InceptionV3_Chexpert_BCE_E30_B32_C0 - TobiasSchmidtDE/DeepL-MedicalImaging GitHub Wiki

InceptionV3_Chexpert_BCE_E30_B32_C0

Version: 1

Trained InceptionV3 architecture using the 'Chexpert_BCE_E30_B32_C0' benchmark. The benchmark was initialized for the chexpert_full dataset with batch size of 32, shuffle set to True and images rescaled to dimension (256, 256). The training was done for 30 epochs using the Adam optimizer and binary_crossentropy loss. A total of 14 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 InceptionV3 architecture using the 'Chexpert_BCE_E30_B32_C0' benchmark.

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


The training was done for 30 epochs using the Adam optimizer and binary_crossentropy loss.


A total of 14 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

                No Finding       0.10      0.07      0.08      4479
Enlarged Cardiomediastinum       0.00      0.00      0.00      2214
              Cardiomegaly       0.10      0.03      0.05      5294
              Lung Opacity       0.48      0.56      0.51     21324
               Lung Lesion       0.00      0.00      0.00      1901
                     Edema       0.23      0.15      0.18     10461
             Consolidation       0.00      0.00      0.00      3063
                 Pneumonia       0.00      0.00      0.00      1225
               Atelectasis       0.00      0.00      0.00      6912
              Pneumothorax       0.11      0.03      0.04      3894
          Pleural Effusion       0.39      0.37      0.38     17656
             Pleural Other       0.00      0.00      0.00       747
                  Fracture       0.00      0.00      0.00      1863
           Support Devices       0.52      0.54      0.53     23648

                 micro avg       0.42      0.32      0.36    104681
                 macro avg       0.14      0.12      0.13    104681
              weighted avg       0.32      0.32      0.31    104681
               samples avg       0.34      0.29      0.29    104681

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:  0.28535911440849304
Test auc:  0.7669256925582886
Test precision:  0.7018487453460693
Test recall:  0.5247657299041748
Test f2_score:  0.5526536703109741
Test binary_accuracy:  0.8837191462516785

Benchmark Details

pp = pprint.PrettyPrinter(indent=4)
if "benchmark" in data.keys():
    pp.pprint(data["benchmark"])
{   'batch_size': 32,
    'benchmark_name': 'Chexpert_BCE_E30_B32_C0',
    'crop': False,
    'dataset_folder': 'data/chexpert/full',
    'dataset_name': 'chexpert_full',
    'dim': [256, 256],
    'drop_last': True,
    'epochs': 30,
    'label_columns': [   'No Finding',
                         'Enlarged Cardiomediastinum',
                         'Cardiomegaly',
                         'Lung Opacity',
                         'Lung Lesion',
                         'Edema',
                         'Consolidation',
                         'Pneumonia',
                         'Atelectasis',
                         'Pneumothorax',
                         'Pleural Effusion',
                         'Pleural Other',
                         'Fracture',
                         'Support Devices'],
    'loss': 'binary_crossentropy',
    'metrics': ['auc', 'precision', 'recall', 'f2_score', 'binary_accuracy'],
    'models_dir': 'models',
    'n_channels': 3,
    'nan_replacement': 0,
    'negative_weights': [   1.1111509799957275,
                            1.0502605438232422,
                            1.137785792350769,
                            1.8928941488265991,
                            1.0430703163146973,
                            1.3037471771240234,
                            1.0706472396850586,
                            1.0274509191513062,
                            1.1762800216674805,
                            1.0968482494354248,
                            1.621975302696228,
                            1.0159274339675903,
                            1.04159677028656,
                            2.0654001235961914],
    'optimizer': 'Adam',
    'path_column': 'Path',
    'path_column_prefix': '',
    'positive_weights': [   9.996768951416016,
                            20.896329879760742,
                            8.257645606994629,
                            2.1199536323547363,
                            24.21783447265625,
                            4.292212009429932,
                            15.154845237731934,
                            37.4287223815918,
                            6.672793865203857,
                            11.325428009033203,
                            2.607780933380127,
                            63.78485107421875,
                            25.04029655456543,
                            1.9386144876480103],
    '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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