DenseNet121_Chexpert_BCE_E5_B32_C1_N5_CTCOMP - TobiasSchmidtDE/DeepL-MedicalImaging GitHub Wiki

DenseNet121_Chexpert_BCE_E5_B32_C1_N5_CTCOMP

Version: 1

Trained DenseNet121 architecture using the 'Chexpert_BCE_E5_B32_C1_N5_CTCOMP' benchmark. The benchmark was initialized for the chexpert_preprocessed-256-crop dataset with batch size of 32, shuffle set to True and images rescaled to dimension (256, 256). The training was done for 5 epochs using the Adam optimizer and binary_crossentropy loss. A total of 5 labels/pathologies were included in the training and encoded using the 'uzeroes' method. The traing set included 142320 number of sample, the validation set 36162, and the test set 44932.

from pathlib import Path
from dotenv import load_dotenv, find_dotenv
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib.pyplot import figure
import json
import os
import re
import pprint

basepath = Path(os.getcwd())
if basepath.name != "idp-radio-1":
    os.chdir(basepath.parent.parent)
    print(os.getcwd())
load_dotenv(find_dotenv())

from src.preprocessing.split.train_test_split import train_test_split
/srv/idp-radio-1
data = json.loads(os.environ['EXP_DATA'])
history = data['history']

Model and Benchmark Summary

for s in data["description"].split(".")[:-1]:
    print(s + ".\n")
Trained DenseNet121 architecture using the 'Chexpert_BCE_E5_B32_C1_N5_CTCOMP' benchmark.

 The benchmark was initialized for the chexpert_preprocessed-256-crop dataset with batch size of 32, shuffle set to True and images rescaled to dimension (256, 256).


The training was done for 5 epochs using the Adam optimizer and binary_crossentropy loss.


A total of 5 labels/pathologies were included in the training and encoded using the 'uzeroes' method.


The traing set included 142320 number of sample, the validation set 36162, and the test set 44932.

Extract and format metrics to be plotted

# if there are any metrics that were renamed, add this new name here as ("default_name":"new_name")
metric_custom_names={"auc":"AUC_ROC"}

metric_names = [re.sub("([a-z0-9])([A-Z])","\g<1> \g<2>",name) for name in data["benchmark"]["metrics"]]
metric_keys = [re.sub("([a-z0-9])([A-Z])","\g<1>_\g<2>",name).lower() for name in data["benchmark"]["metrics"]]

for default_name, custom_name in metric_custom_names.items():
    if not default_name in history.keys() and default_name in metric_keys:
        #replace default name with custom name
        metric_keys[metric_keys.index(default_name)]=custom_name

Plot training & validation accuracy values

def print_or_plot_metric(metric_key, metric_name, figure_name):
    if len(history[metric_key]) == 1:
        print("Data for {m_name} only available for a single epoch. \nSkipping plot and printing data...".format(m_name=metric_name))
        print('Train {}: '.format(metric_name), history[metric_key])
        print('Validation {}: '.format(metric_name), history['val_'+metric_key])
        print()        
    else:
        plot_epoch_metric(metric_key, metric_name, figure_name)
        
def plot_epoch_metric(metric_key, metric_name, figure_name):
    figure(num=None, figsize=(10, 6))
    plt.plot(history[metric_key])
    if 'val_'+metric_key in history.keys():
        plt.plot(history['val_'+metric_key])
    plt.title(figure_name)
    plt.ylabel(metric_name)
    plt.xlabel('Epoch')
    if 'val_'+metric_key in history.keys():
        plt.legend(['Train', 'Validation'], loc='upper left')
    plt.show()

for i, metric_key in enumerate(metric_keys):
    print_or_plot_metric(metric_key, metric_names[i], "Model "+metric_names[i])

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Plot training & validation loss values

print_or_plot_metric("loss", "Loss", "Model loss")

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if "lr" in history.keys():
    plot_epoch_metric("lr", "Learning Rate", "Learning Rate")

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Classification Report

if 'classification_report' in data.keys() and data['classification_report']:
    print(data['classification_report'])
               precision    recall  f1-score   support

        Edema       0.21      0.01      0.01     10461
  Atelectasis       0.00      0.00      0.00      6912
    Pneumonia       0.00      0.00      0.00      1225
 Lung Opacity       0.47      0.27      0.34     21324
Consolidation       0.00      0.00      0.00      3063

    micro avg       0.47      0.13      0.21     42985
    macro avg       0.14      0.05      0.07     42985
 weighted avg       0.29      0.13      0.17     42985
  samples avg       0.13      0.10      0.11     42985

Test Scores

if 'test' in data.keys() and data['test']:
    for score_name, score in data["test"].items():
        print('Test {}: '.format(score_name), score)
Test loss:  0.40162837505340576
Test auc:  0.6654490232467651
Test precision:  0.6579886674880981
Test recall:  0.18874025344848633
Test f2_score:  0.22013890743255615
Test binary_accuracy:  0.8261523246765137

Benchmark Details

pp = pprint.PrettyPrinter(indent=4)
if "benchmark" in data.keys():
    pp.pprint(data["benchmark"])
{   'batch_size': 32,
    'benchmark_name': 'Chexpert_BCE_E5_B32_C1_N5_CTCOMP',
    'crop': False,
    'dataset_folder': 'data/chexpert/preprocessed-256-crop',
    'dataset_name': 'chexpert_preprocessed-256-crop',
    'dim': [256, 256],
    'drop_last': True,
    'epochs': 5,
    'label_columns': [   'Edema',
                         'Atelectasis',
                         'Pneumonia',
                         'Lung Opacity',
                         'Consolidation'],
    'loss': 'binary_crossentropy',
    'metrics': ['auc', 'precision', 'recall', 'f2_score', 'binary_accuracy'],
    'models_dir': 'models',
    'n_channels': 3,
    'nan_replacement': 0,
    'negative_weights': [   1.3037351369857788,
                            1.1763091087341309,
                            1.0274509191513062,
                            1.8928438425064087,
                            1.0706472396850586],
    'optimizer': 'Adam',
    'path_column': 'Path',
    'path_column_prefix': '',
    'positive_weights': [   4.292341709136963,
                            6.671855449676514,
                            37.4287223815918,
                            2.120016574859619,
                            15.154845237731934],
    'shuffle': True,
    'split_seed': 6122156,
    'test_num_samples': 44932,
    'train_num_samples': 142320,
    'u_enc': 'uzeroes',
    'unc_value': -1,
    'use_class_weights': False,
    'valid_num_samples': 36162}

Data Distribution

if 'benchmark' in data.keys() and 'split_seed' in data['benchmark']:
    benchmark = data['benchmark']

    dataset_path = Path(benchmark['dataset_folder'])
    train_labels = benchmark['train_labels'] if 'train_labels' in benchmark.keys() else 'train.csv'
    split_test_size =  benchmark['split_test_size'] if 'split_test_size' in benchmark.keys() else 0.2
    split_valid_size =  benchmark['split_valid_size'] if 'split_valid_size' in benchmark.keys() else 0.2
    split_group = benchmark['split_group'] if 'split_group' in benchmark.keys() else 'patient_id'
    split_seed = benchmark['split_seed']

    all_labels = pd.read_csv(dataset_path / train_labels)
    train_labels, test_labels = train_test_split(all_labels, test_size=split_test_size, group=split_group, seed=split_seed)
    train_labels, validation_labels = train_test_split(train_labels, test_size=split_valid_size, group=split_group, seed=split_seed)
from src.datasets.u_encoding import uencode

def get_distribution(labels):
    if 'nan_replacement' in benchmark.keys():
        labels = labels.fillna(benchmark['nan_replacement'])
    data = labels.to_numpy()
    data = uencode(benchmark['u_enc'], data, unc_value=benchmark['unc_value'])
    data = pd.DataFrame(data, columns=labels.columns)

    labels = data[benchmark['label_columns']]

    d = {'Pathology': [], 'Positive': [], 'Positive %': [], 'Negative': [], 'Negative %': [],}
    for label in labels.columns:
        values = labels.groupby(label)
        d['Pathology'].append(label)

        positive = values.size()[1.0] if 1.0 in values.size() else 0
        positive_percent = positive / labels.shape[0] * 100
        d['Positive'].append(positive)
        d['Positive %'].append(round(positive_percent))

        negative = values.size()[-0.0] if -0.0 in values.size() else 0
        negative_percent = negative / labels.shape[0] * 100
        d['Negative'].append(negative)
        d['Negative %'].append(round(negative_percent))
    
    df = pd.DataFrame(d)
    df = df.set_index('Pathology')

    return df
if 'benchmark' in data.keys() and 'split_seed' in data['benchmark']:
    train = get_distribution(train_labels)
    val = get_distribution(validation_labels)
    test = get_distribution(test_labels)
    
    positives = train[['Positive %']].merge(val[['Positive %']], left_index=True, right_index=True).merge(test[['Positive %']], left_index=True,  right_index=True).rename(columns={"Positive %_x": "Positives Train", "Positive %_y": "Positives Validation", "Positive %": "Positives Test", })
    positives.copy().plot(kind='bar', figsize=(10,7), title="Positive Labels Distribution")
    
    negatives = train[['Negative %']].merge(val[['Negative %']], left_index=True, right_index=True).merge(test[['Negative %']], left_index=True,  right_index=True).rename(columns={"Negative %_x": "Negative Train", "Negative %_y": "Negative Validation", "Negative %": "Negative Test", })
    negatives.copy().plot(kind='bar', figsize=(10,7), title="Negative Labels Distribution")

    train[['Positive %', 'Negative %']].copy().plot(kind='bar', figsize=(10,7), title="Training set")
    val[['Positive %', 'Negative %']].copy().plot(kind='bar', figsize=(10,7), title="Validation set")
    test[['Positive %', 'Negative %']].copy().plot(kind='bar', figsize=(10,7), title="Test set")

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