Using Scikit-learn with the SageMaker Python SDK¶
With Scikit-learn Estimators, you can train and host Scikit-learn models on Amazon SageMaker.
For information about supported versions of Scikit-learn, see the Chainer README.
For general information about using the SageMaker Python SDK, see Using the SageMaker Python SDK.
Contents
Train a Model with Scikit-learn¶
To train a Scikit-learn model by using the SageMaker Python SDK:
- Prepare a training script
- Create a
sagemaker.sklearn.SKLearn
Estimator - Call the estimator’s
fit
method
Prepare a Scikit-learn Training Script¶
Your Scikit-learn training script must be a Python 2.7 or 3.6 compatible source file.
The training script is similar to a training script you might run outside of SageMaker, but you can access useful properties about the training environment through various environment variables. For example:
SM_MODEL_DIR
: A string representing the path to the directory to write model artifacts to. These artifacts are uploaded to S3 for model hosting.SM_OUTPUT_DATA_DIR
: A string representing the filesystem path to write output artifacts to. Output artifacts may include checkpoints, graphs, and other files to save, not including model artifacts. These artifacts are compressed and uploaded to S3 to the same S3 prefix as the model artifacts.
Supposing two input channels, ‘train’ and ‘test’, were used in the call to the Scikit-learn estimator’s fit()
method,
the following will be set, following the format “SM_CHANNEL_[channel_name]”:
SM_CHANNEL_TRAIN
: A string representing the path to the directory containing data in the ‘train’ channelSM_CHANNEL_TEST
: Same as above, but for the ‘test’ channel.
A typical training script loads data from the input channels, configures training with hyperparameters, trains a model, and saves a model to model_dir so that it can be hosted later. Hyperparameters are passed to your script as arguments and can be retrieved with an argparse.ArgumentParser instance. For example, a training script might start with the following:
import argparse
import os
if __name__ =='__main__':
parser = argparse.ArgumentParser()
# hyperparameters sent by the client are passed as command-line arguments to the script.
parser.add_argument('--epochs', type=int, default=50)
parser.add_argument('--batch-size', type=int, default=64)
parser.add_argument('--learning-rate', type=float, default=0.05)
# Data, model, and output directories
parser.add_argument('--output-data-dir', type=str, default=os.environ.get('SM_OUTPUT_DATA_DIR'))
parser.add_argument('--model-dir', type=str, default=os.environ.get('SM_MODEL_DIR'))
parser.add_argument('--train', type=str, default=os.environ.get('SM_CHANNEL_TRAIN'))
parser.add_argument('--test', type=str, default=os.environ.get('SM_CHANNEL_TEST'))
args, _ = parser.parse_known_args()
# ... load from args.train and args.test, train a model, write model to args.model_dir.
Because the SageMaker imports your training script, you should put your training code in a main guard
(if __name__=='__main__':
) if you are using the same script to host your model, so that SageMaker does not
inadvertently run your training code at the wrong point in execution.
For more on training environment variables, please visit https://github.com/aws/sagemaker-containers.
Save the Model¶
In order to save your trained Scikit-learn model for deployment on SageMaker, your training script should save your
model to a certain filesystem path called model_dir. This value is accessible through the environment variable
SM_MODEL_DIR
. The following code demonstrates how to save a trained Scikit-learn model named model
as
model.joblib
at the end of training:
from sklearn.externals import joblib
import argparse
import os
if __name__=='__main__':
# default to the value in environment variable `SM_MODEL_DIR`. Using args makes the script more portable.
parser.add_argument('--model-dir', type=str, default=os.environ['SM_MODEL_DIR'])
args, _ = parser.parse_known_args()
# ... train classifier `clf`, then save it to `model_dir` as file 'model.joblib'
joblib.dump(clf, os.path.join(args.model_dir, "model.joblib"))
After your training job is complete, SageMaker will compress and upload the serialized model to S3, and your model data
will available in the s3 output_path
you specified when you created the Scikit-learn Estimator.
Using third-party libraries¶
When running your training script on SageMaker, it has access to some pre-installed third-party libraries including scikit-learn
, numpy
, and pandas
.
For more information on the runtime environment, including specific package versions, see SageMaker Scikit-learn Docker Container.
If there are other packages you want to use with your script, you can include a requirements.txt
file in the same directory as your training script to install other dependencies at runtime.
A requirements.txt
file is a text file that contains a list of items that are installed by using pip install
. You can also specify the version of an item to install.
For information about the format of a requirements.txt
file, see Requirements Files in the pip documentation.
Create an Estimator¶
You run Scikit-learn training scripts on SageMaker by creating SKLearn
Estimators.
Call the fit
method on a SKLearn
Estimator to start a SageMaker training job.
The following code sample shows how you train a custom Scikit-learn script named “sklearn-train.py”, passing
in three hyperparameters (‘epochs’, ‘batch-size’, and ‘learning-rate’), and using two input channel
directories (‘train’ and ‘test’).
sklearn_estimator = SKLearn('sklearn-train.py',
train_instance_type='ml.m4.xlarge',
framework_version='0.20.0',
hyperparameters = {'epochs': 20, 'batch-size': 64, 'learning-rate': 0.1})
sklearn_estimator.fit({'train': 's3://my-data-bucket/path/to/my/training/data',
'test': 's3://my-data-bucket/path/to/my/test/data'})
Call the fit Method¶
You start your training script by calling fit
on a SKLearn
Estimator. fit
takes both required and optional
arguments.
fit Required arguments¶
inputs
: This can take one of the following forms: A string s3 URI, for examples3://my-bucket/my-training-data
. In this case, the s3 objects rooted at themy-training-data
prefix will be available in the defaulttrain
channel. A dict from string channel names to s3 URIs. In this case, the objects rooted at each s3 prefix will available as files in each channel directory.
For example:
{'train':'s3://my-bucket/my-training-data',
'eval':'s3://my-bucket/my-evaluation-data'}
fit Optional arguments¶
wait
: Defaults to True, whether to block and wait for the training script to complete before returning.logs
: Defaults to True, whether to show logs produced by training job in the Python session. Only meaningful when wait is True.
Deploy a Scikit-learn Model¶
After you fit a Scikit-learn Estimator, you can host the newly created model in SageMaker.
After you call fit
, you can call deploy
on an SKLearn
estimator to create a SageMaker endpoint.
The endpoint runs a SageMaker-provided Scikit-learn model server and hosts the model produced by your training script,
which was run when you called fit
. This was the model you saved to model_dir
.
deploy
returns a Predictor
object, which you can use to do inference on the Endpoint hosting your Scikit-learn
model. Each Predictor
provides a predict
method which can do inference with numpy arrays or Python lists.
Inference arrays or lists are serialized and sent to the Scikit-learn model server by an InvokeEndpoint
SageMaker
operation.
predict
returns the result of inference against your model. By default, the inference result a NumPy array.
# Train my estimator
sklearn_estimator = SKLearn(entry_point='train_and_deploy.py',
train_instance_type='ml.m4.xlarge',
framework_version='0.20.0')
sklearn_estimator.fit('s3://my_bucket/my_training_data/')
# Deploy my estimator to a SageMaker Endpoint and get a Predictor
predictor = sklearn_estimator.deploy(instance_type='ml.m4.xlarge',
initial_instance_count=1)
# `data` is a NumPy array or a Python list.
# `response` is a NumPy array.
response = predictor.predict(data)
You use the SageMaker Scikit-learn model server to host your Scikit-learn model when you call deploy
on an SKLearn
Estimator. The model server runs inside a SageMaker Endpoint, which your call to deploy
creates.
You can access the name of the Endpoint by the name
property on the returned Predictor
.
SageMaker Scikit-learn Model Server¶
The Scikit-learn Endpoint you create with deploy
runs a SageMaker Scikit-learn model server.
The model server loads the model that was saved by your training script and performs inference on the model in response
to SageMaker InvokeEndpoint API calls.
You can configure two components of the SageMaker Scikit-learn model server: Model loading and model serving. Model loading is the process of deserializing your saved model back into an Scikit-learn model. Serving is the process of translating InvokeEndpoint requests to inference calls on the loaded model.
You configure the Scikit-learn model server by defining functions in the Python source file you passed to the Scikit-learn constructor.
Load a Model¶
Before a model can be served, it must be loaded. The SageMaker Scikit-learn model server loads your model by invoking a
model_fn
function that you must provide in your script. The model_fn
should have the following signature:
def model_fn(model_dir)
SageMaker will inject the directory where your model files and sub-directories, saved by save
, have been mounted.
Your model function should return a model object that can be used for model serving.
SageMaker provides automated serving functions that work with Gluon API net
objects and Module API Module
objects. If you return either of these types of objects, then you will be able to use the default serving request handling functions.
The following code-snippet shows an example model_fn
implementation.
This loads returns a Scikit-learn Classifier from a model.joblib
file in the SageMaker model directory
model_dir
.
from sklearn.externals import joblib
import os
def model_fn(model_dir):
clf = joblib.load(os.path.join(model_dir, "model.joblib"))
return clf
Serve a Model¶
After the SageMaker model server has loaded your model by calling model_fn
, SageMaker will serve your model.
Model serving is the process of responding to inference requests, received by SageMaker InvokeEndpoint API calls.
The SageMaker Scikit-learn model server breaks request handling into three steps:
- input processing,
- prediction, and
- output processing.
In a similar way to model loading, you configure these steps by defining functions in your Python source file.
Each step involves invoking a python function, with information about the request and the return-value from the previous function in the chain. Inside the SageMaker Scikit-learn model server, the process looks like:
# Deserialize the Invoke request body into an object we can perform prediction on
input_object = input_fn(request_body, request_content_type)
# Perform prediction on the deserialized object, with the loaded model
prediction = predict_fn(input_object, model)
# Serialize the prediction result into the desired response content type
output = output_fn(prediction, response_content_type)
The above code-sample shows the three function definitions:
input_fn
: Takes request data and deserializes the data into an object for prediction.predict_fn
: Takes the deserialized request object and performs inference against the loaded model.output_fn
: Takes the result of prediction and serializes this according to the response content type.
The SageMaker Scikit-learn model server provides default implementations of these functions. You can provide your own implementations for these functions in your hosting script. If you omit any definition then the SageMaker Scikit-learn model server will use its default implementation for that function.
The RealTimePredictor
used by Scikit-learn in the SageMaker Python SDK serializes NumPy arrays to the NPY format
by default, with Content-Type application/x-npy
. The SageMaker Scikit-learn model server can deserialize NPY-formatted
data (along with JSON and CSV data).
If you rely solely on the SageMaker Scikit-learn model server defaults, you get the following functionality:
- Prediction on models that implement the
__call__
method - Serialization and deserialization of NumPy arrays.
The default input_fn
and output_fn
are meant to make it easy to predict on NumPy arrays. If your model expects
a NumPy array and returns a NumPy array, then these functions do not have to be overridden when sending NPY-formatted
data.
In the following sections we describe the default implementations of input_fn, predict_fn, and output_fn. We describe the input arguments and expected return types of each, so you can define your own implementations.
Process Input¶
When an InvokeEndpoint operation is made against an Endpoint running a SageMaker Scikit-learn model server, the model server receives two pieces of information:
- The request Content-Type, for example “application/x-npy”
- The request data body, a byte array
The SageMaker Scikit-learn model server will invoke an “input_fn” function in your hosting script,
passing in this information. If you define an input_fn
function definition,
it should return an object that can be passed to predict_fn
and have the following signature:
def input_fn(request_body, request_content_type)
Where request_body
is a byte buffer and request_content_type
is a Python string
The SageMaker Scikit-learn model server provides a default implementation of input_fn
.
This function deserializes JSON, CSV, or NPY encoded data into a NumPy array.
Default NPY deserialization requires request_body
to follow the NPY format. For Scikit-learn, the Python SDK
defaults to sending prediction requests with this format.
Default json deserialization requires request_body
contain a single json list.
Sending multiple json objects within the same request_body
is not supported.
The list must have a dimensionality compatible with the model loaded in model_fn
.
The list’s shape must be identical to the model’s input shape, for all dimensions after the first (which first
dimension is the batch size).
Default csv deserialization requires request_body
contain one or more lines of CSV numerical data.
The data is loaded into a two-dimensional array, where each line break defines the boundaries of the first dimension.
The example below shows a custom input_fn
for preparing pickled NumPy arrays.
import numpy as np
def input_fn(request_body, request_content_type):
"""An input_fn that loads a pickled numpy array"""
if request_content_type == "application/python-pickle":
array = np.load(StringIO(request_body))
return array
else:
# Handle other content-types here or raise an Exception
# if the content type is not supported.
pass
Get Predictions¶
After the inference request has been deserialized by input_fn
, the SageMaker Scikit-learn model server invokes
predict_fn
on the return value of input_fn
.
As with input_fn
, you can define your own predict_fn
or use the SageMaker Scikit-learn model server default.
The predict_fn
function has the following signature:
def predict_fn(input_object, model)
Where input_object
is the object returned from input_fn
and
model
is the model loaded by model_fn
.
The default implementation of predict_fn
invokes the loaded model’s predict
function on input_object
,
and returns the resulting value. The return-type should be a NumPy array to be compatible with the default
output_fn
.
The example below shows an overridden predict_fn
for a Logistic Regression classifier. This model accepts a
Python list and returns a tuple of predictions and prediction probabilities from the model in a NumPy array.
This predict_fn
can rely on the default input_fn
and output_fn
because input_data
is a NumPy array,
and the return value of this function is a NumPy array.
import sklearn
import numpy as np
def predict_fn(input_data, model):
prediction = model.predict(input_data)
pred_prob = model.predict_proba(input_data)
return np.array([prediction, pred_prob])
If you implement your own prediction function, you should take care to ensure that:
- The first argument is expected to be the return value from input_fn. If you use the default input_fn, this will be a NumPy array.
- The second argument is the loaded model.
- The return value should be of the correct type to be passed as the
first argument to
output_fn
. If you use the defaultoutput_fn
, this should be a NumPy array.
Process Output¶
After invoking predict_fn
, the model server invokes output_fn
, passing in the return-value from predict_fn
and the InvokeEndpoint requested response content-type.
The output_fn
has the following signature:
def output_fn(prediction, content_type)
Where prediction
is the result of invoking predict_fn
and
content_type
is the InvokeEndpoint requested response content-type.
The function should return a byte array of data serialized to content_type.
The default implementation expects prediction
to be an NumPy and can serialize the result to JSON, CSV, or NPY.
It accepts response content types of “application/json”, “text/csv”, and “application/x-npy”.
Working with existing model data and training jobs¶
Attach to Existing Training Jobs¶
You can attach an Scikit-learn Estimator to an existing training job using the
attach
method.
my_training_job_name = "MyAwesomeSKLearnTrainingJob"
sklearn_estimator = SKLearn.attach(my_training_job_name)
After attaching, if the training job is in a Complete status, it can be
deploy
ed to create a SageMaker Endpoint and return a
Predictor
. If the training job is in progress,
attach will block and display log messages from the training job, until the training job completes.
The attach
method accepts the following arguments:
training_job_name (str):
The name of the training job to attach to.sagemaker_session (sagemaker.Session or None):
The Session used to interact with SageMaker
Deploy an Endpoint from Model Data¶
As well as attaching to existing training jobs, you can deploy models directly from model data in S3.
The following code sample shows how to do this, using the SKLearnModel
class.
sklearn_model = SKLearnModel(model_data="s3://bucket/model.tar.gz", role="SageMakerRole",
entry_point="transform_script.py")
predictor = sklearn_model.deploy(instance_type="ml.c4.xlarge", initial_instance_count=1)
The sklearn_model constructor takes the following arguments:
model_data (str):
An S3 location of a SageMaker model data .tar.gz fileimage (str):
A Docker image URIrole (str):
An IAM role name or Arn for SageMaker to access AWS resources on your behalf.predictor_cls (callable[string,sagemaker.Session]):
A function to call to create a predictor. If not None,deploy
will return the result of invoking this function on the created endpoint nameenv (dict[string,string]):
Environment variables to run withimage
when hosted in SageMaker.name (str):
The model name. If None, a default model name will be selected on eachdeploy.
entry_point (str):
Path (absolute or relative) to the Python file which should be executed as the entry point to model hosting.source_dir (str):
Optional. Path (absolute or relative) to a directory with any other training source code dependencies including tne entry point file. Structure within this directory will be preserved when training on SageMaker.enable_cloudwatch_metrics (boolean):
Optional. If true, training and hosting containers will generate Cloudwatch metrics under the AWS/SageMakerContainer namespace.container_log_level (int):
Log level to use within the container. Valid values are defined in the Python logging module.code_location (str):
Optional. Name of the S3 bucket where your custom code will be uploaded to. If not specified, will use the SageMaker default bucket created by sagemaker.Session.sagemaker_session (sagemaker.Session):
The SageMaker Session object, used for SageMaker interaction”””
Your model data must be a .tar.gz file in S3. SageMaker Training Job model data is saved to .tar.gz files in S3, however if you have local data you want to deploy, you can prepare the data yourself.
Assuming you have a local directory containg your model data named “my_model” you can tar and gzip compress the file and upload to S3 using the following commands:
tar -czf model.tar.gz my_model
aws s3 cp model.tar.gz s3://my-bucket/my-path/model.tar.gz
This uploads the contents of my_model to a gzip compressed tar file to S3 in the bucket “my-bucket”, with the key “my-path/model.tar.gz”.
To run this command, you’ll need the aws cli tool installed. Please refer to our FAQ for more information on installing this.
Scikit-learn Training Examples¶
Amazon provides an example Jupyter notebook that demonstrate end-to-end training on Amazon SageMaker using Scikit-learn:
https://github.com/awslabs/amazon-sagemaker-examples/tree/master/sagemaker-python-sdk
These are also available in SageMaker Notebook Instance hosted Jupyter notebooks under the “sample notebooks” folder.
sagemaker.sklearn.SKLearn Class¶
The SKLearn constructor takes both required and optional arguments.
Required arguments¶
The following are required arguments to the SKLearn
constructor. When you create a Scikit-learn object, you must
include these in the constructor, either positionally or as keyword arguments.
entry_point
Path (absolute or relative) to the Python file which should be executed as the entry point to training.role
An AWS IAM role (either name or full ARN). The Amazon SageMaker training jobs and APIs that create Amazon SageMaker endpoints use this role to access training data and model artifacts. After the endpoint is created, the inference code might use the IAM role, if accessing AWS resource.train_instance_type
Type of EC2 instance to use for training, for example, ‘ml.m4.xlarge’. Please note that Scikit-learn does not have GPU support.
Optional arguments¶
The following are optional arguments. When you create a SKLearn
object, you can specify these as keyword arguments.
source_dir
Path (absolute or relative) to a directory with any other training source code dependencies including the entry point file. Structure within this directory will be preserved when training on SageMaker.hyperparameters
Hyperparameters that will be used for training. Will be made accessible as a dict[str, str] to the training code on SageMaker. For convenience, accepts other types besides str, but str() will be called on keys and values to convert them before training.py_version
Python version you want to use for executing your model training code.train_volume_size
Size in GB of the EBS volume to use for storing input data during training. Must be large enough to store training data if input_mode=’File’ is used (which is the default).train_max_run
Timeout in seconds for training, after which Amazon SageMaker terminates the job regardless of its current status.input_mode
The input mode that the algorithm supports. Valid modes: ‘File’ - Amazon SageMaker copies the training dataset from the s3 location to a directory in the Docker container. ‘Pipe’ - Amazon SageMaker streams data directly from s3 to the container via a Unix named pipe.output_path
s3 location where you want the training result (model artifacts and optional output files) saved. If not specified, results are stored to a default bucket. If the bucket with the specific name does not exist, the estimator creates the bucket during the fit() method execution.output_kms_key
Optional KMS key ID to optionally encrypt training output with.base_job_name
Name to assign for the training job that the fit() method launches. If not specified, the estimator generates a default job name, based on the training image name and current timestampimage_name
An alternative docker image to use for training and serving. If specified, the estimator will use this image for training and hosting, instead of selecting the appropriate SageMaker official image based on framework_version and py_version. Refer to: SageMaker Scikit-learn Docker Containers for details on what the official images support and where to find the source code to build your custom image.
SageMaker Scikit-learn Docker Containers¶
You can visit the SageMaker Scikit-Learn containers repository here: hhttps://github.com/aws/sagemaker-scikit-learn-container
For information about SageMaker TensorFlow Docker containers and their dependencies, see SageMaker Scikit-learn Docker Containers.