Model Building with BoFire

This notebooks shows how to setup and analyze models trained with BoFire.

Imports

import numpy as np
import pandas as pd
import shap

import bofire.surrogates.api as surrogates
from bofire.data_models.domain.api import Inputs, Outputs
from bofire.data_models.enum import RegressionMetricsEnum
from bofire.data_models.features.api import ContinuousInput, ContinuousOutput
from bofire.data_models.surrogates.api import SingleTaskGPSurrogate
from bofire.plot.cv_folds import plot_cv_folds_plotly
from bofire.plot.feature_importance import plot_feature_importance_by_feature_plotly
from bofire.plot.gp_slice import plot_gp_slice_plotly
from bofire.surrogates.feature_importance import (
    combine_lengthscale_importances,
    combine_permutation_importances,
    lengthscale_importance_hook,
    permutation_importance_hook,
    shap_importance,
    shap_importance_hook,
)

Problem Setup

For didactic purposes, we sample data from a Himmelblau benchmark function and use them to train a SingleTaskGP.

input_features = Inputs(
    features=[ContinuousInput(key=f"x_{i+1}", bounds=(-4, 4)) for i in range(3)],
)
output_features = Outputs(features=[ContinuousOutput(key="y")])
experiments = input_features.sample(n=50)
experiments.eval("y=((x_1**2 + x_2 - 11)**2+(x_1 + x_2**2 -7)**2)", inplace=True, engine = "python")
experiments["valid_y"] = 1

experiments["labcode"] = "exp_" + experiments.index.astype(str)

Cross Validation

Run the cross validation

data_model = SingleTaskGPSurrogate(
    inputs=input_features,
    outputs=output_features,
)

model = surrogates.map(data_model=data_model)
train_cv, test_cv, pi = model.cross_validate(
    experiments,
    folds=5,
    include_X = True,
    include_labcodes = True,
    hooks={
        "permutation_importance": permutation_importance_hook,
        "lengthscale_importance": lengthscale_importance_hook,
        "shap_importance": shap_importance_hook,
    },
)

/opt/hostedtoolcache/Python/3.12.13/x64/lib/python3.12/site-packages/bofire/surrogates/botorch.py:185: UserWarning: The given NumPy array is not writable, and PyTorch does not support non-writable tensors. This means writing to this tensor will result in undefined behavior. You may want to copy the array to protect its data or make it writable before converting it to a tensor. This type of warning will be suppressed for the rest of this program. (Triggered internally at /pytorch/torch/csrc/utils/tensor_numpy.cpp:213.)
  torch.from_numpy(Y.values).to(**tkwargs),

Plot feature importance

shap_folds = pi["shap_importance"]  # list[dict[str, shap.Explanation]]
shap_mean_abs_per_fold = pd.DataFrame(
    [
        pd.Series(
            np.mean(np.abs(fold["y"].values), axis=0),
            index=fold["y"].feature_names,
        )
        for fold in shap_folds
    ]
)

combined_importances = {
    m.name: combine_permutation_importances(pi["permutation_importance"], m).describe()
    for m in RegressionMetricsEnum
}
combined_importances["lengthscale"] = combine_lengthscale_importances(
    pi["lengthscale_importance"],
).describe()
combined_importances["shap"] = shap_mean_abs_per_fold.describe()

plot_feature_importance_by_feature_plotly(
    combined_importances,
    relative=False,
    caption="Feature Importances",
    show_std=True,
    importance_measure="Importance",
)

Analyze the cross validation

# Performance on test sets
test_cv.get_metrics(combine_folds=False)

	MAE	MSD	R2	MAPE	PEARSON	SPEARMAN	FISHER
0	11.395786	223.991679	0.966159	0.467075	0.983823	0.939394	0.003968
1	8.672040	139.631353	0.876523	2.319987	0.944297	0.939394	0.003968
2	5.440700	55.573390	0.964980	0.075173	0.985667	0.975758	0.003968
3	11.496241	369.273141	0.883749	0.109988	0.949433	0.866667	0.103175
4	10.339850	202.398167	0.929351	0.430028	0.972547	0.890909	0.103175

display(test_cv.get_metrics(combine_folds=False))
display(test_cv.get_metrics(combine_folds=False).describe())

	MAE	MSD	R2	MAPE	PEARSON	SPEARMAN	FISHER
0	11.395786	223.991679	0.966159	0.467075	0.983823	0.939394	0.003968
1	8.672040	139.631353	0.876523	2.319987	0.944297	0.939394	0.003968
2	5.440700	55.573390	0.964980	0.075173	0.985667	0.975758	0.003968
3	11.496241	369.273141	0.883749	0.109988	0.949433	0.866667	0.103175
4	10.339850	202.398167	0.929351	0.430028	0.972547	0.890909	0.103175

	MAE	MSD	R2	MAPE	PEARSON	SPEARMAN	FISHER
count	5.000000	5.000000	5.000000	5.000000	5.000000	5.000000	5.000000
mean	9.468924	198.173546	0.924152	0.680450	0.967153	0.922424	0.043651
std	2.522050	115.889481	0.042894	0.933824	0.019275	0.043366	0.054338
min	5.440700	55.573390	0.876523	0.075173	0.944297	0.866667	0.003968
25%	8.672040	139.631353	0.883749	0.109988	0.949433	0.890909	0.003968
50%	10.339850	202.398167	0.929351	0.430028	0.972547	0.939394	0.003968
75%	11.395786	223.991679	0.964980	0.467075	0.983823	0.939394	0.103175
max	11.496241	369.273141	0.966159	2.319987	0.985667	0.975758	0.103175

Plot Folds

plot_cv_folds_plotly(test_cv, plot_X=True, plot_labcodes=True, plot_uncertainties=True)

Plot a slice of the GP

In this slice plot, we vary the inputs x_1 and x_2 across their full bounds to create a grid, while keeping x_3 fixed at a selected value.

The outputs are two Plotly figures: one showing the GP’s predicted mean (fig_mean) and the other showing the predicted standard deviation or uncertainty (fig_sd) over the slice.

If observed_data=experiments is provided, the mean plot will also display the measured data points, with those matching the fixed value of x_3 highlighted separately.

fixed_input_features = [model.inputs.get_by_key("x_3")]
fixed_values = [0.0]
varied_input_features = [
    model.inputs.get_by_key("x_1"),
    model.inputs.get_by_key("x_2"),
]
output_feature = model.outputs.get_by_key("y")

fixed_values = [experiments.iloc[0]["x_3"]]
fig_mean, fig_sd = plot_gp_slice_plotly(
    surrogate=model,
    fixed_input_features=fixed_input_features,
    fixed_values=fixed_values,
    varied_input_features=varied_input_features,
    output_feature=output_feature,
    resolution=80,
    observed_data=experiments,
)
display(fig_mean)
display(fig_sd)

Shapley Plots

shap_explanations = shap_importance(
    predictor=model,
    experiments=experiments,
    bg_experiments=experiments,   # background for KernelSHAP
    bg_sample_size=50,
    seed=42,
)

exp = shap_explanations['y']
shap.summary_plot(exp.values, exp.data, feature_names=exp.feature_names)

--- title: Model Building with BoFire jupyter: python3 --- This notebooks shows how to setup and analyze models trained with BoFire. ## Imports ```{python} #| papermill: {duration: 2.690868, end_time: '2024-10-10T20:34:24.683197', exception: false, start_time: '2024-10-10T20:34:21.992329', status: completed} #| tags: [] import numpy as np import pandas as pd import shap import bofire.surrogates.api as surrogates from bofire.data_models.domain.api import Inputs, Outputs from bofire.data_models.enum import RegressionMetricsEnum from bofire.data_models.features.api import ContinuousInput, ContinuousOutput from bofire.data_models.surrogates.api import SingleTaskGPSurrogate from bofire.plot.cv_folds import plot_cv_folds_plotly from bofire.plot.feature_importance import plot_feature_importance_by_feature_plotly from bofire.plot.gp_slice import plot_gp_slice_plotly from bofire.surrogates.feature_importance import ( combine_lengthscale_importances, combine_permutation_importances, lengthscale_importance_hook, permutation_importance_hook, shap_importance, shap_importance_hook, ) ``` ## Problem Setup For didactic purposes, we sample data from a Himmelblau benchmark function and use them to train a SingleTaskGP. ```{python} #| papermill: {duration: 0.010285, end_time: '2024-10-10T20:34:24.696815', exception: false, start_time: '2024-10-10T20:34:24.686530', status: completed} #| tags: [] input_features = Inputs( features=[ContinuousInput(key=f"x_{i+1}", bounds=(-4, 4)) for i in range(3)], ) output_features = Outputs(features=[ContinuousOutput(key="y")]) experiments = input_features.sample(n=50) experiments.eval("y=((x_1**2 + x_2 - 11)**2+(x_1 + x_2**2 -7)**2)", inplace=True, engine = "python") experiments["valid_y"] = 1 experiments["labcode"] = "exp_" + experiments.index.astype(str) ``` ## Cross Validation ### Run the cross validation ```{python} #| papermill: {duration: 0.229142, end_time: '2024-10-10T20:34:24.929279', exception: true, start_time: '2024-10-10T20:34:24.700137', status: failed} #| tags: [] data_model = SingleTaskGPSurrogate( inputs=input_features, outputs=output_features, ) model = surrogates.map(data_model=data_model) train_cv, test_cv, pi = model.cross_validate( experiments, folds=5, include_X = True, include_labcodes = True, hooks={ "permutation_importance": permutation_importance_hook, "lengthscale_importance": lengthscale_importance_hook, "shap_importance": shap_importance_hook, }, ) ``` ### Plot feature importance ```{python} #| papermill: {duration: null, end_time: null, exception: null, start_time: null, status: pending} #| tags: [] shap_folds = pi["shap_importance"] # list[dict[str, shap.Explanation]] shap_mean_abs_per_fold = pd.DataFrame( [ pd.Series( np.mean(np.abs(fold["y"].values), axis=0), index=fold["y"].feature_names, ) for fold in shap_folds ] ) combined_importances = { m.name: combine_permutation_importances(pi["permutation_importance"], m).describe() for m in RegressionMetricsEnum } combined_importances["lengthscale"] = combine_lengthscale_importances( pi["lengthscale_importance"], ).describe() combined_importances["shap"] = shap_mean_abs_per_fold.describe() plot_feature_importance_by_feature_plotly( combined_importances, relative=False, caption="Feature Importances", show_std=True, importance_measure="Importance", ) ``` ### Analyze the cross validation ```{python} #| papermill: {duration: null, end_time: null, exception: null, start_time: null, status: pending} #| tags: [] # Performance on test sets test_cv.get_metrics(combine_folds=False) ``` ```{python} #| papermill: {duration: null, end_time: null, exception: null, start_time: null, status: pending} #| tags: [] display(test_cv.get_metrics(combine_folds=False)) display(test_cv.get_metrics(combine_folds=False).describe()) ``` ### Plot Folds ```{python} plot_cv_folds_plotly(test_cv, plot_X=True, plot_labcodes=True, plot_uncertainties=True) ``` ### Plot a slice of the GP In this slice plot, we vary the inputs x_1 and x_2 across their full bounds to create a grid, while keeping x_3 fixed at a selected value. The outputs are two Plotly figures: one showing the GP's predicted mean (fig_mean) and the other showing the predicted standard deviation or uncertainty (fig_sd) over the slice. If observed_data=experiments is provided, the mean plot will also display the measured data points, with those matching the fixed value of x_3 highlighted separately. ```{python} fixed_input_features = [model.inputs.get_by_key("x_3")] fixed_values = [0.0] varied_input_features = [ model.inputs.get_by_key("x_1"), model.inputs.get_by_key("x_2"), ] output_feature = model.outputs.get_by_key("y") fixed_values = [experiments.iloc[0]["x_3"]] fig_mean, fig_sd = plot_gp_slice_plotly( surrogate=model, fixed_input_features=fixed_input_features, fixed_values=fixed_values, varied_input_features=varied_input_features, output_feature=output_feature, resolution=80, observed_data=experiments, ) display(fig_mean) display(fig_sd) ``` ### Shapley Plots ```{python} shap_explanations = shap_importance( predictor=model, experiments=experiments, bg_experiments=experiments, # background for KernelSHAP bg_sample_size=50, seed=42, ) exp = shap_explanations['y'] shap.summary_plot(exp.values, exp.data, feature_names=exp.feature_names) ```