Scientific Skill: 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

```bash
# 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

```python
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

```python
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:

```bash
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:

```bash
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

1. **Load and explore data**
   ```python
   import pandas as pd
   df = pd.read_csv('data.csv')
   X = df.drop('target', axis=1)
   y = df['target']
   ```

2. **Split data with stratification**
   ```python
   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
   )
   ```

3. **Create preprocessing pipeline**
   ```python
   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)
   ])
   ```

4. **Build complete pipeline**
   ```python
   model = Pipeline([
       ('preprocessor', preprocessor),
       ('classifier', RandomForestClassifier(random_state=42))
   ])
   ```

5. **Tune hyperparameters**
   ```python
   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)
   ```

6. **Evaluate on test set**
   ```python
   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

1. **Preprocess data**
   ```python
   from sklearn.preprocessing import StandardScaler

   scaler = StandardScaler()
   X_scaled = scaler.fit_transform(X)
   ```

2. **Find optimal number of clusters**
   ```python
   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)]
   ```

3. **Apply clustering**
   ```python
   model = KMeans(n_clusters=optimal_k, random_state=42)
   labels = model.fit_predict(X_scaled)
   ```

4. **Visualize with dimensionality reduction**
   ```python
   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:
```python
# 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:
```python
# 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:
```python
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
```python
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
```python
model = LogisticRegression(max_iter=1000)
```

### Poor Performance on Test Set
**Issue:** Overfitting
**Solution:** Use regularization, cross-validation, or simpler model
```python
# 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
```python
# 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