combo 0.1.3
A Python Toolbox for Machine Learning Model Combination
Keywords: ensemble learning,model combination,outlier ensembles,data mining,machine learning,clustering,python

combo: A Python Toolbox for Machine Learning Model Combination
==============================================================


**Deployment & Documentation & Stats**

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----


**Build Status & Coverage & Maintainability & License**

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----


**combo** is a comprehensive Python toolbox for **combining machine learning (ML) models and scores**.
**Model combination** can be considered as a subtask of `ensemble learning <https://en.wikipedia.org/wiki/Ensemble_learning>`_,
and has been widely used in real-world tasks and data science competitions like Kaggle [#Bell2007Lessons]_.
**combo** has been used/introduced in various research works since its inception [#Raschka2020Machine]_ [#Zhao2019PyOD]_.

**combo** library supports the combination of models and score from
key ML libraries such as `scikit-learn <https://scikit-learn.org/stable/index.html>`_,
`xgboost <https://xgboost.ai/>`_, and `LightGBM <https://github.com/microsoft/LightGBM>`_,
for crucial tasks including classification, clustering, anomaly detection.
See figure below for some representative combination approaches.

.. image:: https://raw.githubusercontent.com/yzhao062/combo/master/docs/figs/framework_demo.png
   :target: https://raw.githubusercontent.com/yzhao062/combo/master/docs/figs/framework_demo.png
   :alt: Combination Framework Demo


**combo** is featured for:

* **Unified APIs, detailed documentation, and interactive examples** across various algorithms.
* **Advanced and latest models**, such as Stacking/DCS/DES/EAC/LSCP.
* **Comprehensive coverage** for classification, clustering, anomaly detection, and raw score.
* **Optimized performance with JIT and parallelization** when possible, using `numba <https://github.com/numba/numba>`_ and `joblib <https://github.com/joblib/joblib>`_.


**API Demo**\ :

.. code-block:: python


   from combo.models.classifier_stacking import Stacking
   # initialize a group of base classifiers
   classifiers = [DecisionTreeClassifier(), LogisticRegression(),
                  KNeighborsClassifier(), RandomForestClassifier(),
                  GradientBoostingClassifier()]

   clf = Stacking(base_estimators=classifiers) # initialize a Stacking model
   clf.fit(X_train, y_train) # fit the model

   # predict on unseen data
   y_test_labels = clf.predict(X_test)  # label prediction
   y_test_proba = clf.predict_proba(X_test)  # probability prediction


**Citing combo**\ :

`combo paper <http://www.andrew.cmu.edu/user/yuezhao2/papers/20-aaai-combo.pdf>`_ is published in
`AAAI 2020 <https://aaai.org/Conferences/AAAI-20/>`_ (demo track).
If you use combo in a scientific publication, we would appreciate citations to the following paper::

    @inproceedings{zhao2020combo,
      title={Combining Machine Learning Models and Scores using combo library},
      author={Zhao, Yue and Wang, Xuejian and Cheng, Cheng and Ding, Xueying},
      booktitle={Thirty-Fourth AAAI Conference on Artificial Intelligence},
      month = {Feb},
      year={2020},
      address = {New York, USA}
    }

or::

    Zhao, Y., Wang, X., Cheng, C. and Ding, X., 2020. Combining Machine Learning Models and Scores using combo library. Thirty-Fourth AAAI Conference on Artificial Intelligence.


**Key Links and Resources**\ :


* `awesome-ensemble-learning <https://github.com/yzhao062/awesome-ensemble-learning>`_ (ensemble learning related books, papers, and more)
* `View the latest codes on Github <https://github.com/yzhao062/combo>`_
* `View the documentation & API <https://pycombo.readthedocs.io/>`_
* `View all examples <https://github.com/yzhao062/combo/tree/master/examples>`_
* `View the demo video for AAAI 2020 <https://youtu.be/PaSJ49Ij7w4>`_
* `Execute Interactive Jupyter Notebooks <https://mybinder.org/v2/gh/yzhao062/combo/master>`_


**Table of Contents**\ :


* `Installation <#installation>`_
* `API Cheatsheet & Reference <#api-cheatsheet--reference>`_
* `Implemented Algorithms <#implemented-algorithms>`_
* `Example 1: Classifier Combination with Stacking/DCS/DES <#example-of-stackingdcsdes>`_
* `Example 2: Simple Classifier Combination <#example-of-classifier-combination>`_
* `Example 3: Clustering Combination <#example-of-clustering-combination>`_
* `Example 4: Outlier Detector Combination <#example-of-outlier-detector-combination>`_
* `Development Status <#development-status>`_
* `Inclusion Criteria <#inclusion-criteria>`_


----


Installation
^^^^^^^^^^^^

It is recommended to use **pip** for installation. Please make sure
**the latest version** is installed, as combo is updated frequently:

.. code-block:: bash

   pip install combo            # normal install
   pip install --upgrade combo  # or update if needed
   pip install --pre combo      # or include pre-release version for new features

Alternatively, you could clone and run setup.py file:

.. code-block:: bash

   git clone https://github.com/yzhao062/combo.git
   cd combo
   pip install .


**Required Dependencies**\ :


* Python 3.5, 3.6, or 3.7
* joblib
* matplotlib (**optional for running examples**)
* numpy>=1.13
* numba>=0.35
* pyod
* scipy>=0.19.1
* scikit_learn>=0.20


**Note on Python 2**\ :
The maintenance of Python 2.7 will be stopped by January 1, 2020 (see `official announcement <https://github.com/python/devguide/pull/344>`_).
To be consistent with the Python change and combo's dependent libraries, e.g., scikit-learn,
**combo only supports Python 3.5+** and we encourage you to use
Python 3.5 or newer for the latest functions and bug fixes. More information can
be found at `Moving to require Python 3 <https://python3statement.org/>`_.


----


API Cheatsheet & Reference
^^^^^^^^^^^^^^^^^^^^^^^^^^

Full API Reference: (https://pycombo.readthedocs.io/en/latest/api.html).
The following APIs are consistent for most of the models
(API Cheatsheet: https://pycombo.readthedocs.io/en/latest/api_cc.html).

* **fit(X, y)**\ : Fit estimator. y is optional for unsupervised methods.
* **predict(X)**\ : Predict on a particular sample once the estimator is fitted.
* **predict_proba(X)**\ : Predict the probability of a sample belonging to each class once the estimator is fitted.
* **fit_predict(X, y)**\ : Fit estimator and predict on X. y is optional for unsupervised methods.

For raw score combination (after the score matrix is generated),
use individual methods from
`"score_comb.py" <https://github.com/yzhao062/combo/blob/master/combo/models/score_comb.py>`_ directly.
Raw score combination API: (https://pycombo.readthedocs.io/en/latest/api.html#score-combination).


----


Implemented Algorithms
^^^^^^^^^^^^^^^^^^^^^^

**combo** groups combination frameworks by tasks. General purpose methods are
fundamental ones which can be applied to various tasks.

===================  ======================================================================================================  =====  ===========================================
Task                 Algorithm                                                                                               Year   Ref
===================  ======================================================================================================  =====  ===========================================
General Purpose      Average & Weighted Average: average across all scores/prediction results, maybe with weights            N/A    [#Zhou2012Ensemble]_
General Purpose      Maximization: simple combination by taking the maximum scores                                           N/A    [#Zhou2012Ensemble]_
General Purpose      Median: take the median value across all scores/prediction results                                      N/A    [#Zhou2012Ensemble]_
General Purpose      Majority Vote & Weighted Majority Vote                                                                  N/A    [#Zhou2012Ensemble]_
Classification       SimpleClassifierAggregator: combining classifiers by general purpose methods above                      N/A    N/A
Classification       DCS: Dynamic Classifier Selection (Combination of multiple classifiers using local accuracy estimates)  1997   [#Woods1997Combination]_
Classification       DES: Dynamic Ensemble Selection (From dynamic classifier selection to dynamic ensemble selection)       2008   [#Ko2008From]_
Classification       Stacking (meta ensembling): use a meta learner to learn the base classifier results                     N/A    [#Gorman2016Kaggle]_
Clustering           Clusterer Ensemble: combine the results of multiple clustering results by relabeling                    2006   [#Zhou2006Clusterer]_
Clustering           Combining multiple clusterings using evidence accumulation (EAC)                                        2002   [#Fred2005Combining]_
Anomaly Detection    SimpleDetectorCombination: combining outlier detectors by general purpose methods above                 N/A    [#Aggarwal2017Outlier]_
Anomaly Detection    Average of Maximum (AOM): divide base detectors into subgroups to take the maximum, and then average    2015   [#Aggarwal2015Theoretical]_
Anomaly Detection    Maximum of Average (MOA): divide base detectors into subgroups to take the average, and then maximize   2015   [#Aggarwal2015Theoretical]_
Anomaly Detection    XGBOD: a semi-supervised combination framework for outlier detection                                    2018   [#Zhao2018XGBOD]_
Anomaly Detection    Locally Selective Combination (LSCP)                                                                    2019   [#Zhao2019LSCP]_
===================  ======================================================================================================  =====  ===========================================


**The comparison among selected implemented models** is made available below
(\ `Figure <https://raw.githubusercontent.com/yzhao062/combo/master/examples/compare_selected_classifiers.png>`_\ ,
`compare_selected_classifiers.py <https://github.com/yzhao062/combo/blob/master/examples/compare_selected_classifiers.py>`_\, `Interactive Jupyter Notebooks <https://mybinder.org/v2/gh/yzhao062/combo/master>`_\ ).
For Jupyter Notebooks, please navigate to **"/notebooks/compare_selected_classifiers.ipynb"**.


.. image:: https://raw.githubusercontent.com/yzhao062/combo/master/examples/compare_selected_classifiers.png
   :target: https://raw.githubusercontent.com/yzhao062/combo/master/examples/compare_selected_classifiers.png
   :alt: Comparison of Selected Models


----


**All implemented modes** are associated with examples, check
`"combo examples" <https://github.com/yzhao062/combo/blob/master/examples>`_
for more information.


Example of Stacking/DCS/DES
^^^^^^^^^^^^^^^^^^^^^^^^^^^


`"examples/classifier_stacking_example.py" <https://github.com/yzhao062/combo/blob/master/examples/classifier_stacking_example.py>`_
demonstrates the basic API of stacking (meta ensembling). `"examples/classifier_dcs_la_example.py" <https://github.com/yzhao062/combo/blob/master/examples/classifier_dcs_la_example.py>`_
demonstrates the basic API of Dynamic Classifier Selection by Local Accuracy. `"examples/classifier_des_la_example.py" <https://github.com/yzhao062/combo/blob/master/examples/classifier_des_la_example.py>`_
demonstrates the basic API of Dynamic Ensemble Selection by Local Accuracy.

It is noted **the basic API is consistent across all these models**.


#. Initialize a group of classifiers as base estimators

   .. code-block:: python


      # initialize a group of classifiers
      classifiers = [DecisionTreeClassifier(random_state=random_state),
                     LogisticRegression(random_state=random_state),
                     KNeighborsClassifier(),
                     RandomForestClassifier(random_state=random_state),
                     GradientBoostingClassifier(random_state=random_state)]


#. Initialize, fit, predict, and evaluate with Stacking

   .. code-block:: python


      from combo.models.classifier_stacking import Stacking

      clf = Stacking(base_estimators=classifiers, n_folds=4, shuffle_data=False,
                   keep_original=True, use_proba=False, random_state=random_state)

      clf.fit(X_train, y_train)
      y_test_predict = clf.predict(X_test)
      evaluate_print('Stacking | ', y_test, y_test_predict)


#. See a sample output of classifier_stacking_example.py

   .. code-block:: bash


      Decision Tree        | Accuracy:0.9386, ROC:0.9383, F1:0.9521
      Logistic Regression  | Accuracy:0.9649, ROC:0.9615, F1:0.973
      K Neighbors          | Accuracy:0.9561, ROC:0.9519, F1:0.9662
      Gradient Boosting    | Accuracy:0.9605, ROC:0.9524, F1:0.9699
      Random Forest        | Accuracy:0.9605, ROC:0.961, F1:0.9693

      Stacking             | Accuracy:0.9868, ROC:0.9841, F1:0.9899


----


Example of Classifier Combination
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^


`"examples/classifier_comb_example.py" <https://github.com/yzhao062/combo/blob/master/examples/classifier_comb_example.py>`_
demonstrates the basic API of predicting with multiple classifiers. **It is noted that the API across all other algorithms are consistent/similar**.

#. Initialize a group of classifiers as base estimators

   .. code-block:: python


      # initialize a group of classifiers
      classifiers = [DecisionTreeClassifier(random_state=random_state),
                     LogisticRegression(random_state=random_state),
                     KNeighborsClassifier(),
                     RandomForestClassifier(random_state=random_state),
                     GradientBoostingClassifier(random_state=random_state)]


#. Initialize, fit, predict, and evaluate with a simple aggregator (average)

   .. code-block:: python


      from combo.models.classifier_comb import SimpleClassifierAggregator

      clf = SimpleClassifierAggregator(classifiers, method='average')
      clf.fit(X_train, y_train)
      y_test_predicted = clf.predict(X_test)
      evaluate_print('Combination by avg   |', y_test, y_test_predicted)



#. See a sample output of classifier_comb_example.py

   .. code-block:: bash


      Decision Tree        | Accuracy:0.9386, ROC:0.9383, F1:0.9521
      Logistic Regression  | Accuracy:0.9649, ROC:0.9615, F1:0.973
      K Neighbors          | Accuracy:0.9561, ROC:0.9519, F1:0.9662
      Gradient Boosting    | Accuracy:0.9605, ROC:0.9524, F1:0.9699
      Random Forest        | Accuracy:0.9605, ROC:0.961, F1:0.9693

      Combination by avg   | Accuracy:0.9693, ROC:0.9677, F1:0.9763
      Combination by w_avg | Accuracy:0.9781, ROC:0.9716, F1:0.9833
      Combination by max   | Accuracy:0.9518, ROC:0.9312, F1:0.9642
      Combination by w_vote| Accuracy:0.9649, ROC:0.9644, F1:0.9728
      Combination by median| Accuracy:0.9693, ROC:0.9677, F1:0.9763


----


Example of Clustering Combination
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^


`"examples/cluster_comb_example.py" <https://github.com/yzhao062/combo/blob/master/examples/cluster_comb_example.py>`_
demonstrates the basic API of combining multiple base clustering estimators. `"examples/cluster_eac_example.py" <https://github.com/yzhao062/combo/blob/master/examples/cluster_eac_example.py>`_
demonstrates the basic API of Combining multiple clusterings using evidence accumulation (EAC).

#. Initialize a group of clustering methods as base estimators

   .. code-block:: python


      # Initialize a set of estimators
      estimators = [KMeans(n_clusters=n_clusters),
                    MiniBatchKMeans(n_clusters=n_clusters),
                    AgglomerativeClustering(n_clusters=n_clusters)]


#. Initialize a Clusterer Ensemble class and fit the model

   .. code-block:: python


      from combo.models.cluster_comb import ClustererEnsemble
      # combine by Clusterer Ensemble
      clf = ClustererEnsemble(estimators, n_clusters=n_clusters)
      clf.fit(X)


#. Get the aligned results

   .. code-block:: python


      # generate the labels on X
      aligned_labels = clf.aligned_labels_
      predicted_labels = clf.labels_



Example of Outlier Detector Combination
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^


`"examples/detector_comb_example.py" <https://github.com/yzhao062/combo/blob/master/examples/detector_comb_example.py>`_
demonstrates the basic API of combining multiple base outlier detectors.

#. Initialize a group of outlier detection methods as base estimators

   .. code-block:: python


      # Initialize a set of estimators
      detectors = [KNN(), LOF(), OCSVM()]


#. Initialize a simple averaging aggregator, fit the model, and make
   the prediction.

   .. code-block:: python


      from combo.models.detector combination import SimpleDetectorAggregator
      clf = SimpleDetectorAggregator(base_estimators=detectors)
      clf_name = 'Aggregation by Averaging'
      clf.fit(X_train)

      y_train_pred = clf.labels_  # binary labels (0: inliers, 1: outliers)
      y_train_scores = clf.decision_scores_  # raw outlier scores

      # get the prediction on the test data
      y_test_pred = clf.predict(X_test)  # outlier labels (0 or 1)
      y_test_scores = clf.decision_function(X_test)  # outlier scores


#. Evaluate the prediction using ROC and Precision @ Rank n.

   .. code-block:: python

      # evaluate and print the results
      print("\nOn Training Data:")
      evaluate_print(clf_name, y_train, y_train_scores)
      print("\nOn Test Data:")
      evaluate_print(clf_name, y_test, y_test_scores)

#. See sample outputs on both training and test data.

   .. code-block:: bash

      On Training Data:
      Aggregation by Averaging ROC:0.9994, precision @ rank n:0.95

      On Test Data:
      Aggregation by Averaging ROC:1.0, precision @ rank n:1.0


----


Development Status
^^^^^^^^^^^^^^^^^^

**combo** is currently **under development** as of Feb, 2020. A concrete plan has
been laid out and will be implemented in the next few months.

Similar to other libraries built by us, e.g., Python Outlier Detection Toolbox
(`pyod <https://github.com/yzhao062/pyod>`_),
**combo** is also targeted to be published in *Journal of Machine Learning Research (JMLR)*,
`open-source software track <http://www.jmlr.org/mloss/>`_. A demo paper has been presented in
*AAAI 2020* for progress update.

**Watch & Star** to get the latest update! Also feel free to send me an email (zhaoy@cmu.edu)
for suggestions and ideas.


----


Inclusion Criteria
^^^^^^^^^^^^^^^^^^

Similarly to scikit-learn, We mainly consider well-established algorithms for inclusion.
A rule of thumb is at least two years since publication, 50+ citations, and usefulness.

However, we encourage the author(s) of newly proposed models to share and add your implementation into combo
for boosting ML accessibility and reproducibility.
This exception only applies if you could commit to the maintenance of your model for at least two year period.


----


Reference
^^^^^^^^^

.. [#Aggarwal2015Theoretical] Aggarwal, C.C. and Sathe, S., 2015. Theoretical foundations and algorithms for outlier ensembles. *ACM SIGKDD Explorations Newsletter*, 17(1), pp.24-47.

.. [#Aggarwal2017Outlier] Aggarwal, C.C. and Sathe, S., 2017. Outlier ensembles: An introduction. Springer.

.. [#Bell2007Lessons] Bell, R.M. and Koren, Y., 2007. Lessons from the Netflix prize challenge. *SIGKDD Explorations*, 9(2), pp.75-79.

.. [#Gorman2016Kaggle] Gorman, B. (2016). A Kaggler's Guide to Model Stacking in Practice. [online] The Official Blog of Kaggle.com. Available at: http://blog.kaggle.com/2016/12/27/a-kagglers-guide-to-model-stacking-in-practice [Accessed 26 Jul. 2019].

.. [#Ko2008From] Ko, A.H., Sabourin, R. and Britto Jr, A.S., 2008. From dynamic classifier selection to dynamic ensemble selection. *Pattern recognition*, 41(5), pp.1718-1731.

.. [#Fred2005Combining] Fred, A. L. N., & Jain, A. K. (2005). Combining multiple clusterings using evidence accumulation. *IEEE Transactions on Pattern Analysis and Machine Intelligence*, 27(6), 835–850. https://doi.org/10.1109/TPAMI.2005.113

.. [#Raschka2020Machine] Raschka, S., Patterson, J. and Nolet, C., 2020. Machine Learning in Python: Main developments and technology trends in data science, machine learning, and artificial intelligence. arXiv preprint arXiv:2002.04803.

.. [#Woods1997Combination] Woods, K., Kegelmeyer, W.P. and Bowyer, K., 1997. Combination of multiple classifiers using local accuracy estimates. *IEEE transactions on pattern analysis and machine intelligence*, 19(4), pp.405-410.

.. [#Zhao2018XGBOD] Zhao, Y. and Hryniewicki, M.K. XGBOD: Improving Supervised Outlier Detection with Unsupervised Representation Learning. *IEEE International Joint Conference on Neural Networks*, 2018.

.. [#Zhao2019LSCP] Zhao, Y., Nasrullah, Z., Hryniewicki, M.K. and Li, Z., 2019, May. LSCP: Locally selective combination in parallel outlier ensembles. In *Proceedings of the 2019 SIAM International Conference on Data Mining (SDM)*, pp. 585-593. Society for Industrial and Applied Mathematics.

.. [#Zhao2019PyOD] Zhao, Y., Nasrullah, Z. and Li, Z., 2019. PyOD: A Python Toolbox for Scalable Outlier Detection. *Journal of Machine Learning Research*, 20, pp.1-7.

.. [#Zhou2006Clusterer] Zhou, Z.H. and Tang, W., 2006. Clusterer ensemble. *Knowledge-Based Systems*, 19(1), pp.77-83.

.. [#Zhou2012Ensemble] Zhou, Z.H., 2012. Ensemble methods: foundations and algorithms. Chapman and Hall/CRC.