Census income classification with LightGBM

This notebook demonstrates how to use LightGBM to predict the probability of an individual making over $50K a year in annual income. It uses the standard UCI Adult income dataset. To download a copy of this notebook visit github.

Gradient boosting machine methods such as LightGBM are state-of-the-art for these types of prediction problems with tabular style input data of many modalities. Tree SHAP (arXiv paper) allows for the exact computation of SHAP values for tree ensemble methods, and has been integrated directly into the C++ LightGBM code base. This allows fast exact computation of SHAP values without sampling and without providing a background dataset (since the background is inferred from the coverage of the trees).

Here we demonstrate how to use SHAP values to understand LightGBM model predictions.

import lightgbm as lgb
from sklearn.model_selection import train_test_split

import shap

# print the JS visualization code to the notebook
shap.initjs()

Load dataset

X, y = shap.datasets.adult()
X_display, y_display = shap.datasets.adult(display=True)

# create a train/test split
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=7)
d_train = lgb.Dataset(X_train, label=y_train)
d_test = lgb.Dataset(X_test, label=y_test)

Train the model

params = {
    "max_bin": 512,
    "learning_rate": 0.05,
    "boosting_type": "gbdt",
    "objective": "binary",
    "metric": "binary_logloss",
    "num_leaves": 10,
    "verbose": -1,
    "min_data": 100,
    "boost_from_average": True,
    "early_stopping_round": 50,
}

model = lgb.train(
    params,
    d_train,
    10000,
    valid_sets=[d_test],
)

Explain predictions

Here we use the Tree SHAP implementation integrated into Light GBM to explain the entire dataset (32561 samples). The Light GBM implementation of Tree SHAP is called from within the shap.TreeExplainer.shap_values method.

explainer = shap.TreeExplainer(model)
shap_values = explainer.shap_values(X)

LightGBM binary classifier with TreeExplainer shap values output has changed to a list of ndarray

Visualize a single prediction

Note that we use the X_display data frame so we get informative feature names instead of category codes.

shap.force_plot(explainer.expected_value[1], shap_values[1][0, :], X_display.iloc[0, :])

Visualization omitted, Javascript library not loaded!
Have you run `initjs()` in this notebook? If this notebook was from another user you must also trust this notebook (File -> Trust notebook). If you are viewing this notebook on github the Javascript has been stripped for security. If you are using JupyterLab this error is because a JupyterLab extension has not yet been written.

Visualize many predictions

To keep the browser happy we only visualize 1,000 individuals.

shap.force_plot(
    explainer.expected_value[1], shap_values[1][:1000, :], X_display.iloc[:1000, :]
)

Visualization omitted, Javascript library not loaded!
Have you run `initjs()` in this notebook? If this notebook was from another user you must also trust this notebook (File -> Trust notebook). If you are viewing this notebook on github the Javascript has been stripped for security. If you are using JupyterLab this error is because a JupyterLab extension has not yet been written.