sklearn Integration

The nimbus-bci classifiers are fully compatible with scikit-learn, allowing seamless integration with pipelines, cross-validation, hyperparameter tuning, and the broader sklearn ecosystem.

sklearn-Compatible API

All nimbus-bci classifiers implement the sklearn estimator interface:

from nimbus_bci import NimbusLDA

clf = NimbusLDA()

# Standard sklearn methods
clf.fit(X_train, y_train)              # Train
predictions = clf.predict(X_test)       # Predict classes
probabilities = clf.predict_proba(X_test)  # Predict probabilities
score = clf.score(X_test, y_test)      # Accuracy score

Pipelines

Basic Pipeline

Combine preprocessing with classification:

from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import StandardScaler
from nimbus_bci import NimbusLDA

# Create pipeline
pipe = make_pipeline(
    StandardScaler(),
    NimbusLDA(mu_scale=3.0)
)

# Fit and predict
pipe.fit(X_train, y_train)
predictions = pipe.predict(X_test)
score = pipe.score(X_test, y_test)
print(f"Accuracy: {score:.2%}")

Multi-Step Pipeline

Add feature selection and normalization:

from sklearn.pipeline import Pipeline
from sklearn.preprocessing import StandardScaler, RobustScaler
from sklearn.feature_selection import SelectKBest, f_classif
from nimbus_bci import NimbusLDA

pipe = Pipeline([
    ('scaler', RobustScaler()),
    ('feature_selection', SelectKBest(f_classif, k=10)),
    ('classifier', NimbusLDA(mu_scale=5.0))
])

pipe.fit(X_train, y_train)
print(f"Selected features: {pipe.named_steps['feature_selection'].get_support()}")

BCI-Specific Pipeline

Complete BCI preprocessing pipeline:

from sklearn.pipeline import Pipeline
from sklearn.preprocessing import StandardScaler
from sklearn.decomposition import PCA
from nimbus_bci import NimbusLDA

# Complete BCI pipeline
bci_pipeline = Pipeline([
    ('normalization', StandardScaler()),
    ('dimensionality_reduction', PCA(n_components=16)),
    ('classifier', NimbusLDA(mu_scale=3.0))
])

# Train on CSP features
bci_pipeline.fit(csp_features, labels)

# Real-time prediction
new_trial = extract_features(eeg_chunk)
prediction = bci_pipeline.predict(new_trial.reshape(1, -1))[0]

Cross-Validation

Basic Cross-Validation

Evaluate model performance:

from sklearn.model_selection import cross_val_score
from nimbus_bci import NimbusLDA

clf = NimbusLDA()
scores = cross_val_score(clf, X, y, cv=5, scoring='accuracy')

print(f"Accuracy: {scores.mean():.2%} (+/- {scores.std():.2%})")

Stratified K-Fold

Maintain class balance in folds:

from sklearn.model_selection import StratifiedKFold, cross_val_score
from nimbus_bci import NimbusQDA

clf = NimbusQDA()
cv = StratifiedKFold(n_splits=5, shuffle=True, random_state=42)
scores = cross_val_score(clf, X, y, cv=cv, scoring='accuracy')

print(f"Stratified CV Accuracy: {scores.mean():.2%}")

Multiple Metrics

Evaluate multiple metrics simultaneously:

from sklearn.model_selection import cross_validate
from nimbus_bci import NimbusLDA

clf = NimbusLDA()
scoring = ['accuracy', 'precision_macro', 'recall_macro', 'f1_macro']
scores = cross_validate(clf, X, y, cv=5, scoring=scoring)

for metric in scoring:
    print(f"{metric}: {scores[f'test_{metric}'].mean():.3f}")

Leave-One-Subject-Out

For BCI with multiple subjects:

from sklearn.model_selection import LeaveOneGroupOut, cross_val_score
from nimbus_bci import NimbusLDA

clf = NimbusLDA()
logo = LeaveOneGroupOut()

# subject_ids: array indicating which subject each trial belongs to
scores = cross_val_score(clf, X, y, groups=subject_ids, cv=logo)

print(f"LOSO Accuracy: {scores.mean():.2%}")
print(f"Per-subject scores: {scores}")

Hyperparameter Tuning

Grid Search

Exhaustive search over parameter grid:

from sklearn.model_selection import GridSearchCV
from nimbus_bci import NimbusLDA

# Define parameter grid
param_grid = {
    'mu_scale': [1.0, 3.0, 5.0, 7.0],
    'class_prior_alpha': [0.5, 1.0, 2.0]
}

# Grid search with cross-validation
grid = GridSearchCV(
    NimbusLDA(),
    param_grid,
    cv=5,
    scoring='accuracy',
    n_jobs=-1,
    verbose=1
)

grid.fit(X_train, y_train)

print(f"Best parameters: {grid.best_params_}")
print(f"Best CV score: {grid.best_score_:.2%}")

# Use best model
best_clf = grid.best_estimator_
test_score = best_clf.score(X_test, y_test)
print(f"Test accuracy: {test_score:.2%}")

Random Search

More efficient for large parameter spaces:

from sklearn.model_selection import RandomizedSearchCV
from scipy.stats import uniform, randint
from nimbus_bci import NimbusQDA

# Define parameter distributions
param_dist = {
    'mu_scale': uniform(1.0, 10.0),
    'class_prior_alpha': uniform(0.1, 5.0)
}

# Random search
random_search = RandomizedSearchCV(
    NimbusQDA(),
    param_dist,
    n_iter=20,
    cv=5,
    scoring='accuracy',
    n_jobs=-1,
    random_state=42
)

random_search.fit(X_train, y_train)
print(f"Best parameters: {random_search.best_params_}")

Pipeline Parameter Tuning

Tune parameters across entire pipeline:

from sklearn.pipeline import Pipeline
from sklearn.preprocessing import StandardScaler
from sklearn.model_selection import GridSearchCV
from nimbus_bci import NimbusLDA

pipe = Pipeline([
    ('scaler', StandardScaler()),
    ('clf', NimbusLDA())
])

# Tune both preprocessing and classifier
param_grid = {
    'scaler__with_mean': [True, False],
    'scaler__with_std': [True, False],
    'clf__mu_scale': [1.0, 3.0, 5.0],
    'clf__class_prior_alpha': [0.5, 1.0, 2.0]
}

grid = GridSearchCV(pipe, param_grid, cv=5, n_jobs=-1)
grid.fit(X_train, y_train)

print(f"Best pipeline: {grid.best_params_}")

Model Selection

Compare Multiple Classifiers

Compare different nimbus-bci classifiers:

from sklearn.model_selection import cross_val_score
from nimbus_bci import NimbusLDA, NimbusQDA, NimbusSoftmax, NimbusSTS

classifiers = {
    'LDA': NimbusLDA(),
    'QDA': NimbusQDA(),
    'Softmax': NimbusSoftmax(),
    'STS': NimbusSTS()
}

results = {}
for name, clf in classifiers.items():
    scores = cross_val_score(clf, X, y, cv=5, scoring='accuracy')
    results[name] = scores
    print(f"{name}: {scores.mean():.2%} (+/- {scores.std():.2%})")

# Select best
best_clf = max(results.items(), key=lambda x: x[1].mean())
print(f"\nBest classifier: {best_clf[0]}")

Compare with sklearn Classifiers

Benchmark against sklearn models:

from sklearn.discriminant_analysis import LinearDiscriminantAnalysis
from sklearn.ensemble import RandomForestClassifier
from sklearn.svm import SVC
from sklearn.model_selection import cross_val_score
from nimbus_bci import NimbusLDA

classifiers = {
    'NimbusLDA': NimbusLDA(),
    'sklearn LDA': LinearDiscriminantAnalysis(),
    'Random Forest': RandomForestClassifier(n_estimators=100),
    'SVM': SVC(probability=True)
}

for name, clf in classifiers.items():
    scores = cross_val_score(clf, X, y, cv=5)
    print(f"{name}: {scores.mean():.2%} (+/- {scores.std():.2%})")

Feature Selection

Univariate Feature Selection

Select best features before classification:

from sklearn.feature_selection import SelectKBest, f_classif
from sklearn.pipeline import Pipeline
from nimbus_bci import NimbusLDA

pipe = Pipeline([
    ('feature_selection', SelectKBest(f_classif, k=10)),
    ('classifier', NimbusLDA())
])

pipe.fit(X_train, y_train)

# Get selected features
selected = pipe.named_steps['feature_selection'].get_support()
print(f"Selected {selected.sum()} features")

Recursive Feature Elimination

Iteratively remove least important features:

from sklearn.feature_selection import RFE
from nimbus_bci import NimbusLDA

clf = NimbusLDA()
rfe = RFE(clf, n_features_to_select=10)
rfe.fit(X_train, y_train)

print(f"Selected features: {rfe.support_}")
print(f"Feature ranking: {rfe.ranking_}")

Ensemble Methods

Voting Classifier

Combine multiple nimbus-bci classifiers:

from sklearn.ensemble import VotingClassifier
from nimbus_bci import NimbusLDA, NimbusQDA, NimbusSoftmax, NimbusSTS

ensemble = VotingClassifier(
    estimators=[
        ('lda', NimbusLDA()),
        ('qda', NimbusQDA()),
        ('softmax', NimbusSoftmax()),
        ('sts', NimbusSTS())
    ],
    voting='soft'  # Use probabilities
)

ensemble.fit(X_train, y_train)
score = ensemble.score(X_test, y_test)
print(f"Ensemble accuracy: {score:.2%}")

Bagging

Bootstrap aggregating for variance reduction:

from sklearn.ensemble import BaggingClassifier
from nimbus_bci import NimbusLDA

bagging = BaggingClassifier(
    base_estimator=NimbusLDA(),
    n_estimators=10,
    random_state=42
)

bagging.fit(X_train, y_train)
score = bagging.score(X_test, y_test)
print(f"Bagging accuracy: {score:.2%}")

Calibration

Probability Calibration

Calibrate predicted probabilities:

from sklearn.calibration import CalibratedClassifierCV
from nimbus_bci import NimbusLDA

# Calibrate with cross-validation
calibrated = CalibratedClassifierCV(
    NimbusLDA(),
    method='isotonic',
    cv=5
)

calibrated.fit(X_train, y_train)
probs = calibrated.predict_proba(X_test)

# Check calibration
from sklearn.calibration import calibration_curve
prob_true, prob_pred = calibration_curve(y_test, probs[:, 1], n_bins=10)

Custom Transformers

BCI-Specific Transformer

Create custom transformer for BCI preprocessing:

from sklearn.base import BaseEstimator, TransformerMixin
import numpy as np

class TemporalAggregator(BaseEstimator, TransformerMixin):
    """Aggregate temporal features for BCI."""
    
    def __init__(self, method='logvar'):
        self.method = method
    
    def fit(self, X, y=None):
        return self
    
    def transform(self, X):
        if self.method == 'logvar':
            return np.log(np.var(X, axis=1))
        elif self.method == 'mean':
            return np.mean(X, axis=1)
        elif self.method == 'rms':
            return np.sqrt(np.mean(X**2, axis=1))
        return X

# Use in pipeline
from sklearn.pipeline import Pipeline
from nimbus_bci import NimbusLDA

pipe = Pipeline([
    ('temporal_agg', TemporalAggregator(method='logvar')),
    ('classifier', NimbusLDA())
])

pipe.fit(X_train, y_train)

Performance Evaluation

Comprehensive Metrics

Evaluate with multiple metrics:

from sklearn.metrics import (
    accuracy_score, precision_score, recall_score, f1_score,
    confusion_matrix, classification_report
)
from nimbus_bci import NimbusLDA

clf = NimbusLDA()
clf.fit(X_train, y_train)
y_pred = clf.predict(X_test)

print(f"Accuracy: {accuracy_score(y_test, y_pred):.2%}")
print(f"Precision: {precision_score(y_test, y_pred, average='macro'):.2%}")
print(f"Recall: {recall_score(y_test, y_pred, average='macro'):.2%}")
print(f"F1: {f1_score(y_test, y_pred, average='macro'):.2%}")

print("\nConfusion Matrix:")
print(confusion_matrix(y_test, y_pred))

print("\nClassification Report:")
print(classification_report(y_test, y_pred))

ROC and AUC

For binary classification:

from sklearn.metrics import roc_curve, auc, roc_auc_score
import matplotlib.pyplot as plt
from nimbus_bci import NimbusQDA

clf = NimbusQDA()
clf.fit(X_train, y_train)
y_probs = clf.predict_proba(X_test)[:, 1]

# ROC curve
fpr, tpr, thresholds = roc_curve(y_test, y_probs)
roc_auc = auc(fpr, tpr)

plt.plot(fpr, tpr, label=f'ROC curve (AUC = {roc_auc:.2f})')
plt.plot([0, 1], [0, 1], 'k--')
plt.xlabel('False Positive Rate')
plt.ylabel('True Positive Rate')
plt.title('ROC Curve')
plt.legend()
plt.show()

print(f"AUC: {roc_auc_score(y_test, y_probs):.3f}")

Saving and Loading

Joblib Persistence

Save entire pipeline:

from sklearn.pipeline import Pipeline
from sklearn.preprocessing import StandardScaler
from nimbus_bci import NimbusLDA
import joblib

# Create and train pipeline
pipe = Pipeline([
    ('scaler', StandardScaler()),
    ('clf', NimbusLDA())
])
pipe.fit(X_train, y_train)

# Save pipeline
joblib.dump(pipe, 'bci_pipeline.pkl')

# Load pipeline
loaded_pipe = joblib.load('bci_pipeline.pkl')
predictions = loaded_pipe.predict(X_test)

Best Practices

1. Always Use Pipelines

Encapsulate preprocessing with classification:

# Good: Preprocessing in pipeline
pipe = make_pipeline(StandardScaler(), NimbusLDA())
pipe.fit(X_train, y_train)
pipe.predict(X_test)

# Bad: Manual preprocessing
X_train_scaled = StandardScaler().fit_transform(X_train)
X_test_scaled = StandardScaler().fit_transform(X_test)  # Wrong!
clf = NimbusLDA().fit(X_train_scaled, y_train)

2. Use Stratified Splits

Maintain class balance:

from sklearn.model_selection import StratifiedKFold

cv = StratifiedKFold(n_splits=5, shuffle=True, random_state=42)
scores = cross_val_score(clf, X, y, cv=cv)

3. Tune Hyperparameters

Always optimize hyperparameters:

from sklearn.model_selection import GridSearchCV

param_grid = {'mu_scale': [1.0, 3.0, 5.0]}
grid = GridSearchCV(NimbusLDA(), param_grid, cv=5)
grid.fit(X_train, y_train)
best_clf = grid.best_estimator_

4. Evaluate on Held-Out Test Set

Never tune on test data:

from sklearn.model_selection import train_test_split

# Split data
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2)

# Tune on train set only
grid = GridSearchCV(NimbusLDA(), param_grid, cv=5)
grid.fit(X_train, y_train)

# Final evaluation on test set
test_score = grid.score(X_test, y_test)

Next Read

Streaming Inference

Real-time BCI with chunk processing

MNE Integration

Complete EEG preprocessing pipeline

API Reference

Complete API documentation

Examples

Working code examples

Getting Started

Core Concepts

Models & Algorithms

Configuration & Setup

Examples

Development

Python SDK

Julia SDK

​sklearn Integration

​sklearn-Compatible API

​Pipelines

​Basic Pipeline

​Multi-Step Pipeline

​BCI-Specific Pipeline

​Cross-Validation

​Basic Cross-Validation

​Stratified K-Fold

​Multiple Metrics

​Leave-One-Subject-Out

​Hyperparameter Tuning

​Grid Search

​Random Search

​Pipeline Parameter Tuning

​Model Selection

​Compare Multiple Classifiers

​Compare with sklearn Classifiers

​Feature Selection

​Univariate Feature Selection

​Recursive Feature Elimination

​Ensemble Methods

​Voting Classifier

​Bagging

​Calibration

​Probability Calibration

​Custom Transformers

​BCI-Specific Transformer

​Performance Evaluation

​Comprehensive Metrics

​ROC and AUC

​Saving and Loading

​Joblib Persistence

​Best Practices

​1. Always Use Pipelines

​2. Use Stratified Splits

​3. Tune Hyperparameters

​4. Evaluate on Held-Out Test Set

​Next Read

Streaming Inference

MNE Integration

API Reference

Examples

sklearn Integration

sklearn-Compatible API

Pipelines

Basic Pipeline

Multi-Step Pipeline

BCI-Specific Pipeline

Cross-Validation

Basic Cross-Validation

Stratified K-Fold

Multiple Metrics

Leave-One-Subject-Out

Hyperparameter Tuning

Grid Search

Random Search

Pipeline Parameter Tuning

Model Selection

Compare Multiple Classifiers

Compare with sklearn Classifiers

Feature Selection

Univariate Feature Selection

Recursive Feature Elimination

Ensemble Methods

Voting Classifier

Bagging

Calibration

Probability Calibration

Custom Transformers

BCI-Specific Transformer

Performance Evaluation

Comprehensive Metrics

ROC and AUC

Saving and Loading

Joblib Persistence

Best Practices

1. Always Use Pipelines

2. Use Stratified Splits

3. Tune Hyperparameters

4. Evaluate on Held-Out Test Set

Next Read