mlblocks 0.3.1

Pipelines and primitives for machine learning and data science.

Pipelines and Primitives for Machine Learning and Data Science.

• Free software: MIT license
• Documentation: https://HDI-Project.github.io/MLBlocks

Overview

MLBlocks is a simple framework for composing end-to-end tunable Machine Learning Pipelines by seamlessly combining tools from any python library with a simple, common and uniform interface.

Features include:

• Build Machine Learning Pipelines combining any Machine Learning Library in Python.
• Access a repository with hundreds of primitives and pipelines ready to be used with little to no python code to write, carefully curated by Machine Learning and Domain experts.
• Extract machine-readable information about which hyperparameters can be tuned and within which ranges, allowing automated integration with Hyperparameter Optimization tools like BTB.
• Complex multi-branch pipelines and DAG configurations, with unlimited number of inputs and outputs per primitive.
• Easy save and load Pipelines using JSON Annotations.

Installation

The simplest and recommended way to install MLBlocks is using pip:

pip install mlblocks

Alternatively, you can also clone the repository and install it from sources

git clone [e-mail]:HDI-Project/MLBlocks.git
cd MLBlocks
make install

For development, you can use make install-develop instead in order to install all the required dependencies for testing and code linting.

MLPrimitives

In order to be usable, MLBlocks requires a compatible primitives library.

The official library, required in order to follow the following MLBlocks tutorial, is MLPrimitives, which you can install with this command:

pip install mlprimitives

Usage Example

Below there is a short example about how to use MLBlocks to create a simple pipeline, fit it using demo data and use it to make predictions.

Please make sure to having installed MLPrimitives before following it.

For advance usage and more detailed explanation about each component, please have a look at the documentation

Creating a pipeline

With MLBlocks, creating a pipeline is as simple as specifying a list of primitives and passing them to the MLPipeline class.

>>> from mlblocks import MLPipeline
... primitives = [
...     'cv2.GaussianBlur',
...     'skimage.feature.hog',
...     'sklearn.ensemble.RandomForestClassifier'
... ]
>>> pipeline = MLPipeline(primitives)

Optionally, specific initialization arguments can be also set by specifying them in a dictionary:

>>> init_params = {
...    'skimage.feature.hog': {
...        'multichannel': True,
...        'visualize': False
...    },
...    'sklearn.ensemble.RandomForestClassifier': {
...         'n_estimators': 100,
...    }
... }
>>> pipeline = MLPipeline(primitives, init_params=init_params)

If you can see which hyperparameters a particular pipeline is using, you can do so by calling its get_hyperparameters method:

>>> import json
>>> hyperparameters = pipeline.get_hyperparameters()
>>> print(json.dumps(hyperparameters, indent=4))
{
    "cv2.GaussianBlur#1": {
        "ksize_width": 3,
        "ksize_height": 3,
        "sigma_x": 0,
        "sigma_y": 0
    },
    "skimage.feature.hog#1": {
        "multichannel": true,
        "visualize": false,
        "orientations": 9,
        "pixels_per_cell_x": 8,
        "pixels_per_cell_y": 8,
        "cells_per_block_x": 3,
        "cells_per_block_y": 3,
        "block_norm": null
    },
    "sklearn.ensemble.RandomForestClassifier#1": {
        "n_jobs": -1,
        "n_estimators": 100,
        "criterion": "entropy",
        "max_features": null,
        "max_depth": 10,
        "min_samples_split": 0.1,
        "min_samples_leaf": 0.1,
        "class_weight": null
    }
}

Making predictions

Once we have created the pipeline with the desired hyperparameters we can fit it and then use it to make predictions on new data.

To do this, we first call the fit method passing the training data and the corresponding labels.

In this case in particular, we will be loading the handwritten digit classification dataset from USPS using the mlblocks.datasets.load_usps method, which returns a dataset object ready to be played with.

>>> from mlblocks.datasets import load_usps
>>> dataset = load_usps()
>>> X_train, X_test, y_train, y_test = dataset.get_splits(1)
>>> pipeline.fit(X_train, y_train)

Once we have fitted our model to our data, we can call the predict method passing new data to obtain predictions from the pipeline.

>>> predictions = pipeline.predict(X_test)
>>> predictions
array([3, 2, 1, ..., 1, 1, 2])

What's Next?

If you want to learn more about how to tune the pipeline hyperparameters, save and load the pipelines using JSON annotations or build complex multi-branched pipelines, please check our documentation.

History

In its first iteration in 2015, MLBlocks was designed for only multi table, multi entity temporal data. A good reference to see our design rationale at that time is Bryan Collazo’s thesis:

• Machine learning blocks. Bryan Collazo. Masters thesis, MIT EECS, 2015.

With recent availability of a multitude of libraries and tools, we decided it was time to integrate them and expand the library to address other data types: images, text, graph, time series and integrate with deep learning libraries.

Changelog

0.3.1 - Pipelines Discovery

• Support flat hyperparameter dictionaries Issue #92 by @csala
• Load pipelines by name and register them as entry_points Issue #88 by @csala
• Implement partial re-fit Issue #61 by @csala
• Move argument parsing to MLBlock Issue #86 by @csala
• Allow getting intermediate outputs Issue #58 by @csala

0.3.0 - New Primitives Discovery

• New primitives discovery system based on entry_points.
• Conditional Hyperparameters filtering in MLBlock initialization.
• Improved logging and exception reporting.

0.2.4 - New Datasets and Unit Tests

• Add a new multi-table dataset.
• Add Unit Tests up to 50% coverage.
• Improve documentation.
• Fix minor bug in newsgroups dataset.

0.2.3 - Demo Datasets

• Add new methods to Dataset class.
• Add documentation for the datasets module.

0.2.2 - MLPipeline Load/Save

• Implement save and load methods for MLPipelines
• Add more datasets

0.2.1 - New Documentation

• Add mlblocks.datasets module with demo data download functions.
• Extensive documentation, including multiple pipeline examples.

0.2.0 - New MLBlocks API

A new MLBlocks API and Primitive format.

This is a summary of the changes:

• Primitives JSONs and Python code has been moved to a different repository, called MLPrimitives
• Optional usage of multiple JSON primitive folders.
• JSON format has been changed to allow more flexibility and features:
  • input and output arguments, as well as argument types, can be specified for each method
  • both classes and function as primitives are supported
  • multitype and conditional hyperparameters fully supported
  • data modalities and primitive classifiers introduced
  • metadata such as documentation, description and author fields added
• Parsers are removed, and now the MLBlock class is responsible for loading and reading the JSON primitive.
• Multiple blocks of the same primitive are supported within the same pipeline.
• Arbitrary inputs and outputs for both pipelines and blocks are allowed.
• Shared variables during pipeline execution, usable by multiple blocks.

0.1.9 - Bugfix Release

• Disable some NetworkX functions for incompatibilities with some types of graphs.

0.1.8 - New primitives and some improvements

• Improve the NetworkX primitives.
• Add String Vectorization and Datetime Featurization primitives.
• Refactor some Keras primitives to work with single dimension y arrays and be compatible with pickle.
• Add XGBClassifier and XGBRegressor primitives.
• Add some keras.applications pretrained networks as preprocessing primitives.
• Add helper class to allow function primitives.

0.1.7 - Nested hyperparams dicts

• Support passing hyperparams as nested dicts.

0.1.6 - Text and Graph Pipelines

• Add LSTM classifier and regressor primitives.
• Add OneHotEncoder and MultiLabelEncoder primitives.
• Add several NetworkX graph featurization primitives.
• Add community.best_partition primitive.

0.1.5 - Collaborative Filtering Pipelines

• Add LightFM primitive.

0.1.4 - Image pipelines improved

• Allow passing init_params on MLPipeline creation.
• Fix bug with MLHyperparam types and Keras.
• Rename produce_params as predict_params.
• Add SingleCNN Classifier and Regressor primitives.
• Simplify and improve Trivial Predictor

0.1.3 - Multi Table pipelines improved

• Improve RandomForest primitive ranges
• Improve DFS primitive
• Add Tree Based Feature Selection primitives
• Fix bugs in TrivialPredictor
• Improved documentation

0.1.2 - Bugfix release

• Fix bug in TrivialMedianPredictor
• Fix bug in OneHotLabelEncoder

0.1.1 - Single Table pipelines improved

• New project structure and primitives for integration into MIT-TA2.
• MIT-TA2 default pipelines and single table pipelines fully working.

0.1.0

• First release on PyPI.