Merge pull request #74 from cmccomb/codex/add-real-world-examples-to-cookbook

Add real-world cookbook examples

Author: cmccomb

README.md

@@ -60,6 +60,17 @@ will perform a comparison of classifier models using cross-validation. Printing
 
 You can then perform inference using the best model with the `predict` method.
 
+## Cookbook
+
+Explore the `automl::cookbook` module for copy-pastable examples that mirror
+real-world workflows:
+
+- `cargo run --example breast_cancer_csv` – load the Wisconsin Diagnostic
+  Breast Cancer dataset from CSV, standardize features, and compare tuned
+  classifiers.
+- `cargo run --example diabetes_regression` – impute, scale, and train
+  regression models for the diabetes progression dataset.
+
 ## Preprocessing pipelines
 
 `automl` now supports composable preprocessing pipelines so you can build

examples/breast_cancer_csv.rs

@@ -0,0 +1,60 @@
+#![allow(clippy::needless_doctest_main)]
+//! Real-world breast cancer classification example.
+//!
+//! This example trains a multi-model comparison on the Wisconsin Diagnostic
+//! Breast Cancer dataset bundled with the repository. The workflow shows how to
+//! load a CSV file, wire up a preprocessing pipeline, and customize the
+//! algorithms that participate in the comparison.
+//!
+//! Run with:
+//!
+//! ```bash
+//! cargo run --example breast_cancer_csv
+//! ```
+
+#[path = "../tests/fixtures/breast_cancer_dataset.rs"]
+mod breast_cancer_dataset;
+
+use std::error::Error;
+
+use automl::settings::{
+    ClassificationSettings, FinalAlgorithm, PreprocessingPipeline, PreprocessingStep,
+    RandomForestClassifierParameters, StandardizeParams,
+};
+use automl::{ClassificationModel, DenseMatrix};
+use breast_cancer_dataset::load_breast_cancer_dataset;
+
+fn main() -> Result<(), Box<dyn Error>> {
+    let (features, targets) = load_breast_cancer_dataset()?;
+
+    let preprocessing = PreprocessingPipeline::new()
+        .add_step(PreprocessingStep::Standardize(StandardizeParams::default()));
+
+    let settings = ClassificationSettings::default()
+        .with_number_of_folds(5)
+        .shuffle_data(true)
+        .with_final_model(FinalAlgorithm::Best)
+        .with_preprocessing(preprocessing)
+        .with_random_forest_classifier_settings(
+            RandomForestClassifierParameters::default()
+                .with_n_trees(200)
+                .with_max_depth(8)
+                .with_min_samples_split(4)
+                .with_min_samples_leaf(2),
+        );
+
+    let mut model = ClassificationModel::new(features, targets, settings);
+    model.train()?;
+
+    println!("{model}");
+
+    let example_patient = DenseMatrix::from_2d_vec(&vec![vec![
+        13.540, 14.360, 87.460, 566.300, 0.097, 0.052, 0.024, 0.015, 0.153, 0.055, 0.284, 0.915,
+        2.376, 23.420, 0.005, 0.013, 0.010, 0.005, 0.018, 0.002, 14.230, 17.730, 91.760, 618.800,
+        0.118, 0.115, 0.068, 0.025, 0.210, 0.062,
+    ]])?;
+    let predictions = model.predict(example_patient)?;
+    println!("Predicted class for the evaluation patient: {predictions:?}");
+
+    Ok(())
+}

examples/diabetes_regression.rs

@@ -0,0 +1,81 @@
+#![allow(clippy::needless_doctest_main)]
+//! Real-world diabetes progression regression example.
+//!
+//! The diabetes dataset includes 10 physiological measurements for 442
+//! individuals. This example demonstrates how to configure a preprocessing
+//! pipeline, tighten algorithm hyperparameters, and evaluate the models via
+//! cross-validation before using the best regressor for inference.
+//!
+//! Run with:
+//!
+//! ```bash
+//! cargo run --example diabetes_regression
+//! ```
+
+#[path = "../tests/fixtures/diabetes_dataset.rs"]
+mod diabetes_dataset;
+
+use std::error::Error;
+
+use automl::settings::{
+    ColumnSelector, FinalAlgorithm, ImputeParams, ImputeStrategy, Kernel, PreprocessingPipeline,
+    PreprocessingStep, RandomForestRegressorParameters, RegressionSettings, SVRParameters,
+    ScaleParams, ScaleStrategy, StandardizeParams,
+};
+use automl::{DenseMatrix, RegressionModel};
+use diabetes_dataset::load_diabetes_dataset;
+
+fn main() -> Result<(), Box<dyn Error>> {
+    let (features, targets) = load_diabetes_dataset()?;
+
+    let preprocessing = PreprocessingPipeline::new()
+        .add_step(PreprocessingStep::Impute(ImputeParams {
+            strategy: ImputeStrategy::Median,
+            selector: ColumnSelector::All,
+        }))
+        .add_step(PreprocessingStep::Scale(ScaleParams {
+            selector: ColumnSelector::All,
+            strategy: ScaleStrategy::Standard(StandardizeParams::default()),
+        }));
+
+    let settings = RegressionSettings::default()
+        .with_number_of_folds(8)
+        .shuffle_data(true)
+        .with_final_model(FinalAlgorithm::Best)
+        .with_preprocessing(preprocessing)
+        .with_random_forest_regressor_settings(
+            RandomForestRegressorParameters::default()
+                .with_n_trees(250)
+                .with_max_depth(6)
+                .with_min_samples_leaf(2)
+                .with_min_samples_split(4),
+        )
+        .with_svr_settings(
+            SVRParameters::default()
+                .with_c(12.5)
+                .with_eps(0.05)
+                .with_kernel(Kernel::RBF(0.35)),
+        );
+
+    let mut model = RegressionModel::new(features, targets, settings);
+    model.train()?;
+
+    println!("{model}");
+
+    let evaluation_visit = DenseMatrix::from_2d_vec(&vec![vec![
+        0.038_075_906,
+        0.050_680_119,
+        0.061_696_207,
+        0.021_872_355,
+        -0.044_223_498,
+        -0.034_820_763,
+        -0.043_400_846,
+        -0.002_592_262,
+        0.019_908_421,
+        -0.017_646_125,
+    ]])?;
+    let predicted_progression = model.predict(evaluation_visit)?;
+    println!("Predicted disease progression: {predicted_progression:?}");
+
+    Ok(())
+}

src/cookbook.rs

@@ -13,3 +13,20 @@
 //! ```rust,ignore
 #![doc = include_str!("../examples/maximal_regression.rs")]
 //! ```
+//!
+//! ## Wisconsin Breast Cancer Classification
+//!
+//! Demonstrates loading data from `data/breast_cancer.csv`, standardizing every
+//! feature, and customizing the random forest search space before running the
+//! leaderboard comparison.
+//! ```rust,ignore
+#![doc = include_str!("../examples/breast_cancer_csv.rs")]
+//! ```
+//!
+//! ## Diabetes Progression Regression
+//!
+//! Shows how to impute, standardize, and tune regression algorithms on the
+//! diabetes dataset that ships with the repository.
+//! ```rust,ignore
+#![doc = include_str!("../examples/diabetes_regression.rs")]
+//! ```

tests/fixtures/breast_cancer_dataset.rs

@@ -0,0 +1,61 @@
+use std::error::Error;
+use std::path::Path;
+
+use csv::ReaderBuilder;
+use smartcore::linalg::basic::matrix::DenseMatrix;
+
+type CsvRows = (Vec<Vec<f64>>, Vec<String>);
+type CsvResult = Result<CsvRows, Box<dyn Error>>;
+
+fn load_feature_rows<P: AsRef<Path>>(path: P) -> CsvResult {
+    let mut reader = ReaderBuilder::new().has_headers(true).from_path(path)?;
+    let mut features = Vec::new();
+    let mut targets = Vec::new();
+
+    for record in reader.records() {
+        let record = record?;
+        let record_len = record.len();
+        if record_len < 2 {
+            return Err("dataset requires at least one feature and a target column".into());
+        }
+        let feature_len = record_len - 1;
+        let mut row = Vec::with_capacity(feature_len);
+        for value in record.iter().take(feature_len) {
+            row.push(value.parse()?);
+        }
+        let target_value = record
+            .get(feature_len)
+            .ok_or("dataset missing target column")?;
+        features.push(row);
+        targets.push(target_value.to_string());
+    }
+
+    Ok((features, targets))
+}
+
+fn parse_label(raw: &str) -> Result<u32, Box<dyn Error>> {
+    let numeric: f64 = raw.parse()?;
+    if (numeric - 1.0).abs() < f64::EPSILON {
+        Ok(1)
+    } else if numeric.abs() < f64::EPSILON {
+        Ok(0)
+    } else {
+        Err("unexpected label".into())
+    }
+}
+
+/// Load the Wisconsin Diagnostic Breast Cancer dataset from `data/breast_cancer.csv`.
+///
+/// # Errors
+///
+/// Returns an error if the CSV file cannot be read or parsed into numeric data.
+pub fn load_breast_cancer_dataset() -> Result<(DenseMatrix<f64>, Vec<u32>), Box<dyn Error>> {
+    let (feature_rows, raw_targets) = load_feature_rows("data/breast_cancer.csv")?;
+    let features = DenseMatrix::from_2d_vec(&feature_rows)?;
+    let targets = raw_targets
+        .into_iter()
+        .map(|value| parse_label(&value))
+        .collect::<Result<Vec<_>, Box<dyn Error>>>()?;
+
+    Ok((features, targets))
+}

tests/fixtures/diabetes_dataset.rs

@@ -0,0 +1,50 @@
+use std::error::Error;
+use std::path::Path;
+
+use csv::ReaderBuilder;
+use smartcore::linalg::basic::matrix::DenseMatrix;
+
+type CsvRows = (Vec<Vec<f64>>, Vec<String>);
+type CsvResult = Result<CsvRows, Box<dyn Error>>;
+
+fn load_feature_rows<P: AsRef<Path>>(path: P) -> CsvResult {
+    let mut reader = ReaderBuilder::new().has_headers(true).from_path(path)?;
+    let mut features = Vec::new();
+    let mut targets = Vec::new();
+
+    for record in reader.records() {
+        let record = record?;
+        let record_len = record.len();
+        if record_len < 2 {
+            return Err("dataset requires at least one feature and a target column".into());
+        }
+        let feature_len = record_len - 1;
+        let mut row = Vec::with_capacity(feature_len);
+        for value in record.iter().take(feature_len) {
+            row.push(value.parse()?);
+        }
+        let target_value = record
+            .get(feature_len)
+            .ok_or("dataset missing target column")?;
+        features.push(row);
+        targets.push(target_value.to_string());
+    }
+
+    Ok((features, targets))
+}
+
+/// Load the diabetes progression dataset from `data/diabetes.csv`.
+///
+/// # Errors
+///
+/// Returns an error if the CSV file cannot be read or parsed into numeric data.
+pub fn load_diabetes_dataset() -> Result<(DenseMatrix<f64>, Vec<f64>), Box<dyn Error>> {
+    let (feature_rows, raw_targets) = load_feature_rows("data/diabetes.csv")?;
+    let features = DenseMatrix::from_2d_vec(&feature_rows)?;
+    let targets = raw_targets
+        .into_iter()
+        .map(|value| -> Result<f64, Box<dyn Error>> { Ok(value.parse()?) })
+        .collect::<Result<Vec<_>, Box<dyn Error>>>()?;
+
+    Ok((features, targets))
+}

tests/real_world_datasets.rs

@@ -0,0 +1,29 @@
+#[path = "fixtures/breast_cancer_dataset.rs"]
+mod breast_cancer_dataset;
+#[path = "fixtures/diabetes_dataset.rs"]
+mod diabetes_dataset;
+
+use breast_cancer_dataset::load_breast_cancer_dataset;
+use diabetes_dataset::load_diabetes_dataset;
+use smartcore::linalg::basic::arrays::Array;
+
+#[test]
+fn breast_cancer_dataset_has_expected_shape() {
+    let (x, y) = load_breast_cancer_dataset().expect("dataset should load");
+    let (rows, cols) = x.shape();
+    assert_eq!(rows, 569);
+    assert_eq!(cols, 30);
+    assert_eq!(y.len(), rows);
+    let positives = y.iter().filter(|label| **label == 1).count();
+    assert_eq!(positives, 212);
+}
+
+#[test]
+fn diabetes_dataset_has_expected_shape() {
+    let (x, y) = load_diabetes_dataset().expect("dataset should load");
+    let (rows, cols) = x.shape();
+    assert_eq!(rows, 442);
+    assert_eq!(cols, 10);
+    assert_eq!(y.len(), rows);
+    assert!(y.iter().all(|value| value.is_finite()));
+}