alzheimers_nn/threshold.py

import pandas as pd
import numpy as np
import os
import tomli as toml
from utils.data.datasets import prepare_datasets
import utils.ensemble as ens
import torch
import matplotlib.pyplot as plt
import sklearn.metrics as metrics
from tqdm import tqdm

RUN = True

# CONFIGURATION
if os.getenv('ADL_CONFIG_PATH') is None:
    with open('config.toml', 'rb') as f:
        config = toml.load(f)
else:
    with open(os.getenv('ADL_CONFIG_PATH'), 'rb') as f:
        config = toml.load(f)


# This function returns a list of the accuracies given a threshold
def threshold(config):
    # First, get the model data
    ts, vs, test_set = prepare_datasets(
        config['paths']['mri_data'],
        config['paths']['xls_data'],
        config['dataset']['validation_split'],
        944,
        config['training']['device'],
    )

    test_set = test_set + vs

    models, _ = ens.load_models(
        config['paths']['model_output'] + config['ensemble']['name'] + '/',
        config['training']['device'],
    )

    indv_model = models[0]

    predictions = []
    indv_predictions = []

    # Evaluate ensemble and uncertainty test set
    for mdata, target in tqdm(test_set, total=len(test_set)):
        mri, xls = mdata
        mri = mri.unsqueeze(0)
        xls = xls.unsqueeze(0)
        mdata = (mri, xls)
        mean, variance = ens.ensemble_predict(models, mdata)
        stdev = torch.sqrt(variance)
        prediction = mean.item()

        target = target[1]

        # Check if the prediction is correct
        correct = (prediction < 0.5 and int(target.item()) == 0) or (
            prediction >= 0.5 and int(target.item()) == 1
        )

        predictions.append(
            {
                'Prediction': prediction,
                'Actual': target.item(),
                'Stdev': stdev.item(),
                'Correct': correct,
            }
        )

        i_mean = indv_model(mdata)[:, 1].item()
        i_correct = (i_mean < 0.5 and int(target.item()) == 0) or (
            i_mean >= 0.5 and int(target.item()) == 1
        )

        indv_predictions.append(
            {
                'Prediction': i_mean,
                'Actual': target.item(),
                'Stdev': 0,
                'Correct': i_correct,
            }
        )

    # Sort the predictions by the uncertainty
    predictions = pd.DataFrame(predictions).sort_values(by='Stdev')

    # Calculate the metrics for the individual model
    indv_predictions = pd.DataFrame(indv_predictions)
    indv_correct = indv_predictions['Correct'].sum()
    indv_accuracy = indv_correct / len(indv_predictions)
    indv_false_pos = len(
        indv_predictions[
            (indv_predictions['Prediction'] >= 0.5) & (indv_predictions['Actual'] == 0)
        ]
    )
    indv_false_neg = len(
        indv_predictions[
            (indv_predictions['Prediction'] < 0.5) & (indv_predictions['Actual'] == 1)
        ]
    )
    indv_f1 = 2 * indv_correct / (2 * indv_correct + indv_false_pos + indv_false_neg)
    indv_auc = metrics.roc_auc_score(
        indv_predictions['Actual'], indv_predictions['Prediction']
    )

    indv_metrics = {'Accuracy': indv_accuracy, 'F1': indv_f1, 'AUC': indv_auc}

    thresholds = []
    quantiles = np.arange(0.1, 1, 0.1)
    # get uncertainty quantiles
    for quantile in quantiles:
        thresholds.append(predictions['Stdev'].quantile(quantile))

    # Calculate the accuracy of the model for each threshold
    accuracies = []
    # Calculate the accuracy of the model for each threshold
    for threshold, quantile in zip(thresholds, quantiles):
        filtered = predictions[predictions['Stdev'] <= threshold]
        correct = filtered['Correct'].sum()
        total = len(filtered)
        accuracy = correct / total

        false_positives = len(
            filtered[(filtered['Prediction'] >= 0.5) & (filtered['Actual'] == 0)]
        )

        false_negatives = len(
            filtered[(filtered['Prediction'] < 0.5) & (filtered['Actual'] == 1)]
        )

        f1 = 2 * correct / (2 * correct + false_positives + false_negatives)

        auc = metrics.roc_auc_score(filtered['Actual'], filtered['Prediction'])

        accuracies.append(
            {
                'Threshold': threshold,
                'Accuracy': accuracy,
                'Quantile': quantile,
                'F1': f1,
                'AUC': auc,
            }
        )

    predictions.to_csv(
        f"{config['paths']['model_output']}{config['ensemble']['name']}/predictions.csv"
    )

    indv_predictions.to_csv(
        f"{config['paths']['model_output']}{config['ensemble']['name']}/indv_predictions.csv"
    )

    return pd.DataFrame(accuracies), indv_metrics


if RUN:
    result, indv = threshold(config)
    result.to_csv(
        f"{config['paths']['model_output']}{config['ensemble']['name']}/coverage.csv"
    )
    indv = pd.DataFrame([indv])
    indv.to_csv(
        f"{config['paths']['model_output']}{config['ensemble']['name']}/indv_metrics.csv"
    )

result = pd.read_csv(
    f"{config['paths']['model_output']}{config['ensemble']['name']}/coverage.csv"
)
predictions = pd.read_csv(
    f"{config['paths']['model_output']}{config['ensemble']['name']}/predictions.csv"
)
indv = pd.read_csv(
    f"{config['paths']['model_output']}{config['ensemble']['name']}/indv_metrics.csv"
)

print(indv)


plt.figure()

plt.plot(result['Quantile'], result['Accuracy'], label='Ensemble Accuracy')

plt.plot(
    result['Quantile'],
    [indv['Accuracy']] * len(result['Quantile']),
    label='Individual Accuracy',
    linestyle='--',
)
plt.legend()

plt.title('Accuracy vs Coverage')

plt.xlabel('Coverage')
plt.ylabel('Accuracy')
plt.gca().invert_xaxis()

plt.savefig(
    f"{config['paths']['model_output']}{config['ensemble']['name']}/coverage.png"
)

plt.figure()
plt.plot(result['Quantile'], result['F1'], label='Ensemble F1')
plt.plot(
    result['Quantile'],
    [indv['F1']] * len(result['Quantile']),
    label='Individual F1',
    linestyle='--',
)
plt.legend()
plt.title('F1 vs Coverage')

plt.xlabel('Coverage')
plt.ylabel('F1')
plt.gca().invert_xaxis()

plt.savefig(
    f"{config['paths']['model_output']}{config['ensemble']['name']}/coverage_f1.png"
)

plt.figure()
plt.plot(result['Quantile'], result['AUC'], label='Ensemble AUC')
plt.plot(
    result['Quantile'],
    [indv['AUC']] * len(result['Quantile']),
    label='Individual AUC',
    linestyle='--',
)
plt.legend()
plt.title('AUC vs Coverage')
plt.xlabel('Coverage')
plt.ylabel('AUC')
plt.gca().invert_xaxis()

plt.savefig(
    f"{config['paths']['model_output']}{config['ensemble']['name']}/coverage_auc.png"
)

# create histogram of the incorrect predictions vs the uncertainty
plt.figure()
plt.hist(predictions[~predictions['Correct']]['Stdev'], bins=10)
plt.xlabel('Uncertainty')
plt.ylabel('Number of incorrect predictions')
plt.savefig(
    f"{config['paths']['model_output']}{config['ensemble']['name']}/incorrect_predictions.png"
)