Create Prediction Intervals such as Quantile Regression, Conformalized Quantile Regression, and bootstrapping using XGBoost

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Project links

repository

Project description

Based off the work done here:

CQR: https://arxiv.org/abs/1905.03222
CQR: poster concise explanation: https://github.com/yromano/cqr/blob/master/poster/CQR_Poster.pdf

macOS users install `libomp` before running the project:

brew install libomp


```python
%pip install xgboost_prediction_interval

import pandas as pd
import numpy as np
from sklearn.model_selection import train_test_split
from xgboost_prediction_interval import XGBoostCQR, XGBoostQuantileRegressor, XGBoostBootstrap

Demo of how to use package:

Creating dummy data

np.random.seed(42)
n_samples = 1000

# Generate some random features
X1 = np.random.normal(loc=0, scale=1, size=n_samples)
X2 = np.random.normal(loc=5, scale=2, size=n_samples)
X3 = np.random.normal(loc=5, scale=2, size=n_samples)
X4 = np.random.normal(loc=5, scale=2, size=n_samples)
X5 = np.random.normal(loc=5, scale=2, size=n_samples)
X6 = np.random.normal(loc=5, scale=2, size=n_samples)
X7 = np.random.normal(loc=5, scale=2, size=n_samples)

# Create a target variable with some noise
# assume a linear relationship with some noise
y = 3 * X1 + 2 * X2 + np.random.normal(loc=0, scale=1, size=n_samples) +X3+X4+X5+X6+X7

df = pd.DataFrame({
    "Feature1": X1,
    "Feature2": X2,
    "Feature3": X3,
    "Feature4": X4,
    "Feature5": X5,
    "Feature6": X6,
    "Feature7": X7,
    "Target": y
})

print(df.head())
print(df.shape)

   Feature1  Feature2  Feature3  Feature4  Feature5  Feature6  Feature7  \
0  0.496714  7.798711  3.649643  1.184385  3.273013  4.152481  2.771837   
1 -0.138264  6.849267  4.710963  3.279230  4.937593  4.093172  3.738138   
2  0.647689  5.119261  3.415160  4.172789  5.036034  1.408714  3.115880   
3  1.523030  3.706126  4.384077  8.775375  5.945261  4.339820  3.904008   
4 -0.234153  6.396447  1.212771  6.113106  2.266283  6.465658  4.571699   

      Target  
0  32.904108  
1  32.265157  
2  30.044909  
3  39.096159  
4  33.427409  
(1000, 8)

To import data saved locally uncomment the following and add full path to dataset in place of path_to_file...

# # Importing data saved locally:
# path = r"path_to_file..."
# data = pd.read_csv(path)

Splitting data

X_data = df.copy()
y_data = X_data.pop("Target")
X_train, X_test, y_train, y_test = train_test_split(X_data, y_data, test_size=0.25)
X_calibration, X_test, y_calibration, y_test = train_test_split(X_test, y_test, test_size=0.5)

xgboost_params = {
    "max_depth": 4,
    "eta": 0.05,
    "gamma": 0.1,
    "subsample": 0.8,
    "min_child_weight": 100,
    "colsample_bytree": 1,
    "alpha": 5,
    "lambda": 0,
    "base_score": 0.57322098
}
cqr_xgboost = XGBoostCQR(
    model_params=xgboost_params,
    num_boost_round=int(100),
    early_stopping_rounds=10,
    alpha=0.9  # coverage probability for the conformal prediction part of CQR - should be set to your final desired coverage level
    )

Using grid search to test different coverage probabilities for the quantile regression portion of CQR

Grid search is NOT a required step - can skip straight to fitting final PI model

The conformal prediction alpha ensures the PIs are padded to maintain the desired coverage probability even with a lower coverage specified for the quantile regression portion

lower_qr_quantile, upper_qr_quantile, conformity_score = cqr_xgboost.cqr_grid_search_alpha(
    [0.1, 0.2, 0.4,],            # lower quantile coverage probability levels
    [0.6, 0.8, 0.9],             # upper quantile coverage probability levels
    X_train.values,         
    y_train.values, 
    X_calibration.values,   # unseen holdout calibration set used for the conformal prediction portion
    y_calibration.values, 
    X_test.values, 
    y_test.values, 
    0.25                    # split size for the training data of the initial quantile regression
    )

Evaluating --- Lower alpha: 0.1 --- Upper alpha 0.6
Evaluating --- Lower alpha: 0.1 --- Upper alpha 0.8
Evaluating --- Lower alpha: 0.1 --- Upper alpha 0.9
Evaluating --- Lower alpha: 0.2 --- Upper alpha 0.6
Evaluating --- Lower alpha: 0.2 --- Upper alpha 0.8
Evaluating --- Lower alpha: 0.2 --- Upper alpha 0.9
Evaluating --- Lower alpha: 0.4 --- Upper alpha 0.6
Evaluating --- Lower alpha: 0.4 --- Upper alpha 0.8
Evaluating --- Lower alpha: 0.4 --- Upper alpha 0.9
best CWC: 2.2498335501828367e-12
best coverage: 0.952
QR Alphas: [0.4, 0.6]
   l_alpha  u_alpha           cwc  coverage  average_PI_width
0      0.1      0.6  3.123635e-12     0.960         19.704405
1      0.1      0.8  4.587595e-12     0.952         16.637457
2      0.1      0.9  7.390271e-12     0.936         16.710157
3      0.2      0.6  4.482768e-12     0.952         17.158796
4      0.2      0.8  3.692294e-12     0.960         16.109138
5      0.2      0.9  7.937115e-12     0.936         15.027287
6      0.4      0.6  2.249834e-12     0.976         16.465689
7      0.4      0.8  3.815250e-12     0.960         15.331766
8      0.4      0.9  4.629115e-12     0.952         16.430967

The output identifies the best quantile values for the quantile regression portion of the prediction interval (0.4 and 0.6)

despite the quantile levels giving a prediction interval width of 0.6-0.4 = 0.2 the overall PI will still have a width of 0.9 due to the alpha defined at the start

Using the results of the grid search we can fit the CQR model with the optimum quantile levels

cqr_xgboost.fit(
    X_train.values, 
    y_train.values, 
    X_calibration.values, 
    y_calibration.values, 
    0.25,                   # training/validation data split proportion used in the quantile regression portion 
    0.4,                    # lower quantile value for quantile regression portion
    0.6,                    # lower quantile value for quantile regression portion
    )

Evaluating --- Lower QR quantile: 0.4 --- Upper QR quantile 0.6 --- CQR alpha 0.9

cqr_preds = cqr_xgboost.predict(X_test)
cqr_preds

{'model_40': <xgboost.core.Booster object at 0x000001A4BE092630>, 'model_60': <xgboost.core.Booster object at 0x000001A4BE091F40>}
(np.float64(6.691801754053905), np.float64(6.691801754053905))





{'model_40_predictions': array([23.486837, 18.67393 , 32.484924, 27.112062, 28.803766, 27.276163,
        22.676764, 31.016535, 33.065357, 29.88289 , 29.197748, 23.760366,
        25.238892, 28.017939, 25.820185, 30.838179, 26.705332, 25.86778 ,
        29.041285, 26.21456 , 30.407969, 27.181593, 29.95053 , 23.81866 ,
        30.059622, 29.288862, 28.555567, 28.5591  , 28.319204, 21.84705 ,
        24.585625, 26.863321, 25.627268, 24.067434, 26.742422, 26.236872,
        33.069336, 24.5562  , 30.418066, 27.926493, 21.664396, 23.109285,
        28.026175, 31.024427, 21.150793, 22.963375, 28.087214, 27.088976,
        24.280598, 22.03742 , 22.731644, 31.532808, 22.613436, 20.83436 ,
        29.681917, 29.690145, 28.256884, 30.230074, 31.142015, 29.283438,
        26.716932, 25.042675, 23.072714, 19.717453, 24.86407 , 29.446177,
        31.87668 , 26.152586, 29.279047, 29.858416, 26.830156, 25.162756,
        27.63354 , 19.20571 , 24.69247 , 25.690577, 30.029097, 30.762701,
        18.25805 , 27.989725, 24.016665, 26.895353, 30.669115, 29.7009  ,
        30.946955, 32.54754 , 24.912683, 27.601076, 31.12282 , 29.557177,
        24.888874, 25.8893  , 30.666895, 28.617975, 21.349886, 23.419872,
        28.527033, 24.727304, 30.481913, 27.833437, 22.214617, 30.06967 ,
        32.49518 , 26.203722, 23.8881  , 25.841269, 24.499422, 29.215921,
        29.807978, 22.654224, 26.073137, 28.352068, 27.04648 , 30.973734,
        31.945948, 26.06415 , 27.427275, 24.810951, 24.995848, 28.251188,
        30.708555, 18.834095, 25.407259, 23.607534, 25.937593],
       dtype=float32),
 'model_60_predictions': array([38.722267, 33.717125, 46.950207, 42.872467, 44.487522, 43.517685,
        36.2037  , 47.33104 , 49.405422, 45.57175 , 45.849594, 40.34343 ,
        42.515392, 45.768757, 41.283974, 47.002872, 43.49001 , 40.70927 ,
        44.985947, 42.033783, 45.824375, 43.750404, 45.824776, 38.606483,
        44.9471  , 44.982548, 43.323177, 44.30441 , 46.64857 , 36.690807,
        42.08947 , 43.14702 , 40.105347, 42.03816 , 42.343517, 42.82062 ,
        47.231827, 39.99295 , 46.01658 , 44.035904, 40.032692, 39.847237,
        43.620773, 45.87897 , 38.059414, 39.671467, 44.383564, 43.294315,
        42.21498 , 37.707195, 39.172314, 48.78219 , 40.33695 , 35.455032,
        45.304146, 44.3602  , 44.47025 , 44.866173, 47.033566, 45.58766 ,
        43.899357, 39.882862, 38.573433, 36.740124, 42.331272, 44.73848 ,
        48.787716, 42.771965, 43.78315 , 46.3867  , 43.134953, 38.920753,
        42.35099 , 34.952   , 40.73547 , 41.644997, 45.818905, 48.361866,
        34.787315, 42.48722 , 39.872192, 43.96925 , 46.86797 , 45.07383 ,
        48.388138, 47.090015, 40.41863 , 44.758327, 45.3852  , 44.541466,
        42.1466  , 43.65617 , 47.54282 , 44.77244 , 36.969772, 41.54296 ,
        43.831978, 39.787712, 46.23097 , 44.46332 , 39.139694, 44.293724,
        49.27917 , 42.516434, 39.81532 , 42.348747, 41.600716, 44.78814 ,
        43.9265  , 38.41995 , 42.405285, 42.678352, 40.930042, 47.90765 ,
        45.33097 , 41.709576, 40.599304, 40.70203 , 40.479744, 41.99648 ,
        48.51149 , 36.695763, 41.383724, 39.570942, 41.64385 ],
       dtype=float32)}

creates a dictionary for the upper and lower prediction interval with the following naming convention: model_{quantile_level}_predictions

the key value changes respect to the quantile level specified during fit()

pd.DataFrame(cqr_preds).head()

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	model_40_predictions	model_60_predictions
0	23.486837	38.722267
1	18.673929	33.717125
2	32.484924	46.950207
3	27.112062	42.872467
4	28.803766	44.487522

lower_quantile_preds = cqr_preds["model_40_predictions"]
upper_quantile_preds = cqr_preds["model_60_predictions"]
cqr_xgboost.plot_pi_line_graph(y_test, lower_quantile_preds, upper_quantile_preds)
print(f"symmetric coverage {cqr_xgboost.coverage(y_test, lower_quantile_preds, upper_quantile_preds)}")
print(f"symmetric average_width {cqr_xgboost.average_width(lower_quantile_preds, upper_quantile_preds)}")
print(f"symmetric cwc {cqr_xgboost.cwc(0.9, y_test, lower_quantile_preds, upper_quantile_preds)}")

png

symmetric coverage 0.96
symmetric average_width 15.935728073120117
symmetric cwc 3.719721652657278e-12

Also have the option for an asymmetric loss function which optimises the upper and lower quantiles separately

# instantiate the model
asymmetric_cqr_xgboost = XGBoostCQR(model_params=xgboost_params,num_boost_round=int(100), alpha=0.90)

# grid search upper and lower quantiles
lower_qr_quantile, upper_qr_quantile, conformity_score = cqr_xgboost.cqr_grid_search_alpha(
    [0.1, 0.2, 0.4,],            # lower quantile coverage probability levels
    [0.6, 0.8, 0.9],             # upper quantile coverage probability levels
    X_train.values,         
    y_train.values, 
    X_calibration.values,   # unseen holdout calibration set used for the conformal prediction portion
    y_calibration.values, 
    X_test.values, 
    y_test.values, 
    0.25                    # split size for the training data of the initial quantile regression
    )

Evaluating --- Lower alpha: 0.1 --- Upper alpha 0.6
Evaluating --- Lower alpha: 0.1 --- Upper alpha 0.8
Evaluating --- Lower alpha: 0.1 --- Upper alpha 0.9
Evaluating --- Lower alpha: 0.2 --- Upper alpha 0.6
Evaluating --- Lower alpha: 0.2 --- Upper alpha 0.8
Evaluating --- Lower alpha: 0.2 --- Upper alpha 0.9
Evaluating --- Lower alpha: 0.4 --- Upper alpha 0.6
Evaluating --- Lower alpha: 0.4 --- Upper alpha 0.8
Evaluating --- Lower alpha: 0.4 --- Upper alpha 0.9
best CWC: 2.2979702687205084e-12
best coverage: 0.944
QR Alphas: [0.1, 0.6]
   l_alpha  u_alpha           cwc  coverage  average_PI_width
0      0.1      0.6  2.297970e-12     0.968         20.983686
1      0.1      0.8  5.785209e-12     0.944         16.820417
2      0.1      0.9  7.639414e-12     0.936         15.943439
3      0.2      0.6  5.581861e-12     0.944         17.615952
4      0.2      0.8  3.708949e-12     0.960         16.003836
5      0.2      0.9  6.238370e-12     0.944         15.047573
6      0.4      0.6  4.770299e-12     0.952         15.728806
7      0.4      0.8  3.616456e-12     0.960         16.588610
8      0.4      0.9  6.010613e-12     0.944         15.938600

The Output for Grid Search shows key metrics (Coverage-Width Criterion, Coverage, average PI width) - best alphas recommended based on lowest CWC which changes based on arbitrary choice of eta parameter in CWC formula (higher eta favours high coverage => wider PIs, lower eta favours narrow PIs => lower coverage) thus for best results experiment with different values of eta or use the full output to also compare coverage and PI width when settling on lower and upper quantile levels. The balance of coverage and PI width will vary based on application

# fit the model
asymmetric_cqr_xgboost.fit(
    X_train.values,
    y_train.values,
    X_calibration.values, 
    y_calibration.values, 0.25, 
    lower_qr_quantile=0.4, 
    upper_qr_quantile=0.6, 
    conformity_score_method="asymmetric"
    )
# make predictions
asym_cqr_preds = asymmetric_cqr_xgboost.predict(X_test)     
# access the lower and upper prediction interval values for the X_test data
asym_lower_quantile_preds = asym_cqr_preds["model_40_predictions"]
asym_upper_quantile_preds = asym_cqr_preds["model_60_predictions"]
# plot the prediction interval against the actual y_test values
asymmetric_cqr_xgboost.plot_pi_line_graph(y_test, asym_lower_quantile_preds, asym_upper_quantile_preds)
# print out some key metrics evaluating the prediction interval
print(f"asymmetric coverage {asymmetric_cqr_xgboost.coverage(y_test, asym_lower_quantile_preds, asym_upper_quantile_preds)}")
print(f"asymmetric average_width {asymmetric_cqr_xgboost.average_width(asym_lower_quantile_preds, asym_upper_quantile_preds)}")
print(f"asymmetric cwc {asymmetric_cqr_xgboost.cwc(0.9, y_test, asym_lower_quantile_preds, asym_upper_quantile_preds)}")

Evaluating --- Lower QR quantile: 0.4 --- Upper QR quantile 0.6 --- CQR alpha 0.9
{'model_40': <xgboost.core.Booster object at 0x000001A4DA37B290>, 'model_60': <xgboost.core.Booster object at 0x000001A4DA3794F0>}
(np.float64(6.199072327530171), np.float64(7.433534967125333))

png

asymmetric coverage 0.96
asymmetric average_width 15.902301788330078
asymmetric cwc 3.725008720146514e-12

Results in a marginally lower coverage probability but a narrower average PI width

XGBoost Quantile Regression Demo

qr_xgboost = XGBoostQuantileRegressor(
    model_params=xgboost_params,
    num_boost_round=int(100),
    early_stopping_rounds=10,
    quantiles=[0.05, 0.95]  # coverage probability for the conformal prediction part of CQR - should be set to your final desired coverage level
    )
qr_xgboost.fit(X_train, y_train, validation_size=0.25)
qr_preds = qr_xgboost.predict(X_test)
# access the lower and upper prediction interval values for the X_test data
lower_qr_preds = qr_preds["model_5_predictions"]
upper_qr_preds = qr_preds["model_95_predictions"]
# plot the prediction interval against the actual y_test values
asymmetric_cqr_xgboost.plot_pi_line_graph(y_test, lower_qr_preds, upper_qr_preds)
# print out some key metrics evaluating the prediction interval
print(f"asymmetric coverage {asymmetric_cqr_xgboost.coverage(y_test, lower_qr_preds, upper_qr_preds)}")
print(f"asymmetric average_width {asymmetric_cqr_xgboost.average_width(lower_qr_preds, upper_qr_preds)}")
print(f"asymmetric cwc {asymmetric_cqr_xgboost.cwc(0.9, y_test, lower_qr_preds, upper_qr_preds)}")

png

asymmetric coverage 0.888
asymmetric average_width 14.869775772094727
asymmetric cwc 3.3716176135545774e-11

bootstrap = XGBoostBootstrap(
    model_params={},
    num_boost_round=int(100),
    alpha=0.98
    )
bootstrap.fit(X_train, y_train, n_bootstrap=100, sample_size_ratio=0.7)
bs_preds = bootstrap.predict(X_test)
# access the lower and upper prediction interval values for the X_test data
lower_qr_preds = bs_preds["model_1_predictions"]
upper_qr_preds = bs_preds["model_99_predictions"]


# plot the prediction interval against the actual y_test values
bootstrap.plot_pi_line_graph(y_test, lower_qr_preds, upper_qr_preds)
# print out some key metrics evaluating the prediction interval
print(f"Bootstrap coverage {bootstrap.coverage(y_test, lower_qr_preds, upper_qr_preds)}")
print(f"Bootstrap average_width {bootstrap.average_width(lower_qr_preds, upper_qr_preds)}")
print(f"Bootstrap cwc {bootstrap.cwc(0.9, y_test, lower_qr_preds, upper_qr_preds)}")

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png

Bootstrap coverage 0.896
Bootstrap average_width 7.640153408050537
Bootstrap cwc 3.4321849985369016e-11

Bootstrap undercovers with the default parameters - introducing randomness via XGBoosts hyperparameters (subsample, colsample_bytree, colsample_bylevel , ...) may reduce this effect

bootstrap.plot_pi_line_graph(y_test, lower_qr_preds, upper_qr_preds, X_test["Feature1"])

png

bootstrap.plot_coverage_probability_binned(y_test, lower_qr_preds, upper_qr_preds, x=X_test["Feature1"])

bootstrap.plot_pi_width(lower_qr_preds, upper_qr_preds, x=X_test["Feature1"])

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0.1.9

Apr 5, 2025

0.1.8

Mar 28, 2025

0.1.7

Mar 28, 2025

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Mar 28, 2025

0.1.5

Mar 28, 2025

0.1.4

Mar 25, 2025

0.1.3

Mar 25, 2025

0.1.2

Mar 24, 2025

0.1.1

Mar 24, 2025

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0.1.0

Mar 24, 2025

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prediction-interval 0.1.0

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macOS users install `libomp` before running the project:

Demo of how to use package:

Creating dummy data

To import data saved locally uncomment the following and add full path to dataset in place of path_to_file...

Splitting data

Using grid search to test different coverage probabilities for the quantile regression portion of CQR

Grid search is NOT a required step - can skip straight to fitting final PI model

The conformal prediction alpha ensures the PIs are padded to maintain the desired coverage probability even with a lower coverage specified for the quantile regression portion

The output identifies the best quantile values for the quantile regression portion of the prediction interval (0.4 and 0.6)

Using the results of the grid search we can fit the CQR model with the optimum quantile levels

Also have the option for an asymmetric loss function which optimises the upper and lower quantiles separately

XGBoost Quantile Regression Demo

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prediction-interval 0.1.0

Navigation

Verified details

Maintainers

Unverified details

Project links

Meta

Classifiers

Project description

macOS users install libomp before running the project:

Demo of how to use package:

Creating dummy data

To import data saved locally uncomment the following and add full path to dataset in place of path_to_file...

Splitting data

Using grid search to test different coverage probabilities for the quantile regression portion of CQR

Grid search is NOT a required step - can skip straight to fitting final PI model

The conformal prediction alpha ensures the PIs are padded to maintain the desired coverage probability even with a lower coverage specified for the quantile regression portion

The output identifies the best quantile values for the quantile regression portion of the prediction interval (0.4 and 0.6)

Using the results of the grid search we can fit the CQR model with the optimum quantile levels

Also have the option for an asymmetric loss function which optimises the upper and lower quantiles separately

XGBoost Quantile Regression Demo

Project details

Verified details

Maintainers

Unverified details

Project links

Meta

Classifiers

Release history Release notifications | RSS feed

Download files

Source Distributions

Built Distribution

File details

File metadata

File hashes

macOS users install `libomp` before running the project: