InceptionV3_Chexpert_WBCE_E10_B32_C1_N12 checkpoint - TobiasSchmidtDE/DeepL-MedicalImaging GitHub Wiki

InceptionV3_Chexpert_WBCE_E10_B32_C1_N12

Version: 1

Trained InceptionV3 architecture using the 'Chexpert_WBCE_E10_B32_C1_N12' 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 10 epochs using the Adam optimizer and binary_crossentropy loss. A total of 12 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_WBCE_E10_B32_C1_N12' 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 10 epochs using the Adam optimizer and binary_crossentropy loss.


A total of 12 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

Enlarged Cardiomediastinum       0.04      0.01      0.02      2214
              Cardiomegaly       0.11      0.09      0.10      5294
              Lung Opacity       0.49      0.14      0.22     21324
               Lung Lesion       0.00      0.00      0.00      1901
                     Edema       0.24      0.18      0.20     10461
             Consolidation       0.08      0.01      0.01      3063
                 Pneumonia       0.00      0.00      0.00      1225
               Atelectasis       0.00      0.00      0.00      6912
              Pneumothorax       0.07      0.01      0.02      3894
          Pleural Effusion       0.39      0.30      0.34     17656
             Pleural Other       0.05      0.00      0.01       747
                  Fracture       0.04      0.00      0.00      1863

                 micro avg       0.32      0.14      0.19     76554
                 macro avg       0.13      0.06      0.08     76554
              weighted avg       0.28      0.14      0.18     76554
               samples avg       0.14      0.11      0.11     76554

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:  0.30407091975212097
Test auc:  0.7227616310119629
Test precision:  0.6466522812843323
Test recall:  0.277425080537796
Test f2_score:  0.3131903409957886
Test binary_accuracy:  0.8758809566497803

Benchmark Details

pp = pprint.PrettyPrinter(indent=4)
if "benchmark" in data.keys():
    pp.pprint(data["benchmark"])
{   'batch_size': 32,
    'benchmark_name': 'Chexpert_WBCE_E10_B32_C1_N12',
    'crop': False,
    'dataset_folder': 'data/chexpert/preprocessed-256-crop',
    'dataset_name': 'chexpert_preprocessed-256-crop',
    'dim': [256, 256],
    'drop_last': True,
    'epochs': 10,
    'label_columns': [   'Enlarged Cardiomediastinum',
                         'Cardiomegaly',
                         'Lung Opacity',
                         'Lung Lesion',
                         'Edema',
                         'Consolidation',
                         'Pneumonia',
                         'Atelectasis',
                         'Pneumothorax',
                         'Pleural Effusion',
                         'Pleural Other',
                         'Fracture'],
    'loss': 'binary_crossentropy',
    'metrics': ['auc', 'precision', 'recall', 'f2_score', 'binary_accuracy'],
    'models_dir': 'models',
    'n_channels': 3,
    'nan_replacement': 0,
    'negative_weights': [   1.050268292427063,
                            1.1378039121627808,
                            1.8928941488265991,
                            1.043062686920166,
                            1.3037351369857788,
                            1.0706310272216797,
                            1.0274434089660645,
                            1.1762994527816772,
                            1.0968397855758667,
                            1.6219568252563477,
                            1.0159274339675903,
                            1.04159677028656],
    'optimizer': 'Adam',
    'path_column': 'Path',
    'path_column_prefix': '',
    'positive_weights': [   20.893260955810547,
                            8.25668716430664,
                            2.1199536323547363,
                            24.22195816040039,
                            4.292341709136963,
                            15.158074378967285,
                            37.438568115234375,
                            6.672168254852295,
                            11.326329231262207,
                            2.6078288555145264,
                            63.78485107421875,
                            25.04029655456543],
    'shuffle': True,
    'split_seed': 6122156,
    'test_num_samples': 44932,
    'train_num_samples': 142320,
    'u_enc': 'uzeroes',
    'unc_value': -1,
    'use_class_weights': True,
    '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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