Convert a pipeline with a LightGBM model

sklearn-onnx only converts scikit-learn models into ONNX but many libraries implement scikit-learn API so that their models can be included in a scikit-learn pipeline. This example considers a pipeline including a LightGBM model. sklearn-onnx can convert the whole pipeline as long as it knows the converter associated to a LGBMClassifier. Let’s see how to do it.

Train a LightGBM classifier

from pyquickhelper.helpgen.graphviz_helper import plot_graphviz
from mlprodict.onnxrt import OnnxInference
import onnxruntime as rt
from skl2onnx import convert_sklearn, update_registered_converter
from skl2onnx.common.shape_calculator import calculate_linear_classifier_output_shapes  # noqa
from onnxmltools.convert.lightgbm.operator_converters.LightGbm import convert_lightgbm  # noqa
from skl2onnx.common.data_types import FloatTensorType
import numpy
from sklearn.datasets import load_iris
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import StandardScaler
from lightgbm import LGBMClassifier

data = load_iris()
X =[:, :2]
y =

ind = numpy.arange(X.shape[0])
X = X[ind, :].copy()
y = y[ind].copy()

pipe = Pipeline([('scaler', StandardScaler()),
                 ('lgbm', LGBMClassifier(n_estimators=3))]), y)


Pipeline(steps=[('scaler', StandardScaler()),
                ('lgbm', LGBMClassifier(n_estimators=3))])

Register the converter for LGBMClassifier

The converter is implemented in onnxmltools: onnxmltools… and the shape calculator: onnxmltools…

    LGBMClassifier, 'LightGbmLGBMClassifier',
    calculate_linear_classifier_output_shapes, convert_lightgbm,
    options={'nocl': [True, False], 'zipmap': [True, False]})

Convert again

model_onnx = convert_sklearn(
    pipe, 'pipeline_lightgbm',
    [('input', FloatTensorType([None, 2]))],

# And save.
with open("pipeline_lightgbm.onnx", "wb") as f:

Compare the predictions

Predictions with LightGbm.

print("predict", pipe.predict(X[:5]))
print("predict_proba", pipe.predict_proba(X[:1]))


predict [0 1 2 2 1]
predict_proba [[0.51995794 0.24549283 0.23454923]]

Predictions with onnxruntime.

sess = rt.InferenceSession("pipeline_lightgbm.onnx")

pred_onx =, {"input": X[:5].astype(numpy.float32)})
print("predict", pred_onx[0])
print("predict_proba", pred_onx[1][:1])


predict [0 1 2 2 1]
predict_proba [[0.51995796 0.24549282 0.23454922]]

Final graph

oinf = OnnxInference(model_onnx)
ax = plot_graphviz(oinf.to_dot())
plot gexternal lightgbm

Total running time of the script: ( 0 minutes 1.359 seconds)

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