Note
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Train, convert and predict with ONNX Runtime¶
This example demonstrates an end to end scenario starting with the training of a machine learned model to its use in its converted from.
Train a logistic regression¶
The first step consists in retrieving the iris datset.
from sklearn.datasets import load_iris
iris = load_iris()
X, y = iris.data, iris.target
from sklearn.model_selection import train_test_split
X_train, X_test, y_train, y_test = train_test_split(X, y)
Then we fit a model.
from sklearn.linear_model import LogisticRegression
clr = LogisticRegression()
clr.fit(X_train, y_train)
Out:
LogisticRegression()
We compute the prediction on the test set and we show the confusion matrix.
from sklearn.metrics import confusion_matrix
pred = clr.predict(X_test)
print(confusion_matrix(y_test, pred))
Out:
[[15 0 0]
[ 0 11 1]
[ 0 2 9]]
Conversion to ONNX format¶
We use module sklearn-onnx to convert the model into ONNX format.
from skl2onnx import convert_sklearn
from skl2onnx.common.data_types import FloatTensorType
initial_type = [('float_input', FloatTensorType([None, 4]))]
onx = convert_sklearn(clr, initial_types=initial_type)
with open("logreg_iris.onnx", "wb") as f:
f.write(onx.SerializeToString())
We load the model with ONNX Runtime and look at its input and output.
import onnxruntime as rt
sess = rt.InferenceSession("logreg_iris.onnx")
print("input name='{}' and shape={}".format(
sess.get_inputs()[0].name, sess.get_inputs()[0].shape))
print("output name='{}' and shape={}".format(
sess.get_outputs()[0].name, sess.get_outputs()[0].shape))
Out:
input name='float_input' and shape=[None, 4]
output name='output_label' and shape=[None]
We compute the predictions.
input_name = sess.get_inputs()[0].name
label_name = sess.get_outputs()[0].name
import numpy
pred_onx = sess.run([label_name], {input_name: X_test.astype(numpy.float32)})[0]
print(confusion_matrix(pred, pred_onx))
Out:
[[15 0 0]
[ 0 13 0]
[ 0 0 10]]
The prediction are perfectly identical.
Probabilities¶
Probabilities are needed to compute other relevant metrics such as the ROC Curve. Let’s see how to get them first with scikit-learn.
prob_sklearn = clr.predict_proba(X_test)
print(prob_sklearn[:3])
Out:
[[1.73218830e-01 8.23426993e-01 3.35417635e-03]
[7.42494153e-02 9.21910775e-01 3.83980986e-03]
[9.74276732e-01 2.57231679e-02 9.98201855e-08]]
And then with ONNX Runtime. The probabilies appear to be
prob_name = sess.get_outputs()[1].name
prob_rt = sess.run([prob_name], {input_name: X_test.astype(numpy.float32)})[0]
import pprint
pprint.pprint(prob_rt[0:3])
Out:
[{0: 0.17321892082691193, 1: 0.8234269618988037, 2: 0.003354174317792058},
{0: 0.07424944639205933, 1: 0.9219107627868652, 2: 0.0038398131728172302},
{0: 0.9742767214775085, 1: 0.025723155587911606, 2: 9.982016280218886e-08}]
Let’s benchmark.
from timeit import Timer
def speed(inst, number=10, repeat=20):
timer = Timer(inst, globals=globals())
raw = numpy.array(timer.repeat(repeat, number=number))
ave = raw.sum() / len(raw) / number
mi, ma = raw.min() / number, raw.max() / number
print("Average %1.3g min=%1.3g max=%1.3g" % (ave, mi, ma))
return ave
print("Execution time for clr.predict")
speed("clr.predict(X_test)")
print("Execution time for ONNX Runtime")
speed("sess.run([label_name], {input_name: X_test.astype(numpy.float32)})[0]")
Out:
Execution time for clr.predict
Average 7.59e-05 min=4.75e-05 max=0.000155
Execution time for ONNX Runtime
Average 3.9e-05 min=3.67e-05 max=6.01e-05
3.902899999999931e-05
Let’s benchmark a scenario similar to what a webservice experiences: the model has to do one prediction at a time as opposed to a batch of prediction.
def loop(X_test, fct, n=None):
nrow = X_test.shape[0]
if n is None:
n = nrow
for i in range(0, n):
im = i % nrow
fct(X_test[im: im+1])
print("Execution time for clr.predict")
speed("loop(X_test, clr.predict, 100)")
def sess_predict(x):
return sess.run([label_name], {input_name: x.astype(numpy.float32)})[0]
print("Execution time for sess_predict")
speed("loop(X_test, sess_predict, 100)")
Out:
Execution time for clr.predict
Average 0.00598 min=0.005 max=0.00753
Execution time for sess_predict
Average 0.00315 min=0.00248 max=0.00516
0.003146542500000038
Let’s do the same for the probabilities.
print("Execution time for predict_proba")
speed("loop(X_test, clr.predict_proba, 100)")
def sess_predict_proba(x):
return sess.run([prob_name], {input_name: x.astype(numpy.float32)})[0]
print("Execution time for sess_predict_proba")
speed("loop(X_test, sess_predict_proba, 100)")
Out:
Execution time for predict_proba
Average 0.00812 min=0.00658 max=0.0116
Execution time for sess_predict_proba
Average 0.00287 min=0.00238 max=0.00362
0.0028650640000000395
This second comparison is better as ONNX Runtime, in this experience, computes the label and the probabilities in every case.
Benchmark with RandomForest¶
We first train and save a model in ONNX format.
from sklearn.ensemble import RandomForestClassifier
rf = RandomForestClassifier()
rf.fit(X_train, y_train)
initial_type = [('float_input', FloatTensorType([1, 4]))]
onx = convert_sklearn(rf, initial_types=initial_type)
with open("rf_iris.onnx", "wb") as f:
f.write(onx.SerializeToString())
We compare.
sess = rt.InferenceSession("rf_iris.onnx")
def sess_predict_proba_rf(x):
return sess.run([prob_name], {input_name: x.astype(numpy.float32)})[0]
print("Execution time for predict_proba")
speed("loop(X_test, rf.predict_proba, 100)")
print("Execution time for sess_predict_proba")
speed("loop(X_test, sess_predict_proba_rf, 100)")
Out:
Execution time for predict_proba
Average 0.594 min=0.506 max=0.727
Execution time for sess_predict_proba
Average 0.00329 min=0.00265 max=0.00614
0.0032889064999999107
Let’s see with different number of trees.
measures = []
for n_trees in range(5, 51, 5):
print(n_trees)
rf = RandomForestClassifier(n_estimators=n_trees)
rf.fit(X_train, y_train)
initial_type = [('float_input', FloatTensorType([1, 4]))]
onx = convert_sklearn(rf, initial_types=initial_type)
with open("rf_iris_%d.onnx" % n_trees, "wb") as f:
f.write(onx.SerializeToString())
sess = rt.InferenceSession("rf_iris_%d.onnx" % n_trees)
def sess_predict_proba_loop(x):
return sess.run([prob_name], {input_name: x.astype(numpy.float32)})[0]
tsk = speed("loop(X_test, rf.predict_proba, 100)", number=5, repeat=5)
trt = speed("loop(X_test, sess_predict_proba_loop, 100)", number=5, repeat=5)
measures.append({'n_trees': n_trees, 'sklearn': tsk, 'rt': trt})
from pandas import DataFrame
df = DataFrame(measures)
ax = df.plot(x="n_trees", y="sklearn", label="scikit-learn", c="blue", logy=True)
df.plot(x="n_trees", y="rt", label="onnxruntime",
ax=ax, c="green", logy=True)
ax.set_xlabel("Number of trees")
ax.set_ylabel("Prediction time (s)")
ax.set_title("Speed comparison between scikit-learn and ONNX Runtime\nFor a random forest on Iris dataset")
ax.legend()
Out:
5
Average 0.0719 min=0.0581 max=0.079
Average 0.00291 min=0.00257 max=0.00326
10
Average 0.0919 min=0.0727 max=0.106
Average 0.00241 min=0.00232 max=0.00248
15
Average 0.129 min=0.119 max=0.141
Average 0.00296 min=0.00266 max=0.00327
20
Average 0.148 min=0.126 max=0.17
Average 0.00345 min=0.00309 max=0.00387
25
Average 0.184 min=0.155 max=0.206
Average 0.00298 min=0.00254 max=0.00355
30
Average 0.208 min=0.162 max=0.256
Average 0.00242 min=0.00238 max=0.00249
35
Average 0.268 min=0.242 max=0.325
Average 0.00326 min=0.00272 max=0.00449
40
Average 0.513 min=0.422 max=0.796
Average 0.00399 min=0.00352 max=0.00489
45
Average 0.44 min=0.399 max=0.499
Average 0.00344 min=0.00336 max=0.00355
50
Average 0.503 min=0.447 max=0.584
Average 0.00342 min=0.00318 max=0.00368
<matplotlib.legend.Legend object at 0x000001878B902EB8>
Total running time of the script: ( 3 minutes 9.986 seconds)
