every couple of rows there is some inconsistency. Like I said, I do not know if it's the case but it may be.
I wrote a code for kNN using sklearn and then compared the predictions using the WEKA kNN. The comparison was done using the 10 test set predictions, out of which, only a single one is showing a high difference of >1.5 but all others are exactly the same. So, I am not sure about if my code is working fine or not. Here is my code:
df = pd.read_csv('xxxx.csv')
X = df.drop(['Name', 'activity'], axis=1)
y = df['activity']
Xstd = StandardScaler().fit_transform(X)
x_train, x_test, y_train, y_test = train_test_split(Xstd, y, test_size=0.2,
shuffle=False, random_state=None)
print(x_train.shape, x_test.shape)
X_train_trans = x_train
X_test_trans = x_test
for i in range(2, 3):
knn_regressor = KNeighborsRegressor(n_neighbors=i, algorithm='brute',
weights='uniform', metric='euclidean', n_jobs=1, p=2)
CV_pred_train = cross_val_predict(knn_regressor, X_train_trans, y_train,
n_jobs=-1, verbose=0, cv=LeaveOneOut())
print("LOO Q2: ", metrics.r2_score(y_train, CV_pred_train).round(2))
# Train Test predictions
knn_regressor.fit(X_train_trans, y_train)
train_r2 = knn_regressor.score(X_train_trans, y_train)
y_train_pred = knn_regressor.predict(X_train_trans).round(3)
train_r2_1 = metrics.r2_score(y_train, y_train_pred)
y_test_pred = knn_regressor.predict(X_test_trans).round(3)
train_r = stats.pearsonr(y_train, y_train_pred)
abs_error_train = (y_train - y_train_pred)
train_predictions = pd.DataFrame({'Actual': y_train, 'Predcited':
y_train_pred, "error": abs_error_train.round(3)})
MAE_train = metrics.mean_absolute_error(y_train, y_train_pred)
abs_error_test = (y_test_pred - y_test)
test_predictions = pd.DataFrame({'Actual': y_test, 'predcited':
y_test_pred, 'error': abs_error_test.round(3)})
test_r = stats.pearsonr(y_test, y_test_pred)
test_r2 = metrics.r2_score(y_test, y_test_pred)
MAE_test = metrics.mean_absolute_error(y_test, y_test_pred).round(3)
print(test_predictions)
The train set statistics are almost same in both sklearn and WEKA kNN.
the sklearn predictions are:
Actual predcited error
6.00 5.285 -0.715
5.44 5.135 -0.305
6.92 6.995 0.075
7.28 7.005 -0.275
5.96 6.440 0.480
7.96 7.150 -0.810
7.30 6.660 -0.640
6.68 7.200 0.520
***4.60 6.950 2.350***
and the weka predictions are:
actual predicted error
6 5.285 -0.715
5.44 5.135 -0.305
6.92 6.995 0.075
7.28 7.005 -0.275
5.96 6.44 0.48
7.96 7.15 -0.81
7.3 6.66 -0.64
6.68 7.2 0.52
***4.6 5.285 0.685***
parameters used in both algorithms are: k =2, brute force for distance calculation, metric: euclidean.
Any suggestions for the difference?