ium_464863/create_model.py

import numpy as np
import pandas as pd
import torch
import torch.nn as nn
import torch.optim as optim

import pathlib

import os
import sys

from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score

from NeuralNetwork import NeuralNetwork

from sacred import Experiment
from sacred.observers import FileStorageObserver, MongoObserver

# Create new sacred experiment
ex = Experiment("s464863")

# Setup observers
ex.observers.append(FileStorageObserver('my_runs'))
ex.observers.append(MongoObserver(url='mongodb://admin:IUM_2021@tzietkiewicz.vm.wmi.amu.edu.pl:27017', db_name='sacred'))

@ex.config
def config():
    # Default parameters
    hidden_size = 128

    # Default learning parameters
    learning_rate = 0.001
    weight_decay = 0.001
    num_epochs = 1000

    # Learning parameters from sys.argv
    if len(sys.argv) > 1:
        num_epochs = int(sys.argv[1])
        learning_rate = float(sys.argv[2])
        weight_decay = float(sys.argv[3])

@ex.automain
def experiment(hidden_size, learning_rate, weight_decay, num_epochs, _run):
    # Seed for reproducibility
    torch.manual_seed(1234)

    # Load data with sacred
    train_data = ex.open_resource('./datasets/train.csv', "r")
    test_data = ex.open_resource('./datasets/test.csv', "r")

    # Convert to pandas dataframe
    train = pd.read_csv(train_data)
    test = pd.read_csv(test_data)

    # Split data
    X_train = train.drop(columns=['id', 'diagnosis']).values
    y_train = train['diagnosis'].values

    X_test = test.drop(columns=['id', 'diagnosis']).values
    y_test = test['diagnosis'].values

    # Convert data to PyTorch tensors
    X_train = torch.FloatTensor(X_train)
    y_train = torch.FloatTensor(y_train).view(-1, 1)

    X_test = torch.FloatTensor(X_test)
    y_test = torch.FloatTensor(y_test).view(-1, 1)

    # Parameters
    input_size = X_train.shape[1]

    # Model initialization
    model = NeuralNetwork(input_size, hidden_size)

    # Loss function and optimizer
    criterion = nn.BCELoss()
    optimizer = optim.Adam(model.parameters(), lr=learning_rate, weight_decay=weight_decay)

    # Training loop
    model.train()

    for epoch in range(num_epochs):
        # Zero the gradients
        optimizer.zero_grad()

        # Forward pass
        outputs = model(X_train)

        # Compute loss
        loss = criterion(outputs, y_train)

        # Backward pass
        loss.backward()

        # Update weights
        optimizer.step()

        # Print loss
        if (epoch + 1) % 100 == 0:
            print(f'Epoch [{epoch + 1}/{num_epochs}], Loss: {loss.item()}')

    # Test the model
    model.eval()

    with torch.no_grad():

        # Make predictions
        y_pred = model(X_test)
        y_pred = np.where(y_pred > 0.5, 1, 0)

        # Calculate metrics
        accuracy = accuracy_score(y_test, y_pred)
        precision = precision_score(y_test, y_pred)
        recall = recall_score(y_test, y_pred)
        f1 = f1_score(y_test, y_pred)

        # Save metrics to sacred
        _run.log_scalar("accuracy", accuracy)
        _run.log_scalar("precision", precision)
        _run.log_scalar("recall", recall)
        _run.log_scalar("f1", f1)

    # If directory models does not exist, create it
    if not os.path.exists('./models'):
        os.makedirs('./models')

    # Save the model
    torch.save(model, './models/model.pth')

    # Add artifact to sacred experiment
    ex.add_artifact('./models/model.pth', content_type="application/x-pythorch")

    # Save id of the run
    with open("experiment_id.txt", "w") as f:
        f.write(str(_run._id))

    # Save sources and resources paths
    with open("sources.txt", "w") as f:
        for source in _run.observers[1].run_entry["experiment"]["sources"]:
            f.write(source[1] + "\n")

    with open("resources.txt", "w") as f:
        for resource in _run.observers[1].run_entry["resources"]:
            f.write(resource[1] + "\n")