scikit-learn

Scikit-learn

Overview

This skill provides comprehensive guidance for machine learning tasks using scikit-learn, the industry-standard Python library for classical machine learning. Use this skill for classification, regression, clustering, dimensionality reduction, preprocessing, model evaluation, and building production-ready ML pipelines.

Installation

# Install scikit-learn using uv
uv uv pip install scikit-learn
Optional: Install visualization dependencies

uv uv pip install matplotlib seaborn
Commonly used with

uv uv pip install pandas numpy

When to Use This Skill

Use the scikit-learn skill when:

Building classification or regression models

Performing clustering or dimensionality reduction

Preprocessing and transforming data for machine learning

Evaluating model performance with cross-validation

Tuning hyperparameters with grid or random search

Creating ML pipelines for production workflows

Comparing different algorithms for a task

Working with both structured (tabular) and text data

Need interpretable, classical machine learning approaches

Quick Start

Classification Example

from sklearn.model_selection import train_test_split
from sklearn.preprocessing import StandardScaler
from sklearn.ensemble import RandomForestClassifier
from sklearn.metrics import classification_report
Split data

X_train, X_test, y_train, y_test = train_test_split(
    X, y, test_size=0.2, stratify=y, random_state=42
)
Preprocess

scaler = StandardScaler()
X_train_scaled = scaler.fit_transform(X_train)
X_test_scaled = scaler.transform(X_test)
Train model

model = RandomForestClassifier(n_estimators=100, random_state=42)
model.fit(X_train_scaled, y_train)
Evaluate

y_pred = model.predict(X_test_scaled)
print(classification_report(y_test, y_pred))

Complete Pipeline with Mixed Data

from sklearn.pipeline import Pipeline
from sklearn.compose import ColumnTransformer
from sklearn.preprocessing import StandardScaler, OneHotEncoder
from sklearn.impute import SimpleImputer
from sklearn.ensemble import GradientBoostingClassifier
Define feature types

numeric_features = ['age', 'income']
categorical_features = ['gender', 'occupation']
Create preprocessing pipelines

numeric_transformer = Pipeline([
    ('imputer', SimpleImputer(strategy='median')),
    ('scaler', StandardScaler())
])
categorical_transformer = Pipeline([
    ('imputer', SimpleImputer(strategy='most_frequent')),
    ('onehot', OneHotEncoder(handle_unknown='ignore'))
])
Combine transformers

preprocessor = ColumnTransformer([
    ('num', numeric_transformer, numeric_features),
    ('cat', categorical_transformer, categorical_features)
])
Full pipeline

model = Pipeline([
    ('preprocessor', preprocessor),
    ('classifier', GradientBoostingClassifier(random_state=42))
])
Fit and predict

model.fit(X_train, y_train)
y_pred = model.predict(X_test)

Core Capabilities

1. Supervised Learning

Comprehensive algorithms for classification and regression tasks.

Key algorithms:

Linear models: Logistic Regression, Linear Regression, Ridge, Lasso, ElasticNet

Tree-based: Decision Trees, Random Forest, Gradient Boosting

Support Vector Machines: SVC, SVR with various kernels

Ensemble methods: AdaBoost, Voting, Stacking

Neural Networks: MLPClassifier, MLPRegressor

Others: Naive Bayes, K-Nearest Neighbors

When to use:

Classification: Predicting discrete categories (spam detection, image classification, fraud detection)

Regression: Predicting continuous values (price prediction, demand forecasting)

See: references/supervised_learning.md for detailed algorithm documentation, parameters, and usage examples.

2. Unsupervised Learning

Discover patterns in unlabeled data through clustering and dimensionality reduction.

Clustering algorithms:

Partition-based: K-Means, MiniBatchKMeans

Density-based: DBSCAN, HDBSCAN, OPTICS

Hierarchical: AgglomerativeClustering

Probabilistic: Gaussian Mixture Models

Others: MeanShift, SpectralClustering, BIRCH

Dimensionality reduction:

Linear: PCA, TruncatedSVD, NMF

Manifold learning: t-SNE, UMAP, Isomap, LLE

Feature extraction: FastICA, LatentDirichletAllocation

When to use:

Customer segmentation, anomaly detection, data visualization

Reducing feature dimensions, exploratory data analysis

Topic modeling, image compression

See: references/unsupervised_learning.md for detailed documentation.

3. Model Evaluation and Selection

Tools for robust model evaluation, cross-validation, and hyperparameter tuning.

Cross-validation strategies:

KFold, StratifiedKFold (classification)

TimeSeriesSplit (temporal data)

GroupKFold (grouped samples)

Hyperparameter tuning:

GridSearchCV (exhaustive search)

RandomizedSearchCV (random sampling)

HalvingGridSearchCV (successive halving)

Metrics:

Classification: accuracy, precision, recall, F1-score, ROC AUC, confusion matrix

Regression: MSE, RMSE, MAE, R², MAPE

Clustering: silhouette score, Calinski-Harabasz, Davies-Bouldin

When to use:

Comparing model performance objectively

Finding optimal hyperparameters

Preventing overfitting through cross-validation

Understanding model behavior with learning curves

See: references/model_evaluation.md for comprehensive metrics and tuning strategies.

4. Data Preprocessing

Transform raw data into formats suitable for machine learning.

Scaling and normalization:

StandardScaler (zero mean, unit variance)

MinMaxScaler (bounded range)

RobustScaler (robust to outliers)

Normalizer (sample-wise normalization)

Encoding categorical variables:

OneHotEncoder (nominal categories)

OrdinalEncoder (ordered categories)

LabelEncoder (target encoding)

Handling missing values:

SimpleImputer (mean, median, most frequent)

KNNImputer (k-nearest neighbors)

IterativeImputer (multivariate imputation)

Feature engineering:

PolynomialFeatures (interaction terms)

KBinsDiscretizer (binning)

Feature selection (RFE, SelectKBest, SelectFromModel)

When to use:

Before training any algorithm that requires scaled features (SVM, KNN, Neural Networks)

Converting categorical variables to numeric format

Handling missing data systematically

Creating non-linear features for linear models

See: references/preprocessing.md for detailed preprocessing techniques.

5. Pipelines and Composition

Build reproducible, production-ready ML workflows.

Key components:

Pipeline: Chain transformers and estimators sequentially

ColumnTransformer: Apply different preprocessing to different columns

FeatureUnion: Combine multiple transformers in parallel

TransformedTargetRegressor: Transform target variable

Benefits:

Prevents data leakage in cross-validation

Simplifies code and improves maintainability

Enables joint hyperparameter tuning

Ensures consistency between training and prediction

When to use:

Always use Pipelines for production workflows

When mixing numerical and categorical features (use ColumnTransformer)

When performing cross-validation with preprocessing steps

When hyperparameter tuning includes preprocessing parameters

See: references/pipelines_and_composition.md for comprehensive pipeline patterns.

Example Scripts

Classification Pipeline

Run a complete classification workflow with preprocessing, model comparison, hyperparameter tuning, and evaluation:

python scripts/classification_pipeline.py

This script demonstrates:

Handling mixed data types (numeric and categorical)

Model comparison using cross-validation

Hyperparameter tuning with GridSearchCV

Comprehensive evaluation with multiple metrics

Feature importance analysis

Clustering Analysis

Perform clustering analysis with algorithm comparison and visualization:

python scripts/clustering_analysis.py

This script demonstrates:

Finding optimal number of clusters (elbow method, silhouette analysis)

Comparing multiple clustering algorithms (K-Means, DBSCAN, Agglomerative, Gaussian Mixture)

Evaluating clustering quality without ground truth

Visualizing results with PCA projection

Reference Documentation

This skill includes comprehensive reference files for deep dives into specific topics:

Quick Reference

File: references/quick_reference.md

Common import patterns and installation instructions

Quick workflow templates for common tasks

Algorithm selection cheat sheets

Common patterns and gotchas

Performance optimization tips

Supervised Learning

File: references/supervised_learning.md

Linear models (regression and classification)

Support Vector Machines

Decision Trees and ensemble methods

K-Nearest Neighbors, Naive Bayes, Neural Networks

Algorithm selection guide

Unsupervised Learning

File: references/unsupervised_learning.md

All clustering algorithms with parameters and use cases

Dimensionality reduction techniques

Outlier and novelty detection

Gaussian Mixture Models

Method selection guide

Model Evaluation

File: references/model_evaluation.md

Cross-validation strategies

Hyperparameter tuning methods

Classification, regression, and clustering metrics

Learning and validation curves

Best practices for model selection

Preprocessing

File: references/preprocessing.md

Feature scaling and normalization

Encoding categorical variables

Missing value imputation

Feature engineering techniques

Custom transformers

Pipelines and Composition

File: references/pipelines_and_composition.md

Pipeline construction and usage

ColumnTransformer for mixed data types

FeatureUnion for parallel transformations

Complete end-to-end examples

Best practices

Common Workflows

Building a Classification Model

Load and explore data

import pandas as pd
   df = pd.read_csv('data.csv')
   X = df.drop('target', axis=1)
   y = df['target']

Split data with stratification

from sklearn.model_selection import train_test_split
   X_train, X_test, y_train, y_test = train_test_split(
       X, y, test_size=0.2, stratify=y, random_state=42
   )

Create preprocessing pipeline

from sklearn.pipeline import Pipeline
   from sklearn.preprocessing import StandardScaler
   from sklearn.compose import ColumnTransformer
   # Handle numeric and categorical features separately
   preprocessor = ColumnTransformer([
       ('num', StandardScaler(), numeric_features),
       ('cat', OneHotEncoder(), categorical_features)
   ])

Build complete pipeline

model = Pipeline([
       ('preprocessor', preprocessor),
       ('classifier', RandomForestClassifier(random_state=42))
   ])

Tune hyperparameters

from sklearn.model_selection import GridSearchCV
   param_grid = {
       'classifier__n_estimators': [100, 200],
       'classifier__max_depth': [10, 20, None]
   }
   grid_search = GridSearchCV(model, param_grid, cv=5)
   grid_search.fit(X_train, y_train)

Evaluate on test set

from sklearn.metrics import classification_report
   best_model = grid_search.best_estimator_
   y_pred = best_model.predict(X_test)
   print(classification_report(y_test, y_pred))

Performing Clustering Analysis

Preprocess data

from sklearn.preprocessing import StandardScaler
   scaler = StandardScaler()
   X_scaled = scaler.fit_transform(X)

Find optimal number of clusters

from sklearn.cluster import KMeans
   from sklearn.metrics import silhouette_score
   scores = []
   for k in range(2, 11):
       kmeans = KMeans(n_clusters=k, random_state=42)
       labels = kmeans.fit_predict(X_scaled)
       scores.append(silhouette_score(X_scaled, labels))
   optimal_k = range(2, 11)[np.argmax(scores)]

Apply clustering

model = KMeans(n_clusters=optimal_k, random_state=42)
   labels = model.fit_predict(X_scaled)

Visualize with dimensionality reduction

from sklearn.decomposition import PCA
   pca = PCA(n_components=2)
   X_2d = pca.fit_transform(X_scaled)
   plt.scatter(X_2d[:, 0], X_2d[:, 1], c=labels, cmap='viridis')

Best Practices

Always Use Pipelines

Pipelines prevent data leakage and ensure consistency:

# Good: Preprocessing in pipeline
pipeline = Pipeline([
    ('scaler', StandardScaler()),
    ('model', LogisticRegression())
])
Bad: Preprocessing outside (can leak information)

X_scaled = StandardScaler().fit_transform(X)

Fit on Training Data Only

Never fit on test data:

# Good
scaler = StandardScaler()
X_train_scaled = scaler.fit_transform(X_train)
X_test_scaled = scaler.transform(X_test)  # Only transform
Bad

scaler = StandardScaler()
X_all_scaled = scaler.fit_transform(np.vstack([X_train, X_test]))

Use Stratified Splitting for Classification

Preserve class distribution:

X_train, X_test, y_train, y_test = train_test_split(
    X, y, test_size=0.2, stratify=y, random_state=42
)

Set Random State for Reproducibility

model = RandomForestClassifier(n_estimators=100, random_state=42)

Choose Appropriate Metrics

Balanced data: Accuracy, F1-score

Imbalanced data: Precision, Recall, ROC AUC, Balanced Accuracy

Cost-sensitive: Define custom scorer

Scale Features When Required

Algorithms requiring feature scaling:

SVM, KNN, Neural Networks

PCA, Linear/Logistic Regression with regularization

K-Means clustering

Algorithms not requiring scaling:

Tree-based models (Decision Trees, Random Forest, Gradient Boosting)

Naive Bayes

Troubleshooting Common Issues

ConvergenceWarning

Issue: Model didn't converge
Solution: Increase max_iter or scale features

model = LogisticRegression(max_iter=1000)

Poor Performance on Test Set

Issue: Overfitting
Solution: Use regularization, cross-validation, or simpler model

# Add regularization
model = Ridge(alpha=1.0)
Use cross-validation

scores = cross_val_score(model, X, y, cv=5)

Memory Error with Large Datasets

Solution: Use algorithms designed for large data

# Use SGD for large datasets
from sklearn.linear_model import SGDClassifier
model = SGDClassifier()
Or MiniBatchKMeans for clustering

from sklearn.cluster import MiniBatchKMeans
model = MiniBatchKMeans(n_clusters=8, batch_size=100)

Additional Resources

Official Documentation: https://scikit-learn.org/stable/

User Guide: https://scikit-learn.org/stable/user_guide.html

API Reference: https://scikit-learn.org/stable/api/index.html

Examples Gallery: https://scikit-learn.org/stable/auto_examples/index.html

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