COVID-19 Cases Prediction (Regression)

Objectives:

• Solve a regression problem with deep neural networks (DNN).
• Understand basic DNN training tips.
• Familiarize yourself with PyTorch.

Task Description

• COVID-19 Cases Prediction

• Source: Delphi group @ CMU

  • A daily survey since April 2020 via facebook.

Try to find out the data and use it to your training is forbidden

• Given survey results in the past 5 days in a specific state in U.S., then predict the percentage of new tested positive cases in the 5th day.

Data

Conducted surveys via facebook (every day & every state) Survey: symptoms, COVID-19 testing, social distancing, mental health, demographics, economic effects, …

• States (37, encoded to one-hot vectors)
• COVID-like illness (4)
  • cli、ili …
• Behavior Indicators (8)
  • wearing_mask、travel_outside_state …
• Mental Health Indicators (3)
  • anxious、depressed …
• Tested Positive Cases (1)
  • tested_positive (this is what we want to predict)

Data – One-hot Vector

• One-hot vectors:
  Vectors with only one element equals to one while others are zero. Usually used to encode discrete values.

the details about One-hot Vector please read the blog:One-Hot

Evaluation Metric

• Mean Squared Error (MSE)

Download data

If the Google Drive links below do not work, you can download data from Kaggle, and upload data manually to the workspace.

!gdown --id '1kLSW_-cW2Huj7bh84YTdimGBOJaODiOS' --output covid.train.csv
!gdown --id '1iiI5qROrAhZn-o4FPqsE97bMzDEFvIdg' --output covid.test.csv

/usr/local/lib/python3.7/dist-packages/gdown/cli.py:131: FutureWarning: Option `--id` was deprecated in version 4.3.1 and will be removed in 5.0. You don't need to pass it anymore to use a file ID.
  category=FutureWarning,
Downloading...
From: https://drive.google.com/uc?id=1kLSW_-cW2Huj7bh84YTdimGBOJaODiOS
To: /content/covid.train.csv
100% 2.49M/2.49M [00:00<00:00, 238MB/s]
/usr/local/lib/python3.7/dist-packages/gdown/cli.py:131: FutureWarning: Option `--id` was deprecated in version 4.3.1 and will be removed in 5.0. You don't need to pass it anymore to use a file ID.
  category=FutureWarning,
Downloading...
From: https://drive.google.com/uc?id=1iiI5qROrAhZn-o4FPqsE97bMzDEFvIdg
To: /content/covid.test.csv
100% 993k/993k [00:00<00:00, 137MB/s]

Import packages

# Numerical Operations
import math
import numpy as np

# Reading/Writing Data
import pandas as pd
import os
import csv

# For Progress Bar
from tqdm import tqdm

# Pytorch
import torch 
import torch.nn as nn
from torch.utils.data import Dataset, DataLoader, random_split

# For plotting learning curve
from torch.utils.tensorboard import SummaryWriter

Some Utility Functions

You do not need to modify this part.

def same_seed(seed): 
    '''Fixes random number generator seeds for reproducibility.'''
    torch.backends.cudnn.deterministic = True
    torch.backends.cudnn.benchmark = False
    np.random.seed(seed)
    torch.manual_seed(seed)
    if torch.cuda.is_available():
        torch.cuda.manual_seed_all(seed)

def train_valid_split(data_set, valid_ratio, seed):
    '''Split provided training data into training set and validation set'''
    valid_set_size = int(valid_ratio * len(data_set)) 
    train_set_size = len(data_set) - valid_set_size
    train_set, valid_set = random_split(data_set, [train_set_size, valid_set_size], generator=torch.Generator().manual_seed(seed))
    return np.array(train_set), np.array(valid_set)

def predict(test_loader, model, device):
    model.eval() # Set your model to evaluation mode.
    preds = []
    for x in tqdm(test_loader):
        x = x.to(device)                        
        with torch.no_grad():                   
            pred = model(x)                     
            preds.append(pred.detach().cpu())   
    preds = torch.cat(preds, dim=0).numpy()  
    return preds

Dataset

class COVID19Dataset(Dataset):
    '''
    x: Features.
    y: Targets, if none, do prediction.
    '''
    def __init__(self, x, y=None):
        if y is None:
            self.y = y
        else:
            self.y = torch.FloatTensor(y)
        self.x = torch.FloatTensor(x)

    def __getitem__(self, idx):
        if self.y is None:
            return self.x[idx]
        else:
            return self.x[idx], self.y[idx]

    def __len__(self):
        return len(self.x)

Neural Network Model

Try out different model architectures by modifying the class below.

class My_Model(nn.Module):
    def __init__(self, input_dim):
        super(My_Model, self).__init__()
        # TODO: modify model's structure, be aware of dimensions. 
        self.layers = nn.Sequential(
            nn.Linear(input_dim, 16),
            nn.ReLU(),
            nn.Linear(16, 8),
            nn.ReLU(),
            nn.Linear(8, 1)
        )

    def forward(self, x):
        x = self.layers(x)
        x = x.squeeze(1) # (B, 1) -> (B)
        return x

Feature Selection

Choose features you deem useful by modifying the function below.

def select_feat(train_data, valid_data, test_data, select_all=True):
    '''Selects useful features to perform regression'''
    y_train, y_valid = train_data[:,-1], valid_data[:,-1]
    raw_x_train, raw_x_valid, raw_x_test = train_data[:,:-1], valid_data[:,:-1], test_data

    if select_all:
        feat_idx = list(range(raw_x_train.shape[1]))
    else:
        feat_idx = [0,1,2,3,4] # TODO: Select suitable feature columns.
        
    return raw_x_train[:,feat_idx], raw_x_valid[:,feat_idx], raw_x_test[:,feat_idx], y_train, y_valid

Training Loop

def trainer(train_loader, valid_loader, model, config, device):

    criterion = nn.MSELoss(reduction='mean') # Define your loss function, do not modify this.

    # Define your optimization algorithm. 
    # TODO: Please check https://pytorch.org/docs/stable/optim.html to get more available algorithms.
    # TODO: L2 regularization (optimizer(weight decay...) or implement by your self).
    optimizer = torch.optim.SGD(model.parameters(), lr=config['learning_rate'], momentum=0.9) 

    writer = SummaryWriter() # Writer of tensoboard.

    if not os.path.isdir('./models'):
        os.mkdir('./models') # Create directory of saving models.

    n_epochs, best_loss, step, early_stop_count = config['n_epochs'], math.inf, 0, 0

    for epoch in range(n_epochs):
        model.train() # Set your model to train mode.
        loss_record = []

        # tqdm is a package to visualize your training progress.
        train_pbar = tqdm(train_loader, position=0, leave=True)

        for x, y in train_pbar:
            optimizer.zero_grad()               # Set gradient to zero.
            x, y = x.to(device), y.to(device)   # Move your data to device. 
            pred = model(x)             
            loss = criterion(pred, y)
            loss.backward()                     # Compute gradient(backpropagation).
            optimizer.step()                    # Update parameters.
            step += 1
            loss_record.append(loss.detach().item())
            
            # Display current epoch number and loss on tqdm progress bar.
            train_pbar.set_description(f'Epoch [{epoch+1}/{n_epochs}]')
            train_pbar.set_postfix({'loss': loss.detach().item()})

        mean_train_loss = sum(loss_record)/len(loss_record)
        writer.add_scalar('Loss/train', mean_train_loss, step)

        model.eval() # Set your model to evaluation mode.
        loss_record = []
        for x, y in valid_loader:
            x, y = x.to(device), y.to(device)
            with torch.no_grad():
                pred = model(x)
                loss = criterion(pred, y)

            loss_record.append(loss.item())
            
        mean_valid_loss = sum(loss_record)/len(loss_record)
        print(f'Epoch [{epoch+1}/{n_epochs}]: Train loss: {mean_train_loss:.4f}, Valid loss: {mean_valid_loss:.4f}')
        writer.add_scalar('Loss/valid', mean_valid_loss, step)

        if mean_valid_loss < best_loss:
            best_loss = mean_valid_loss
            torch.save(model.state_dict(), config['save_path']) # Save your best model
            print('Saving model with loss {:.3f}...'.format(best_loss))
            early_stop_count = 0
        else: 
            early_stop_count += 1

        if early_stop_count >= config['early_stop']:
            print('\nModel is not improving, so we halt the training session.')
            return

Configurations

config contains hyper-parameters for training and the path to save your model.

device = 'cuda' if torch.cuda.is_available() else 'cpu'
config = {
    'seed': 5201314,      # Your seed number, you can pick your lucky number. :)
    'select_all': True,   # Whether to use all features.
    'valid_ratio': 0.2,   # validation_size = train_size * valid_ratio
    'n_epochs': 3000,     # Number of epochs.            
    'batch_size': 256, 
    'learning_rate': 1e-5,              
    'early_stop': 400,    # If model has not improved for this many consecutive epochs, stop training.     
    'save_path': './models/model.ckpt'  # Your model will be saved here.
}

Dataloader

Read data from files and set up training, validation, and testing sets. You do not need to modify this part.

# Set seed for reproducibility
same_seed(config['seed'])


# train_data size: 2699 x 118 (id + 37 states + 16 features x 5 days) 
# test_data size: 1078 x 117 (without last day's positive rate)
train_data, test_data = pd.read_csv('./covid.train.csv').values, pd.read_csv('./covid.test.csv').values
train_data, valid_data = train_valid_split(train_data, config['valid_ratio'], config['seed'])

# Print out the data size.
print(f"""train_data size: {train_data.shape} 
valid_data size: {valid_data.shape} 
test_data size: {test_data.shape}""")

# Select features
x_train, x_valid, x_test, y_train, y_valid = select_feat(train_data, valid_data, test_data, config['select_all'])

# Print out the number of features.
print(f'number of features: {x_train.shape[1]}')

train_dataset, valid_dataset, test_dataset = COVID19Dataset(x_train, y_train), \
                                            COVID19Dataset(x_valid, y_valid), \
                                            COVID19Dataset(x_test)

# Pytorch data loader loads pytorch dataset into batches.
train_loader = DataLoader(train_dataset, batch_size=config['batch_size'], shuffle=True, pin_memory=True)
valid_loader = DataLoader(valid_dataset, batch_size=config['batch_size'], shuffle=True, pin_memory=True)
test_loader = DataLoader(test_dataset, batch_size=config['batch_size'], shuffle=False, pin_memory=True)

Start training!

it may take lots of time(depends on GPU you drew),be sure stay front your computer or get some scripts or devices to make your screen stay light.

model = My_Model(input_dim=x_train.shape[1]).to(device) # put your model and data on the same computation device.
trainer(train_loader, valid_loader, model, config, device)

and if you never modify any above code,it may train 1883 times

Plot learning curves with tensorboard (optional)

tensorboard is a tool that allows you to visualize your training progress.

If this block does not display your learning curve, please wait for few minutes, and re-run this block. It might take some time to load your logging information.

%reload_ext tensorboard
%tensorboard --logdir=./runs/

you will get a picture like this.

Testing

The predictions of your model on testing set will be stored at pred.csv.

def save_pred(preds, file):
    ''' Save predictions to specified file '''
    with open(file, 'w') as fp:
        writer = csv.writer(fp)
        writer.writerow(['id', 'tested_positive'])
        for i, p in enumerate(preds):
            writer.writerow([i, p])

model = My_Model(input_dim=x_train.shape[1]).to(device)
model.load_state_dict(torch.load(config['save_path']))
preds = predict(test_loader, model, device) 
save_pred(preds, 'pred.csv')         

100%|██████████| 5/5 [00:00<00:00, 554.88it/s]

after these cells,you will get a pred.csv in the files

you can download this doc and submit it in kaggle

and the kaggle will give you a score,if you never modify,you may have a low score like this:

Some optimization

if you work above code,you will pass the Simple Baseline. About how can pass Medium Baseline & Strong Baseline, i will try to give the answer in the future(maybe in 09/2022), teaching assistant gave some hints:

• 特征选择(Feature selection-what other features are useful?)
• DNN结构：层数，维度，激活函数(DNN construction-layers, dimension, activation function)
• 训练(training-mini batch, optimizer, leaning rate)
• L2 regularization

Reference

all the code was from HUNG-Yi LEE(李宏毅),you can study the 《MACHINE LEARNING 2022 SPRING》 in https://speech.ee.ntu.edu.tw/~hylee/ml/2022-spring.php

above all was my study note, if you have any suggestions, welcome to comment.