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ANN_Training.py 14.91 KiB
# -*- coding: utf-8 -*-
"""
@author: Laura C. Kühle, Soraya Terrab (sorayaterrab)
Code-Style: E226, W503
Docstring-Style: D200, D400
TODO: Add README for ANN training
"""
import numpy as np
import time
import matplotlib
from matplotlib import pyplot as plt
import os
import torch
import json
from torch.utils.data import TensorDataset, DataLoader, random_split
from sklearn.model_selection import KFold
from sklearn.metrics import accuracy_score, precision_recall_fscore_support, \
roc_auc_score
import ANN_Model
from Plotting import plot_classification_barplot, plot_classification_boxplot
matplotlib.use('Agg')
class ModelTrainer:
"""Class for ANN model training.
Trains and tests a model with set loss function and optimizer.
Attributes
----------
model : torch.nn.Module
ANN model instance for evaluation.
loss_function : torch.nn.modules.loss
Function to evaluate loss during model training.
optimizer : torch.optim
Optimizer for model training.
validation_loss : torch.Tensor
List of validation loss values during training.
Methods
-------
epoch_training(dataset, num_epochs, verbose)
Trains model for a given number of epochs.
test_model(training_set, test_set)
Evaluates predictions of a model.
save_model(directory, model_name)
Saves state and validation loss of a model.
"""
def __init__(self, config: dict) -> None:
"""Initializes ModelTrainer.
Parameters
----------
config : dict
Additional parameters for model trainer.
"""
self._reset(config)
def _reset(self, config: dict) -> None:
"""Resets instance variables.
Parameters
----------
config : dict
Additional parameters for model trainer.
"""
self._batch_size = config.pop('batch_size', 500)
self._num_epochs = config.pop('num_epochs', 1000)
self._threshold = config.pop('threshold', 1e-5)
model = config.pop('model', 'ThreeLayerReLu')
model_config = config.pop('model_config', {})
loss_function = config.pop('loss_function', 'BCELoss')
loss_config = config.pop('loss_config', {})
optimizer = config.pop('optimizer', 'Adam')
optimizer_config = config.pop('optimizer_config', {})
# Set learning rate
learning_rate = config.pop('learning_rate', 1e-2)
optimizer_config['lr'] = learning_rate
if not hasattr(ANN_Model, model):
raise ValueError('Invalid model: "%s"' % model)
if not hasattr(torch.nn.modules.loss, loss_function):
raise ValueError('Invalid loss function: "%s"' % loss_function)
if not hasattr(torch.optim, optimizer):
raise ValueError('Invalid optimizer: "%s"' % optimizer)
self._model = getattr(ANN_Model, model)(model_config)
self._loss_function = getattr(torch.nn.modules.loss, loss_function)(
**loss_config)
self._optimizer = getattr(torch.optim, optimizer)(
self._model.parameters(), **optimizer_config)
self._validation_loss = torch.zeros(self._num_epochs//10)
def epoch_training(self, dataset: torch.utils.data.dataset.TensorDataset,
num_epochs: int = None, verbose: bool = True) -> None:
"""Trains model for a given number of epochs.
Trains model and saves the validation loss. The training stops after
the given number of epochs or if the threshold is reached.
Parameters
----------
dataset : torch.utils.data.dataset.TensorDataset
Training dataset.
num_epochs : int, optional
Number of epochs for training.
Default: None (i.e. instance variable).
verbose : bool, optional
Flag whether commentary in console is wanted. Default: False.
"""
tic = time.perf_counter()
if num_epochs is None:
num_epochs = self._num_epochs
# Split data into training and validation set
num_samples = len(dataset)
if verbose:
print('Splitting data randomly into training and validation set.')
train_ds, valid_ds = random_split(dataset, [round(num_samples*0.8),
round(num_samples*0.2)])
# Load sets
train_dl = DataLoader(train_ds, batch_size=self._batch_size,
shuffle=True)
valid_dl = DataLoader(valid_ds, batch_size=self._batch_size * 2)
# Train with validation
if verbose:
print('\nTraining model...')
print('Number of epochs:', num_epochs)
tic_train = time.perf_counter()
for epoch in range(num_epochs):
self._model.train()
for x_batch, y_batch in train_dl:
pred = self._model(x_batch.float())
loss = self._loss_function(pred, y_batch.float()).mean()
# Run back propagation, update the weights,
# and zero gradients for next epoch
loss.backward()
self._optimizer.step()
self._optimizer.zero_grad()
# Determine validation loss
self._model.eval()
with torch.no_grad():
valid_loss = sum(
self._loss_function(self._model(x_batch_valid.float()),
y_batch_valid.float())
for x_batch_valid, y_batch_valid in valid_dl)
# Report validation loss
if (epoch+1) % 100 == 0:
self._validation_loss[int((epoch+1) / 100)-1] \
= valid_loss / len(valid_dl)
if verbose:
print(epoch+1, 'epochs completed. Loss:',
valid_loss / len(valid_dl))
# Interrupt if threshold is reached
if valid_loss / len(valid_dl) < self._threshold:
break
toc_train = time.perf_counter()
if verbose:
print('Finished training model!')
print(f'Training time: {toc_train-tic_train:0.4f}s\n')
toc = time.perf_counter()
if verbose:
print(f'Total runtime: {toc-tic:0.4f}s\n')
def test_model(self, training_set: torch.utils.data.dataset.TensorDataset,
test_set: torch.utils.data.dataset.TensorDataset) -> dict:
"""Evaluates predictions of a model.
Trains a model and compares the predicted and true results by
evaluating precision, recall, and f-score for both classes,
as well as accuracy and AUROC score.
Parameters
----------
training_set : torch.utils.data.dataset.TensorDataset
Training dataset.
test_set : torch.utils.data.dataset.TensorDataset
Test dataset.
Returns
-------
dict
Dictionary containing classification evaluation data.
"""
# Train model
self.epoch_training(training_set, num_epochs=50, verbose=False)
self._model.eval()
# Classify data
x_test, y_test = test_set
model_score = self._model(x_test.float())
model_output = torch.argmax(model_score, dim=1)
# Evaluate classification
y_true = y_test.detach().numpy()[:, 1]
y_pred = model_output.detach().numpy()
accuracy = accuracy_score(y_true, y_pred)
precision, recall, f_score, support = precision_recall_fscore_support(
y_true, y_pred, zero_division=0)
auroc = roc_auc_score(y_true, y_pred)
return {'Precision_Smooth': precision[0],
'Precision_Troubled': precision[1],
'Recall_Smooth': recall[0],
'Recall_Troubled': recall[1],
'F-Score_Smooth': f_score[0],
'F-Score_Troubled': f_score[1],
'Accuracy': accuracy,
'AUROC': auroc}
def save_model(self, directory: str,
model_name: str = 'test_model') -> None:
"""Saves state and validation loss of a model.
Parameters
----------
directory : str
Path to directory in which model is saved.
model_name : str, optional
Name of model for saving. Default: 'test_model'.
"""
# Set paths for files if not existing already
model_dir = directory + '/trained models'
if not os.path.exists(model_dir):
os.makedirs(model_dir)
# Save model and loss
torch.save(self._model.state_dict(), model_dir + '/' +
model_name + '.model.pt')
torch.save(self._validation_loss, model_dir + '/' +
model_name + '.loss.pt')
def read_training_data(directory: str, normalized: bool = True) -> \
torch.utils.data.dataset.TensorDataset:
"""Reads training data from directory.
Parameters
----------
directory : str
Path to directory in which training data is saved.
normalized : bool, optional
Flag whether normalized data should be used. Default: True.
Returns
-------
torch.utils.data.dataset.TensorDataset
Training dataset.
"""
# Get training dataset from saved file and map to Torch tensor and dataset
input_file = directory + ('/input_data.normalized.npy'
if normalized else '/input_data.raw.npy')
output_file = directory + '/output_data.npy'
return TensorDataset(*map(torch.tensor, (np.load(input_file),
np.load(output_file))))
def evaluate_models(models: dict, directory: str, num_iterations: int = 100,
compare_normalization: bool = False) -> None:
"""Evaluates the classification of a given set of models.
Evaluates the classification and saves the results in a JSON file.
Parameters
----------
models : dict
Dictionary of models to evaluate.
directory : str
Path to directory for saving resulting plots.
num_iterations : int, optional
Number of iterations for evaluation. Default: 100.
compare_normalization : bool, optional
Flag whether both normalized and raw data should be evaluated.
Default: False.
"""
tic = time.perf_counter()
# Read training data
print('Read normalized training data.')
datasets = {'normalized': read_training_data(directory)}
if compare_normalization:
print('Read raw, non-normalized training data.')
datasets['raw'] = read_training_data(directory, False)
# Train models for evaluation
print('\nTraining models with 5-fold cross validation...')
print('Number of iterations:', num_iterations)
tic_train = time.perf_counter()
classification_stats = {}
for iteration in range(num_iterations):
# Split data for cross validation
for train_index, test_index in KFold(
n_splits=5, shuffle=True).split(datasets['normalized']):
for dataset in datasets.keys():
training_set = TensorDataset(*datasets[dataset][train_index])
test_set = datasets[dataset][test_index]
# Save results for each model on split dataset
for model in models:
result = models[model].test_model(training_set, test_set)
for measure in result.keys():
if measure not in classification_stats.keys():
classification_stats[measure] = \
{model + ' (' + dataset + ')': []
for model in models
for dataset in datasets}
classification_stats[measure][model + ' (' + dataset +
')'].append(
result[measure])
# Report status
if iteration+1 % max(10, 10*(num_iterations//100)):
print(iteration+1, 'iterations completed.')
toc_train = time.perf_counter()
print('Finished training models with 5-fold cross validation!')
print(f'Training time: {toc_train - tic_train:0.4f}s\n')
# Set paths for plot files if not existing already
plot_dir = directory + '/model evaluation'
if not os.path.exists(plot_dir):
os.makedirs(plot_dir)
# Save evaluation results in JSON format
print('Saving evaluation results in JSON format.')
with open(plot_dir + '/' + '_'.join(models.keys()) + '.json', 'w')\
as json_file:
json_file.write(json.dumps(classification_stats))
toc = time.perf_counter()
print(f'Total runtime: {toc - tic:0.4f}s')
def plot_evaluation_results(evaluation_file: str, directory: str,
colors: dict = None) -> None:
"""Plots given evaluation results of model classifications.
Plots evaluation results for all measures for which a color is given. If
colors is set to None, all measures are plotted with a default color
scheme.
Parameters
----------
evaluation_file: str
Path to file containing evaluation results.
directory : str
Path to directory for saving resulting plots.
colors : dict, optional
Dictionary containing plotting colors. If None, set to default colors.
Default: None.
"""
tic = time.perf_counter()
# Set colors if not given
if colors is None:
colors = {'Accuracy': 'magenta', 'Precision_Smooth': 'red',
'Precision_Troubled': '#8B0000', 'Recall_Smooth': 'blue',
'Recall_Troubled': '#00008B', 'F-Score_Smooth': 'green',
'F-Score_Troubled': '#006400', 'AUROC': 'yellow'}
# Read evaluation results
print('Reading evaluation results.')
with open(evaluation_file) as json_file:
classification_stats = json.load(json_file)
# Plot data
print('\nPlotting evaluation of trained models...')
print('Plotting data in boxplot.')
models = classification_stats[list(colors.keys())[0]].keys()
plot_classification_boxplot(classification_stats, colors)
print('Plotting averaged data in barplot.')
classification_stats = {measure: {model: np.array(
classification_stats[measure][model]).mean()
for model in models}
for measure in colors}
plot_classification_barplot(classification_stats, colors)
print('Finished plotting evaluation of trained models!\n')
# Set paths for plot files if not existing already
plot_dir = directory + '/model evaluation'
if not os.path.exists(plot_dir):
os.makedirs(plot_dir)
# Save plots
print('Saving plots.')
file_name = evaluation_file.split('/')[-1].rstrip('.json')
for identifier in plt.get_figlabels():
plt.figure(identifier)
plt.savefig(plot_dir + '/' + file_name + '.' + identifier + '.pdf')
toc = time.perf_counter()
print(f'Total runtime: {toc - tic:0.4f}s')