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Trained model pipelines

Both Keras and TensorFlow handle data that has been packaged into tensors gracefully. However, real-world data is often not properly formatted, especially at the time of prediction. It may come as a collection (a list, set, or generator) of urls, have non-numeric metadata that needs to be converted into tensor format, etc. Some of the data may actually be missing or cause exceptions in preprocessing / prediction stages.

Keras provides some features for image preprocessing to address this issue, and TensorFlow has functions to include non-tensor values into the computational graph. Both approaches have limitations - neither of them can handle missing data while retaining performance. As a concrete example, let us consider the following (which is a basis of the unit test ModelPipeTest.test_model_pipe_mnist_urls in studio/tests/model_util_test.py):

We are training a network to classify mnist digits, and then trying to predict images from urls. The simplest way to achieve this would be:

from PIL import Image
from io import BytesIO
import urlllib
import numpy as np

from studio import model_util

# setup and train keras model
#
# urls is a list of urls

labels = []
for url in urls:
    data = urllib.urlopen(url).read()
    img = Image.open(BytesIO(data))

    # resize image to model input, and convert to tensor:
    img_t = model_util.resize_to_model_input(model)(img)

    labels.append(np.argmax(model.predict(img_t)))

The function model_util.resize_to_model_input(model) is used for brevity and performes conversion of an image into a tensor with values between 0 and 1, and shaped accoring to model input size. np.argmax in the last line is used to convert output class probablilities into the class label.

Ok, so why do we need anything else? The code above has two problems: 1) it does not handle exceptions (though that is easy to fix) and 2) it processes the data sequentially. To address 2, we could have spawned a bunch of child processes, and if the model is evaluated on a CPU that probably would have been ok. But modern neural networks get a substantial speed boost from using GPUs that don't do well with hundreds of processes trying to run different instructions. To leverage GPU speedup, we'll need to create batches of data and feed them to the GPU (preferrably in parallel with urls being fetched).

Keras offers a built in mechanism to do this: keras.models.predict_generator. The relevant part of the code above can then become:

labels = []
batch_size = 32
tensor_generator = (model_util.resize_to_model_input(model)(Image.open(BytesIO(urllib.urlopen(url).read()))) for url in urls)
output = model.predict_generator(tensor_generator, batch_size = batch_size, num_workers=4, no_batches = len(urls) / batch_size)

for out_t in output:
    labels = np.stack(labels, np.argmax(out_t, axis=1))

We are handling de-batching implicitly when doing stacking of the labels from different batches. This code will spin up 4 workers that will read from the tensor_generator and prepare the next batch in the background at the same time as the heavy lifting of prediction is handled by GPU. So is that good enough? Not really. Rememeber our problem 1) - what if there is an exception in the pre-processing / url is missing etc? By default the entire script will come to a halt at that point. We could filter out the missing urls by passing an exception-handling function into the generator, but filtering out bad values will ruin the mapping from url to label, rendering values after exception just as useless as if the script were to stop.

The least ugly solution using Keras is to add another input to the model, so that model applies to a key:tensor value; and then after prediction sort out which ones were successfull. But this process really doesn't have to be that complicated.

Studio provides primitives that make this job (that is conceptually very simple) simple in code; and similar in usage to Keras. The code above becomes (see unit test ModelPipeTest.test_model_pipe_mnist_urls in studio/tests/model_util_test.py)

pipe = model_util.ModelPipe()
pipe.add(lambda url: urllib.urlopen(url).read(), num_workers=4, timeout=5)
pipe.add(lambda img: Image.open(BytesIO(img)))
pipe.add(model_util.resize_to_model_input(model))
pipe.add(lambda x: 1-x)
pipe.add(model, num_workers=1, batch_size=32, batcher=np.vstack)
pipe.add(lambda x: np.argmax(x, axis=1))

output_dict = pipe({url:url for url in urls})

This runs the preprocessing logic (getting the url, converting it to an image, resizing the image, and convering to a tensor) using 4 workers that populate the queue. The prediction is run using 1 worker with batch size 32 using the same queue as input. Conversion of class probabilities to class labels is also now a part of the model pipeline. In this example the input is a dictionary mapping url to url. The functions will be applied only to the values, so the output will become url: label. The pipeline can also be applied to lists, generators and sets, in which case it returns the same type of collection (if the input was list, it returns list etc) with tuples (index, label) If any step of the preprocessing raises an exception, it is caught, and corresponding output is filtered out. We are using additional function lambda x: 1-x because in the mnist dataset the digits are white on black background, whereas in the test urls digits are black on white background.

The timeout parameter controls how long the workers wait if the queue is empty (e.g. when urls take too long to fetch). Note that this also means that the call pipe() will not return for a number of seconds specified by the last (closest to output) timeout value.

Note that pipe.add() calls that don't specify a number of workers, timeout, batch_size, or batcher (function to assemble list of values into a batch digestable by a function that operates on batches) are composed with the function in previous calls to pipe.add() directly, so that there is no unnecessary queues / buffers / workers.

Benchmark

For a benchmark, we use StyleNet inference on a dataset of 7k urls, some of which are missing / broken. The benchmark is being run using EC2 p2.xlarge instances (with nVidia Tesla K80 gpus). The one-by-one experiment is running inference one image at a time, pipe is using model pipe primitives as described above. Batch size is number of images being processed as a single call to model.predict, and workers is number of prefetching workers

Experiment Time (s) Time per url (s)
One-by-one 6994 ~ 0.98
Pipe (batch 64, workers 4) 1581 ~ 0.22
Pipe (batch 128, workers 32) 157 ~ 0.02