Run in Google Colab

Meta Estimators in SciKeras

In this notebook, we implement sklearn ensemble and tree meta-estimators backed by a Keras MLP model.

Table of contents

• 1. Setup

• 2. Defining the Keras Model

  • 2.1 Building a boosting ensemble

• 3. Testing with a toy dataset

• 4. Bagging ensemble

1. Setup

try:
    import scikeras
except ImportError:
    !python -m pip install scikeras[tensorflow]

Silence TensorFlow logging to keep output succinct.

import warnings
from tensorflow import get_logger
get_logger().setLevel('ERROR')
warnings.filterwarnings("ignore", message="Setting the random state for TF")

import numpy as np
from scikeras.wrappers import KerasClassifier, KerasRegressor
import keras

2. Defining the Keras Model

We borrow our MLPClassifier implementation from the MLPClassifier notebook.

from typing import Dict, Iterable, Any


def get_clf_model(hidden_layer_sizes: Iterable[int], meta: Dict[str, Any], compile_kwargs: Dict[str, Any]):
    model = keras.Sequential()
    inp = keras.layers.Input(shape=(meta["n_features_in_"],))
    model.add(inp)
    for hidden_layer_size in hidden_layer_sizes:
        layer = keras.layers.Dense(hidden_layer_size, activation="relu")
        model.add(layer)
    if meta["target_type_"] == "binary":
        n_output_units = 1
        output_activation = "sigmoid"
        loss = "binary_crossentropy"
    elif meta["target_type_"] == "multiclass":
        n_output_units = meta["n_classes_"]
        output_activation = "softmax"
        loss = "sparse_categorical_crossentropy"
    else:
        raise NotImplementedError(f"Unsupported task type: {meta['target_type_']}")
    out = keras.layers.Dense(n_output_units, activation=output_activation)
    model.add(out)
    model.compile(loss=loss, optimizer=compile_kwargs["optimizer"])
    return model

Next we wrap this Keras model with SciKeras

clf = KerasClassifier(
    model=get_clf_model,
    hidden_layer_sizes=(100, ),
    optimizer="adam",
    optimizer__learning_rate=0.001,
    verbose=0,
    random_state=0,
)

2.1 Building a boosting ensemble

Because SciKeras estimators are fully compliant with the Scikit-Learn API, we can make use of Scikit-Learn’s built in utilities. In particular example, we will use AdaBoostClassifier from sklearn.ensemble.AdaBoostClassifier, but the process is the same for most Scikit-Learn meta-estimators.

from sklearn.ensemble import AdaBoostClassifier


adaboost = AdaBoostClassifier(estimator=clf, random_state=0)

3. Testing with a toy dataset

Before continouing, we will run a small test to make sure we get somewhat reasonable results.

from sklearn.datasets import make_moons


X, y = make_moons()

single_score = clf.fit(X, y).score(X, y)

adaboost_score = adaboost.fit(X, y).score(X, y)

print(f"Single score: {single_score:.2f}")
print(f"AdaBoost score: {adaboost_score:.2f}")

/home/runner/work/scikeras/scikeras/.venv/lib/python3.12/site-packages/sklearn/ensemble/_weight_boosting.py:519: FutureWarning: The SAMME.R algorithm (the default) is deprecated and will be removed in 1.6. Use the SAMME algorithm to circumvent this warning.
  warnings.warn(

Single score: 0.50
AdaBoost score: 0.87

We see that the score for the AdaBoost classifier is slightly higher than that of an individual MLPRegressor instance. We can explore the individual classifiers, and see that each one is composed of a Keras Model with it’s own individual weights.

print(adaboost.estimators_[0].model_.get_weights()[0][0, :5])  # first sub-estimator
print(adaboost.estimators_[1].model_.get_weights()[0][0, :5])  # second sub-estimator

[-0.00940828  0.04692359  0.08673294 -0.20467542  0.11149351]
[ 0.22922313  0.20061073  0.21357909  0.0311804  -0.09936447]

4. Bagging ensemble

For comparison, we run the same test with an ensemble built using sklearn.ensemble.BaggingClassifier.

from sklearn.ensemble import BaggingClassifier


bagging = BaggingClassifier(estimator=clf, random_state=0, n_jobs=-1)

bagging_score = bagging.fit(X, y).score(X, y)

print(f"Bagging score: {bagging_score:.2f}")

WARNING:tensorflow:5 out of the last 9 calls to <function TensorFlowTrainer.make_predict_function.<locals>.one_step_on_data_distributed at 0x7f9b64cc16c0> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for  more details.
WARNING:tensorflow:6 out of the last 12 calls to <function TensorFlowTrainer.make_predict_function.<locals>.one_step_on_data_distributed at 0x7f9b64cc16c0> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for  more details.
WARNING:tensorflow:5 out of the last 9 calls to <function TensorFlowTrainer.make_predict_function.<locals>.one_step_on_data_distributed at 0x7f7858710f40> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for  more details.

Bagging score: 0.73

WARNING:tensorflow:6 out of the last 12 calls to <function TensorFlowTrainer.make_predict_function.<locals>.one_step_on_data_distributed at 0x7f7858710f40> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for  more details.