dryml 0.2.0

Don't Repeat Yourself Machine Learning: A Machine Learning library to reduce code duplication, and increase portability and interoperability in the Machine Learning Space.

DRYML

Don't Repeat Yourself Machine Learning: A Machine Learning library to reduce code duplication, automate testing, perform hyper paramter searches, and ease model serialization.

DRYML aims to empower the Machine Learning practitioner to spend less time writing boilerplate code, and more time implementing new techniques. DRYML provides a model serialization framework along with serialization implementation for many common ML frameworks and model types, a framework for defining and training models on a specific problem, and a system to compare models from different ML frameworks on the same footing.

DRYML Programming Philosophy

Easy Object Serialization

All DRYML Objects can be uniquely identified, and serialized to disk. Once saved, you can load Objects directly from disk without having to first build a holding object as originally constructed. This allows for instance, Neural Net objects to be initialized with the correct parameters before loading the model weights without user intervention. Loading an Object consists of a single command load_object. Basic save/load logic is available for some major ML platforms, but the user is able and encouraged to implement new Objects with custom save/load methods and so is extendable to any ML system.

Reuse Model Components

DRYML borrows from the Entity Component System programming pattern, and many Model types are created from components which are attached to the model, and can be reused. These can include training procedure, optimization algorithm, loss function, and the underlying NN model itself. This compartmentalization allows us to enable hyperparameter searches over nearly any parameter of your ML algorithm from the NN topology, from the optimizer learning rate, to the training procedure. It also allows the user to define a complex training procedure once, and then reuse it for multiple related problems in the future. DRYML also has defined training procedures for some common ML frameworks.

Compare Models Between Frameworks

Many ML Problems can be tackled by different ML Frameworks. DRYML's API places all supported Frameworks on equal footing. All models output data in the form of DRYML Datasets. This means metrics on Datasets can be reused for models in different frameworks and models from different frameworks can be compared directly, allowing the ML practictioner to make decisions about which method is best for their problem. Models can also be easily chained together

Allow Frameworks to work together

Modern ML frameworks such as tensorflow and pytorch are greedy about GPU use. DRYML implements a context system to enforce constraints on these frameworks when possible. The context system also provides a resource request API to allow the user to request the types of resources each framework is allowed to use. This allows elements from multiple frameworks to co-exist within the same data pipeline. For example, we can use a pytorch dataset and preprocessing with a tensorflow machine learning model.

Bringing ML Frameworks together

The following ML Frameworks are currently supported, or planned to be supported

• Tensorflow (Initial support complete)
• Pytorch (Initial support complete)
• Sklearn (Initial support complete)
• XGBoost (Initial support complete)
• Statsmodels (support planned)

DRYML Major Components

DRYML Object and ObjectDef

The DRYML API provides the Object class which automatically implements all basic machinery for automatic object serialization. Any class you create which you want to serialize must inherit from the Object class. Here's a simple example:

>>> from dryml import Object
>>> class Data(Object):
...     def __init__(self, data):
...         pass
... 
>>> data_obj = Data([1, 2, 3, 4, 5])
>>> data_obj.dry_args
([1, 2, 3, 4, 5],)
>>> data_obj.dry_kwargs
{'dry_id': 'e18d670c-b3b8-41b3-a941-3c2f7bf0b11e'}

We can see that Object gives the new Data class some extra powers! It remembers the arguments used to create it, and it receives a unique identifier (if you don't specify it yourself!). data_obj can also be easily serialized to disk with the save_self member method or save_object global method. Let's see that here:

>>> from dryml import save_object, load_object
>>> save_object(data_obj, 'test.dry')
True
>>> new_obj = load_object('test.dry')
>>> new_obj
{'cls': <class '__main__.Data'>, 'dry_mut': False, 'dry_args': ([1, 2, 3, 4, 5],), 'dry_kwargs': {'dry_id': 'e18d670c-b3b8-41b3-a941-3c2f7bf0b11e'}}

Now, why not just use pickle or dill? There is one major issue with that. pickle and dill tries to save every python object contained within the object you're trying to save. This will fail if your model object contains data which isn't supported by these major serialization platforms! Tensorflow tensors for example aren't supported.

If we want to add the ability for an Object to store an internal state, we need to implement the save_object_imp and load_object_imp methods as well.

data_obj has another ability too. It has the method definition which builds an ObjectDef object matching the arguments data_obj was constructed with. Let's take a quick look at that.

>>> obj_def = data_obj.definition()
>>> obj_def
{'cls': <class '__main__.Data'>, 'dry_mut': False, 'dry_args': ([1, 2, 3, 4, 5],), 'dry_kwargs': {'dry_id': 'e18d670c-b3b8-41b3-a941-3c2f7bf0b11e'}}
>>> new_obj_2 = obj_def.build()
>>> new_obj_2
{'cls': <class '__main__.Data'>, 'dry_mut': False, 'dry_args': ([1, 2, 3, 4, 5],), 'dry_kwargs': {'dry_id': 'e18d670c-b3b8-41b3-a941-3c2f7bf0b11e'}}
>>> new_obj_2.dry_args
([1, 2, 3, 4, 5],)

So we can see that ObjectDef is a factory object creating objects matching the arguments used to initially construct data_obj!.

We can create new ObjectDefs directly and use it to create new objects with different definitions! Let's look at that here:

>>> from dryml import ObjectDef
>>> obj_def_2 = ObjectDef(Data, 3)
>>> obj_def_2
{'cls': <class '__main__.Data'>, 'dry_mut': False, 'dry_args': (3,), 'dry_kwargs': {}}
>>> test_obj_2 = obj_def_2.build()
>>> test_obj_2.dry_args
(3,)

This is great for creating copies of an object which contains internal data that is randomly initialized. We can for example, create many copies of the same neural network, train them, and see how well each network trains.

DRYML Repo and Selector

A major issue working with many machine learning models is we want to try different things, which means different models and parameters. This can get unyieldy as the variety of models we're interested in trying gets larger. DRYML introduces the Repo and Selector types to help solve this issue. Any Object can be added to a Repo, and Repos methods can be used to automate saving, loading, and application of a method across a collection of Objects. Selector is a type which can match properties of an Object. It's created similarly to ObjectDef and is a callable object. When passed an ObjectDef or Object, it indicates with a bool whether that object is compatible with the Selector. With Selector, Repo can return only those objects contained which match the Selector. Let's look at this now.

First, let's create a Repo and save a few objects.

>>> repo = Repo(directory='./test', create=True)
>>> obj_def = ObjectDef(Data, 1)
>>> obj_def
{'cls': <class '__main__.Data'>, 'dry_mut': False, 'dry_args': (1,), 'dry_kwargs': {}}
>>> for i in range(5):
...     obj = obj_def.build()
...     repo.add_object(obj)
... 
>>> obj_def_2 = ObjectDef(Data, 2)
>>> for i in range(5):
...     obj = obj_def_2.build()
...     repo.add_object(obj)
... 
>>> len(repo)
10

Do now our repo has 10 objects, 5 of each type. Let's use a Selector to grab only those Objects with a 2.

>>> repo.get(Selector(Data, obj_args=(2,)))
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: __init__() got an unexpected keyword argument 'obj_args'
>>> repo.get(Selector(Data, args=(2,)))
[{'cls': <class '__main__.Data'>, 'dry_mut': False, 'dry_args': (2,), 'dry_kwargs': {'dry_id': '99d796f9-6bc6-4341-947e-94b1b89a9ff3'}}, {'cls': <class '__main__.Data'>, 'dry_mut': False, 'dry_args': (2,), 'dry_kwargs': {'dry_id': 'b9208924-8714-448a-b280-d63eefa758a7'}}, {'cls': <class '__main__.Data'>, 'dry_mut': False, 'dry_args': (2,), 'dry_kwargs': {'dry_id': 'deb0b98b-6ec7-4a98-a98f-81cd0c9b3f3f'}}, {'cls': <class '__main__.Data'>, 'dry_mut': False, 'dry_args': (2,), 'dry_kwargs': {'dry_id': '77561cf0-bdf5-4ae0-b7d8-9b9302544cd8'}}, {'cls': <class '__main__.Data'>, 'dry_mut': False, 'dry_args': (2,), 'dry_kwargs': {'dry_id': 'c256d4c2-45d0-495a-8b67-e29f4d5e824f'}}]
>>> len(repo.get(Selector(Data, args=(2,))))
5

And now we can work with the selected models!

DRYML Dataset

The DRYML API provides the Dataset class which represents a machine learning dataset. It presents a number of useful methods for working with data, and also transformations to change datasets defined within major machine learning systems like tensorflow or pytorch into a more relevant framework or data type. We'll create a small Dataset here, and look at the unbatch, and peek methods.

>>> import numpy as np
>>> num_examples = 32
>>> data_shape = (10, 10)
>>> data = np.random.random((num_examples,)+data_shape)
>>> data.shape
(32, 10, 10)
>>> from dryml.data import NumpyDataset
>>> data_ds = NumpyDataset(data)
>>> data_ds.peek().shape
(32, 10, 10)
>>> type(data_ds.peek())
<class 'numpy.ndarray'>
>>> type(data_ds.tf().unbatch().peek())
<class 'tensorflow.python.framework.ops.EagerTensor'>
>>> data_ds.tf().peek().shape
TensorShape([32, 10, 10])
>>> data_ds.tf().unbatch().peek().shape
TensorShape([10, 10])
>>> type(data_ds.torch().peek())
<class 'torch.Tensor'>

We can also see that tf turns the Dataset into a TFDataset which is backed by a tf.data.Dataset. Thus the elements retrievable become tensorflow Tensors. Similarly, torch turns the Dataset into a TorchDataset which is backed by a torch.utils.data.IterableDataset.

DRYML Context

The DRYML API provides a context system to manage the allocation of compute devices like GPUs. It also provides a decorator dryml.context.compute_context which can be applied to any method we want to launch in a separate process with a specific set of context requirements. This allows the user to prevent code which allocates memory on a device like a GPU from running unless you explicitly allow it. Object supports this as well with the load_compute_imp and save_compute_imp methods which manage an Object's transition into and out of 'compute mode' in which an Object may allocate memory on a device. This is especially useful for situations when we may want to compare results from a tensorflow based model and a pytorch based model. We can wrap a method with compute_context and then request a context with requirements {'tf': {}} for the tensorflow model, and requirements {'torch': {}} for the pytorch model.

The user can specify the amount or even specific resources with a context requirement for example:

{
    'tf': {'gpu/1': 0.5},
    'torch': {'gpu/1': 0.5},
}

Let's look at a simple example. We'll first define a method which loads a tensorflow dataset, but first checks whether the context can support it. It then returns the first element of that dataset. Then we'll decorate that method so we can execute it in a separate process with certain contexts. We'll then try a couple contexts and see what happens!

>>> def test_method():
...     import dryml
...     import tensorflow_datasets as tfds
...     from dryml.data.tf import TFDataset
...     dryml.context.context_check({'tf': {}})
...     (test_ds,) = tfds.load(
...         'mnist',
...         split=['test'],
...         shuffle_files=True,
...         as_supervised=True)
...     test_ds = TFDataset(
...         test_ds,
...         supervised=True)
...     return test_ds.unbatch().numpy().peek()
...
>>> test_method = dryml.context.compute_context()(test_method)
>>> test_method()
Exception encountered in context thread! pid: 724396
Traceback (most recent call last):
  File "/data0/matthew/Software/NCSA/DRYML/src/dryml/context/process.py", line 34, in run
    super().run()
  File "/data0/matthew/Software/NCSA/DRYML/venv_dryml_dev/lib/python3.8/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/data0/matthew/Software/NCSA/DRYML/src/dryml/context/process.py", line 186, in __call__
    self.final_call(f, ctx_send_q, ctx_ret_q, *args, **kwargs)
  File "/data0/matthew/Software/NCSA/DRYML/src/dryml/context/process.py", line 129, in final_call
    res = f(*args, **kwargs)
  File "<stdin>", line 5, in test_method
  File "/data0/matthew/Software/NCSA/DRYML/src/dryml/context/context_tracker.py", line 420, in context_check
    raise ContextIncompatibilityError(
dryml.context.context_tracker.ContextIncompatibilityError: Context doesn't satisfy requirements {'tf': {}}

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/data0/matthew/Software/NCSA/DRYML/src/dryml/context/process.py", line 370, in wrapped_func
    raise e
dryml.context.context_tracker.ContextIncompatibilityError: Context doesn't satisfy requirements {'tf': {}}
>>> x, y = test_method(call_context_reqs={'tf': {}})
2022-10-06 15:27:33.318424: W tensorflow/core/kernels/data/cache_dataset_ops.cc:768] The calling iterator did not fully read the dataset being cached. In order to avoid unexpected truncation of the dataset, the partially cached contents of the dataset  will be discarded. This can happen if you have an input pipeline similar to `dataset.cache().take(k).repeat()`. You should use `dataset.take(k).cache().repeat()` instead.
>>> x.shape
(28, 28, 1)
>>> y.shape
()