SHAP analysis of an improved EEG-based mental workload classification framework: utilizing data augmentation and explainable AI.
The 6 matches
- [1] § Results › SHAP analysis ↔ code_with_smote.py.py, lines 190–298 · score 0.65 · Local Explanation Summary, Gradient Explainer, Global Feature Importance, SHAP, training, Class
- [2] § Results › SHAP analysis ↔ code_without_smote.py.py, lines 200–308 · score 0.65 · Local Explanation Summary, Gradient Explainer, Global Feature Importance, SHAP, training, Class
- [3] § Results ↔ code_with_smote.py.py, lines 343–397 · score 0.60 · loss curve, confusion matrix, validation accuracy, epochs, SMOTE, trained
- [4] § Results ↔ code_without_smote.py.py, lines 311–400 · score 0.59 · loss curve, confusion matrix, validation accuracy, epochs, trained, model
- [5] § Methodology › EEGNet model ↔ code_with_smote.py.py, lines 82–104 · score 0.53 · batch normalization, ELU, dropout, kernel, separable, EEGNet
- [6] § Methodology › EEGNet model ↔ code_without_smote.py.py, lines 53–75 · score 0.53 · batch normalization, ELU, dropout, kernel, separable, EEGNet
Paper
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The authors' code
Python · 399 lines · 16 KB · no license · 3 matches
- import itertools
- import os
- import numpy as np
- import pandas as pd
- import mne
- import warnings
- import time
- import tensorflow as tf
- from scipy.io import loadmat
- from sklearn.utils import shuffle
- from sklearn.model_selection import train_test_split
- from sklearn.metrics import classification_report, confusion_matrix, precision_score, recall_score, f1_score
- from tensorflow.keras.models import Model
- from tensorflow.keras.layers import Dense, Activation, Permute, Dropout, Conv2D, MaxPooling2D, AveragePooling2D, SeparableConv2D, DepthwiseConv2D, BatchNormalization, SpatialDropout2D, Input, Flatten
- from tensorflow.keras.regularizers import l1_l2
- from tensorflow.keras.constraints import max_norm
- from tensorflow.keras.utils import to_categorical
- from tensorflow.keras.callbacks import EarlyStopping, ReduceLROnPlateau
- from tensorflow.keras.optimizers import Adam
- import shap
- import matplotlib.pyplot as plt
- # Suppress warnings
- warnings.filterwarnings('ignore')
- # Set random seeds
- np.random.seed(42)
- tf.random.set_seed(42)
- # Load the Dataset
- def load_data(data_path, tasks, n_subs, n_sessions):
- x, y = [], []
- for sub_n, session_n in itertools.product(range(n_subs), range(n_sessions)):
- epochs_data, labels = [], []
- for lab_idx, level in enumerate(tasks):
- sub = 'P{0:02d}'.format(sub_n + 1)
- sess = f'S{session_n + 1}'
- path = os.path.join(os.path.join(data_path, sub), sess) + f'/eeg/alldata_sbj{str(sub_n + 1).zfill(2)}_sess{session_n + 1}_{level}.set'
- epochs = mne.io.read_epochs_eeglab(path, verbose=False)
- epochs.pick_channels(channel_names)
- tmp = epochs.get_data()
- epochs_data.extend(tmp)
- labels.extend([lab_idx] * len(tmp))
- x.extend(epochs_data)
- y.extend(labels)
- return np.array(x), np.array(y)
- # SMOTE Function
- from imblearn.over_sampling import SMOTE
- def apply_smote_3d(X, y, target_ratio=2.0):
- """
- Applies SMOTE to EEG data.
- Parameters:
- X (numpy array): Shape (samples, channels, time points, 1)
- y (numpy array): Class labels (1D array)
- target_ratio (float): Desired increase factor for each class.
- Returns:
- X_resampled, y_resampled: Augmented dataset
- """
- n_samples, n_channels, n_timepoints, _ = X.shape
- # Flatten EEG data for SMOTE
- X_flattened = X.reshape(n_samples, -1) # Shape: (samples, channels*timepoints)
- # Determine sampling strategy
- class_counts = np.bincount(y)
- target_samples = {cls: int(count * target_ratio) for cls, count in enumerate(class_counts)}
- smote = SMOTE(sampling_strategy=target_samples, random_state=42)
- X_resampled, y_resampled = smote.fit_resample(X_flattened, y)
- # Reshape back to 3D EEG format
- X_resampled = X_resampled.reshape(-1, n_channels, n_timepoints, 1)
- return X_resampled, y_resampled
- # EEGNet Model Definition
- def build_eegnet(nb_classes, Chans=61, Samples=500, dropoutRate=0.5, kernLength=64, F1=64, D=4, F2=128):
- input1 = Input(shape=(Chans, Samples, 1))
- block1 = Conv2D(F1, (1, kernLength), padding='same', use_bias=False)(input1)
- block1 = BatchNormalization()(block1)
- block1 = DepthwiseConv2D((Chans, 1), use_bias=False, depth_multiplier=D, depthwise_constraint=max_norm(1.))(block1)
- block1 = BatchNormalization()(block1)
- block1 = Activation('elu')(block1)
- block1 = AveragePooling2D((1, 4))(block1)
- block1 = Dropout(dropoutRate)(block1)
- block2 = SeparableConv2D(F2, (1, 16), use_bias=False, padding='same')(block1)
- block2 = BatchNormalization()(block2)
- block2 = Activation('elu')(block2)
- block2 = AveragePooling2D((1, 8))(block2)
- block2 = Dropout(dropoutRate)(block2)
- flatten = Flatten(name='flatten')(block2)
- dense = Dense(nb_classes, name='dense', kernel_constraint=max_norm(0.25))(flatten)
- softmax = Activation('softmax', name='softmax')(dense)
- return Model(inputs=input1, outputs=softmax)
- # Train the Model
- def train_model(model, X_train, y_train, X_test, y_test, batch_size=64, epochs=50):
- lr_scheduler = ReduceLROnPlateau(monitor='val_loss', factor=0.1, patience=10, verbose=1)
- early_stopping = EarlyStopping(monitor='val_loss', patience=20, restore_best_weights=True)
- history = model.fit(
- X_train, y_train,
- batch_size=batch_size,
- epochs=epochs,
- validation_data=(X_test, y_test),
- callbacks=[lr_scheduler, early_stopping],
- verbose=1
- )
- return history
- # Evaluate the Model
- def evaluate_model(model, X_test, y_test):
- y_pred = model.predict(X_test)
- y_pred_classes = np.argmax(y_pred, axis=1)
- y_true_classes = np.argmax(y_test, axis=1)
- # Calculate metrics
- precision = precision_score(y_true_classes, y_pred_classes, average='weighted')
- recall = recall_score(y_true_classes, y_pred_classes, average='weighted')
- f1 = f1_score(y_true_classes, y_pred_classes, average='weighted')
- print("Classification Report:")
- print(classification_report(y_true_classes, y_pred_classes))
- print("Confusion Matrix:")
- print(confusion_matrix(y_true_classes, y_pred_classes))
- return precision, recall, f1
- # Plot and Save Accuracy and Loss Curves
- def plot_accuracy_loss_curves(history, trial):
- plt.figure(figsize=(12, 6))
- # Plot accuracy
- plt.subplot(1, 2, 1)
- plt.plot(history.history['accuracy'], label='Train Accuracy')
- plt.plot(history.history['val_accuracy'], label='Validation Accuracy')
- plt.title(f'Trial {trial + 1} - Accuracy Curves')
- plt.xlabel('Epoch')
- plt.ylabel('Accuracy')
- plt.legend()
- # Plot loss
- plt.subplot(1, 2, 2)
- plt.plot(history.history['loss'], label='Train Loss')
- plt.plot(history.history['val_loss'], label='Validation Loss')
- plt.title(f'Trial {trial + 1} - Loss Curves')
- plt.xlabel('Epoch')
- plt.ylabel('Loss')
- plt.legend()
- plt.tight_layout()
- plt.savefig(f'Trial_{trial + 1}_Accuracy_Loss_Curves.png')
- plt.close()
- # Plot and Save Confusion Matrix
- def plot_confusion_matrix(model, X_test, y_test, trial):
- y_pred = model.predict(X_test)
- y_pred_classes = np.argmax(y_pred, axis=1)
- y_true_classes = np.argmax(y_test, axis=1)
- cm = confusion_matrix(y_true_classes, y_pred_classes)
- plt.figure(figsize=(8, 6))
- plt.imshow(cm, interpolation='nearest', cmap=plt.cm.Blues)
- plt.title(f'Trial {trial + 1} - Confusion Matrix')
- plt.colorbar()
- tick_marks = np.arange(len(np.unique(y_true_classes)))
- plt.xticks(tick_marks, np.unique(y_true_classes))
- plt.yticks(tick_marks, np.unique(y_true_classes))
- plt.xlabel('Predicted Label')
- plt.ylabel('True Label')
- for i, j in itertools.product(range(cm.shape[0]), range(cm.shape[1])):
- plt.text(j, i, cm[i, j], horizontalalignment="center", color="white" if cm[i, j] > cm.max() / 2 else "black")
- plt.tight_layout()
- plt.savefig(f'Trial_{trial + 1}_Confusion_Matrix.png')
- plt.close()
- # SHAP Analysis Function
- def shap_analysis(model, X_train, X_test, output_dir, sample_size=50):
- # Create output directory if it doesn't exist
- os.makedirs(output_dir, exist_ok=True)
- print(f"Plots will be saved to: {os.path.abspath(output_dir)}")
- # Explain the model's predictions using SHAP
- explainer = shap.GradientExplainer(model, X_train[:sample_size])
- shap_values = explainer.shap_values(X_test[:sample_size])
- # Debug: Check SHAP values shape
- print("SHAP values shape:", np.array(shap_values).shape)
- # Aggregate SHAP values across the time dimension
- shap_values_aggregated = [np.mean(shap_values[class_idx], axis=2) for class_idx in range(len(shap_values))] # Shape: (3, 50, 11)
- shap_values_aggregated = [np.squeeze(shap_values_aggregated[class_idx]) for class_idx in range(len(shap_values_aggregated))] # Remove the last dimension
- # Aggregate X_test across the time dimension
- X_test_aggregated = np.mean(X_test[:sample_size], axis=2) # Shape: (50, 11, 1)
- X_test_aggregated = np.squeeze(X_test_aggregated) # Remove the last dimension
- # Save SHAP summary plot for each class
- print("Saving SHAP summary plot...")
- for class_idx in range(len(shap_values_aggregated)):
- # Select SHAP values for the current class
- shap_values_class = shap_values_aggregated[class_idx] # Shape: (50, 11)
- # Plot SHAP summary for the current class
- shap.summary_plot(shap_values_class, X_test_aggregated, plot_type="bar", feature_names=channel_names,max_display=61, show=False)
- plt.savefig(os.path.join(output_dir, f"shap_summary_plot_class_{class_idx}.png"), dpi=300, bbox_inches='tight')
- plt.close()
- print("SHAP summary plots saved.")
- # Save SHAP image plot
- print("Saving SHAP image plot...")
- plt.figure(figsize=(14, 12)) # Set figure size
- shap.image_plot(shap_values, X_test[:sample_size], show=False)
- plt.savefig(os.path.join(output_dir, "shap_image_plot.svg"), bbox_inches='tight')
- plt.close()
- print("SHAP image plot saved.")
- # Save SHAP heatmap for a sample
- print("Saving SHAP heatmap...")
- sample_idx = 9 # Choose a sample index
- shap_values_np = np.array(shap_values)
- if len(shap_values_np.shape) == 5:
- shap_values_sample = shap_values_np[0, sample_idx, :, :, 0] # Select first class
- else:
- shap_values_sample = shap_values_np[sample_idx, :, :, 0]
- plt.imshow(shap_values_sample, aspect='auto', cmap='RdBu')
- plt.colorbar()
- plt.xlabel("Time")
- plt.ylabel("Channels")
- plt.title(f"SHAP Heatmap for Sample {sample_idx}")
- plt.savefig(os.path.join(output_dir, "shap_heatmap.png"), dpi=300, bbox_inches='tight')
- plt.close()
- print("SHAP heatmap saved.")
- # Save SHAP dependence plot for each feature
- print("Saving SHAP dependence plots...")
- for feature_idx in range(X_test_aggregated.shape[1]):
- shap.dependence_plot(
- feature_idx,
- shap_values_aggregated[0], # Use SHAP values for the first class
- X_test_aggregated,
- feature_names=channel_names,
- show=False
- )
- plt.savefig(os.path.join(output_dir, f"shap_dependence_plot_feature_{feature_idx}.png"), dpi=300, bbox_inches='tight')
- plt.close()
- print("SHAP dependence plots saved.")
- # Save SHAP class comparison plot
- print("Saving SHAP class comparison plot...")
- shap.summary_plot(shap_values_aggregated, X_test_aggregated, plot_type="bar", feature_names=channel_names, max_display=61,show=False)
- plt.savefig(os.path.join(output_dir, "shap_class_comparison_plot.png"), dpi=300, bbox_inches='tight')
- plt.close()
- print("SHAP class comparison plot saved.")
- # Save Global Feature Importance Plot
- print("Saving Global Feature Importance Plot...")
- # Aggregate SHAP values across time and samples
- shap_values_global = np.mean(np.abs(shap_values), axis=(1, 3)) # Shape: (3, 11)
- shap_values_global = np.squeeze(shap_values_global) # Remove the last dimension
- # Plot global feature importance
- shap.summary_plot(shap_values_global, X_test_aggregated, plot_type="bar", feature_names=channel_names, max_display=61,show=False)
- plt.savefig(os.path.join(output_dir, "global_feature_importance.png"), dpi=300, bbox_inches='tight')
- plt.close()
- print("Global Feature Importance Plot saved.")
- # Save Local Explanation Summary Plot
- print("Saving Local Explanation Summary Plot...")
- # Aggregate SHAP values across time and samples for the first class
- shap_values_local = np.mean(shap_values[0], axis=2) # Shape: (50, 11)
- shap_values_local = np.squeeze(shap_values_local) # Remove the last dimension
- # Plot local explanation summary for the first class
- shap.summary_plot(shap_values_local, X_test_aggregated, plot_type="dot", feature_names=channel_names, max_display=61,show=False)
- plt.savefig(os.path.join(output_dir, "local_explanation_summary.png"), dpi=300, bbox_inches='tight')
- plt.close()
- print("Local Explanation Summary Plot saved.")
- print("All SHAP plots saved successfully!")
- # Main Workflow
- if __name__ == "__main__":
- # Dataset Parameters
- data_path = 'Dataset_path'
- tasks = ['MATBeasy', 'MATBmed', 'MATBdiff']
- n_subs, n_sessions = 15, 2
- channel_names =['Fp1', 'Fz', 'F3', 'F7', 'FT9', 'FC5', 'FC1', 'C3', 'T7', 'CP5', 'CP1', 'Pz', 'P3', 'P7', 'O1', 'Oz', 'O2', 'P4', 'P8', 'TP10', 'CP6', 'CP2', 'FCz', 'C4', 'T8', 'FT8', 'FC6', 'FC2', 'F4', 'F8', 'Fp2', 'AF7', 'AF3', 'AFz', 'F1', 'F5', 'FT7', 'FC3', 'C1', 'C5', 'TP7', 'CP3', 'P1', 'P5', 'PO7', 'PO3', 'POz', 'PO4', 'PO8', 'P6', 'P2', 'CPz', 'CP4', 'TP8', 'C6', 'C2', 'FC4', 'FT10', 'F6', 'AF8', 'AF4','F2']
- # Load Data
- X, Y = load_data(data_path, tasks, n_subs, n_sessions)
- X = (X - np.mean(X, axis=(0, 2), keepdims=True)) / (np.std(X, axis=(0, 2), keepdims=True) + 1e-10)
- X, Y = shuffle(X, Y, random_state=42)
- X = X.reshape((X.shape[0], X.shape[1], X.shape[2], 1))
- Y = to_categorical(Y, len(np.unique(Y)))
- # Initialize DataFrame to store metrics
- results_df = pd.DataFrame(columns=['Trial', 'Train_Accuracy', 'Train_Loss', 'Validation_Accuracy', 'Validation_Loss', 'Test_Accuracy', 'Precision', 'Recall', 'F1_Score', 'Training_Time'])
- # Variables to hold last SMOTE'd training set for shape print
- X_smote = None
- Y_smote = None
- # Run 5 trials
- for trial in range(5):
- print(f"\n=== Trial {trial + 1} ===")
- # Train-Test Split (first split, then apply SMOTE ONLY on training set)
- X_train, X_test, y_train, y_test = train_test_split(
- X, Y,
- test_size=0.25,
- random_state=42
- )
- # Apply SMOTE on training set only
- y_train_int = np.argmax(y_train, axis=1)
- X_train_smote, y_train_smote_int = apply_smote_3d(X_train, y_train_int)
- y_train_smote = to_categorical(y_train_smote_int, num_classes=3)
- # Save last trial's SMOTE shapes for printing later
- X_smote = X_train_smote
- Y_smote = y_train_smote
- # Build and Compile Model
- model = build_eegnet(nb_classes=3) # Ensure nb_classes matches the number of unique classes
- model.compile(optimizer=Adam(learning_rate=0.0001), loss='categorical_crossentropy', metrics=['accuracy'])
- # Measure training time
- start_time = time.time()
- # Train Model (using SMOTE'd training set, original test set)
- history = train_model(model, X_train_smote, y_train_smote, X_test, y_test, batch_size=64, epochs=50)
- end_time = time.time()
- training_time = end_time - start_time
- # Evaluate Model
- train_accuracy = history.history['accuracy'][-1]
- train_loss = min(history.history['loss'])
- val_accuracy = history.history['val_accuracy'][-1]
- val_loss = min(history.history['val_loss'])
- test_accuracy = model.evaluate(X_test, y_test, verbose=0)[1]
- precision, recall, f1 = evaluate_model(model, X_test, y_test)
- # Save metrics
- results_df = results_df.append({
- 'Trial': trial + 1,
- 'Train_Accuracy': train_accuracy,
- 'Train_Loss': train_loss,
- 'Validation_Accuracy': val_accuracy,
- 'Validation_Loss': val_loss,
- 'Test_Accuracy': test_accuracy,
- 'Precision': precision,
- 'Recall': recall,
- 'F1_Score': f1,
- 'Training_Time': training_time
- }, ignore_index=True)
- # Save the .h5 file
- model.save(f"EEGNet_Trial_{trial + 1}.h5")
- # Plot and save accuracy and loss curves
- plot_accuracy_loss_curves(history, trial)
- # Plot and save confusion matrix
- plot_confusion_matrix(model, X_test, y_test, trial)
- # Save SHAP plots for this trial
- shap_output_dir = f"Trial_{trial + 1}_SHAP_Plots"
- shap_analysis(model, X_train_smote, X_test, shap_output_dir, sample_size=50)
- # Save results to Excel
- results_df.to_excel("Trial_Results.xlsx", index=False)
- print("Results saved to Trial_Results.xlsx")
- print(X.shape)
- print(Y.shape)
- print(X_smote.shape)
- print(Y_smote.shape)
- # print("All trials completed and plots saved successfully!")
code_with_smote.py.py at commit 5de4da8, no license · at the source
Overview
Abstract
Mental workload (MWL) classification using electroencephalogram (EEG) signals is crucial for cognitive neuroscience and is also a challenging research area in brain-computer interface (BCI). Since the EEG signals fluctuate a lot across sessions and individuals, there is a need for a robust classification model that generalizes well for real-world applications. In this work, we used the publicly available dataset “An EEG dataset for cross-session mental workload estimation: passive BCI competition of the Neuroergonomics Conference 2021”, and the standard EEGNet model to classify the MWL into three classes (Low, Med, and High). To improve the performance of the model, a synthetic minority oversampling technique (SMOTE) was used by creating synthetic EEG samples, and key hyperparameters (F1, F2, and D) of EEGNet were systematically varied to identify the optimal configuration. Furthermore, Shapley Additive Explanations (SHAP) analysis was performed to identify the most influential EEG channels for model prediction. The proposed approach achieves the highest accuracy of 80.5% and 82.7% without and with SMOTE, respectively. The comparative analysis showed that applying SMOTE resulted in an average performance improvement of approximately 3%. A Wilcoxon signed-rank test confirmed that this improvement was statistically significant (p < 0.05). Finally, the SHAP analysis revealed that the most informative EEG channels were located over the parieto-occipital and temporal regions, which is consistent with established neurophysiological evidence related to MWL processing. The proposed framework improves both performance and explainability in EEG-based MWL classification, representing a systematic integration of SMOTE and SHAP analysis.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
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213112003/EEG-Based-Mental-Workload-Classification
5de4da8ae9549f2149b7369f4b5bb18d7646ef60, 30 April 2026Availability: 1 check, the latest on 28 September 2026: the link answers
- 28 September 2026: the link answers
3 files
- code_with_smote.py.py, Python, 399 lines, 3 matches
- code_without_smote.py.py
, Python, 400 lines, 3 matches - README.md, Text, 30 lines
Code availability
The code used in this work is publicly available at: https://
Reproduced under the paper's license (CC BY), from the paper cited above.
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Data
Datasets cited
- zenodo:5055046, at Zenodo; found in the text, “Datasets”
Data availability
The dataset used in this work is open access (online available) and can be found at: 10.5281/
Reproduced under the paper's license (CC BY), from the paper cited above.
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Recorded: type, language, journal, volume, issue, pages, dates, 2 authors, 9 keywords, 7 MeSH terms, 24 references.
Cite
This paper
Chaturvedi, S., & Ahirwal, M. K. (2026). SHAP analysis of an improved EEG-based mental workload classification framework: utilizing data augmentation and explainable AI. Scientific reports, 16(1), 22886. https://
BibTeX
@article{chaturvedi2026s
author = {Chaturvedi, Sushil and Ahirwal, Mitul Kumar},
title = {{SHAP analysis of an improved EEG-based mental workload classification framework: utilizing data augmentation and explainable AI}},
journal = {Scientific reports},
year = {2026},
month = may,
volume = {16},
number = {1},
pages = {22886},
publisher = {Nature Publishing Group},
issn = {2045-2322},
doi = {10.1038/
url = {https://
pmid = {42162083},
pmcid = {PMC13389205}
}
RIS
TY - JOUR
AU - Chaturvedi, Sushil
AU - Ahirwal, Mitul Kumar
TI - SHAP analysis of an improved EEG-based mental workload classification framework: utilizing data augmentation and explainable AI
T2 - Scientific reports
J2 - Sci Rep
PY - 2026
DA - 2026/
VL - 16
IS - 1
SP - 22886
SN - 2045-2322
PB - Nature Publishing Group
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
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"id": "10.1038/
"type": "article-journal",
"title": "SHAP analysis of an improved EEG-based mental workload classification framework: utilizing data augmentation and explainable AI",
"container-title": "Scientific reports",
"author": [
{
"family": "Chaturvedi",
"given": "Sushil"
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{
"family": "Ahirwal",
"given": "Mitul Kumar"
}
],
"container-title-short":
"volume": "16",
"issue": "1",
"page": "22886",
"DOI": "10.1038/
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"PMCID": "PMC13389205",
"ISSN": "2045-2322",
"publisher": "Nature Publishing Group",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
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20
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]
}
}
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