maxjoshua 0.4.3
Feature selection for hard voting classifier and NN sparse weight initialization.
License: Apache License 2.0
Requires Python: >=3.7

|PyPI version| |Language grade: Python| |Total alerts|

maxjoshua
=========

Feature selection for hard voting classifier and NN sparse weight
initialization.

Preface
-------

I am naming this software package in memory of my late nephew Max Joshua
Hamster (\* 2005 to † June 18, 2022).

Usage
-----

Forward Selection for Hard Voting Classifier
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Load toy data set and convert features to binary.

.. code:: py

   from sklearn.datasets import load_breast_cancer
   from sklearn.preprocessing import scale
   X = scale(load_breast_cancer().data, axis=0) > 0  # convert to binary features
   y = load_breast_cancer().target

Select binary features. Each row in the ``results`` list contains the
``n_select`` column indices of ``X``, the notice if the binary features
were negated, and the sum of absolute MCC correlation coeffcients
between the selected features.

.. code:: py

   import maxjoshua as mh
   idx, neg, rho, results = mh.binsel(
       X, y, preselect=0.8, oob_score=True, subsample=0.5, 
       n_select=5, unique=True, n_draws=100, random_state=42)

**Algorithm**. The task is to select e.g. ``n_select`` features from a
pool of many features. These features might be the prediction of binary
classifiers. The selected features are then combined into one
hard-voting classifier.

A voting classifier should have the following properties

-  each voter (a binary feature) should be highly correlated to the
   target variable
-  the selected features should be uncorrelated.

The algorithm works as follows

1. Generate multiple correlation matrices by bootstrapping. This
   includes ``corr(X_i, X_j)`` as well as ``corr(Y, X_i)`` computation.
   Also store the oob samples for evaluation.
2. For each correlation matrix do …

   a. Preselect the ``i*`` with the highest ``abs(corr(Y, X_i))``
      estimates (e.g. pick the ``n_pre=?`` highest absolute
      correlations)
   b. Slice a correlation matrix ``corr(X_i*, X_j*)`` and find the least
      correlated combination of ``n_select`` features. (see
      ```korr.mincorr`` <https://github.com/kmedian/korr/blob/master/korr/mincorr.py>`__)
   c. Compute the out-of-bag (OOB) performance (see step 1) of the
      hard-voter with the selected ``n_select=?`` features

3. Select the feature combination with the best OOB performance as final
   model.

Forward Selection for Linear Regression
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Load toy dataset.

.. code:: py

   from sklearn.preprocessing import scale
   from sklearn.datasets import fetch_california_housing
   housing = fetch_california_housing()
   X = scale(housing["data"], axis=0)
   y = scale(housing["target"])

Select real-numbered features. Each row in the ``results`` list contains
the ``n_select`` column indices of ``X``, the ridge regression
coefficents ``beta`` and the RMSE ``loss``. Warning! Please note that
the features ``X`` and the target ``y`` must be scaled because
``mh.fltsel`` uses an L2-penalty on ``beta`` coefficients, and doesn’t
used an intercept term to shift ``y``.

.. code:: py

   import maxjoshua as mh
   from sklearn.preprocessing import scale

   idx, beta, loss, results = mh.fltsel(
       scale(X), scale(y), preselect=0.8, oob_score=True, subsample=0.5, 
       n_select=5, unique=True, n_draws=100, random_state=42, l2=0.01)

Initialize Sparse NN Layer
~~~~~~~~~~~~~~~~~~~~~~~~~~

The idea is to run ``mh.fltsel`` to generate an ensemble of linear
models, and combine them in a sparse linear neural network layer, i.e.,
the number of output neurons is the ensemble size. In case of small
datasets, the sparse NN layer is non-trainable because because each
submodel was already estimated and selected with two-way data splits in
``mh.fltsel`` (see ``oob_scores`` and ``subsample``). The sparse NN
layers basically produces submodel predictions for meta model in the
next layer, i.e., a simple dense linear layer. The inputs of the sparse
NN layer must be normalized for which a layer normalization layers is
trained.

.. code:: py

   import maxjoshua as mh
   import tensorflow as tf
   import sklearn.preprocessing

   # create toy dataset
   import sklearn.datasets
   X, y = sklearn.datasets.make_regression(
       n_samples=1000, n_features=100, n_informative=20, n_targets=3)

   # feature selection
   # - always scale the inputs and targets -
   indices, values, num_in, num_out = mh.pretrain_submodels(
       sklearn.preprocessing.scale(X), 
       sklearn.preprocessing.scale(y), 
       num_out=64, n_select=3)

   # specify the model
   model = tf.keras.models.Sequential([
       # sub-models
       mh.SparseLayerAsEnsemble(
           num_in=num_in, 
           num_out=num_out, 
           sp_indices=indices, 
           sp_values=values,
           sp_trainable=False,
           norm_trainable=True,
       ),
       # meta model
       tf.keras.layers.Dense(
           units=3, use_bias=False,
           # kernel_constraint=tf.keras.constraints.NonNeg()
       ),
       # scale up
       mh.InverseTransformer(
           units=3,
           init_bias=y.mean(), 
           init_scale=y.std()
       )
   ])
   model.compile(
       optimizer=tf.keras.optimizers.Adam(
           learning_rate=3e-4, beta_1=.9, beta_2=.999, epsilon=1e-7, amsgrad=True),
       loss='mean_squared_error'
   )

   # train
   history = model.fit(X, y, epochs=3)

Appendix
--------

Installation
~~~~~~~~~~~~

The ``maxjoshua`` `git repo <http://github.com/ulf1/maxjoshua>`__ is
available as `PyPi package <https://pypi.org/project/maxjoshua>`__

.. code:: sh

   pip install maxjoshua

Install a virtual environment
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: sh

   python3.7 -m venv .venv
   source .venv/bin/activate
   pip install --upgrade pip
   pip install -r requirements.txt
   pip install -r requirements-dev.txt
   pip install -r requirements-demo.txt

(If your git repo is stored in a folder with whitespaces, then don’t use
the subfolder ``.venv``. Use an absolute path without whitespaces.)

Python commands
~~~~~~~~~~~~~~~

-  Jupyter for the examples: ``jupyter lab``
-  Check syntax:
   ``flake8 --ignore=F401 --exclude=$(grep -v '^#' .gitignore | xargs | sed -e 's/ /,/g')``
-  Run Unit Tests: ``pytest``

Publish

.. code:: sh

   pandoc README.md --from markdown --to rst -s -o README.rst
   python setup.py sdist 
   twine upload -r pypi dist/*

Clean up
~~~~~~~~

::

   find . -type f -name "*.pyc" | xargs rm
   find . -type d -name "__pycache__" | xargs rm -r
   rm -r .venv

Support
-------

Please `open an issue <https://github.com/ulf1/maxjoshua/issues/new>`__
for support.

Contributing
------------

Please contribute using `Github
Flow <https://guides.github.com/introduction/flow/>`__. Create a branch,
add commits, and `open a pull
request <https://github.com/ulf1/maxjoshua/compare/>`__.

.. |PyPI version| image:: https://badge.fury.io/py/maxjoshua.svg
   :target: https://badge.fury.io/py/maxjoshua
.. |Language grade: Python| image:: https://img.shields.io/lgtm/grade/python/g/ulf1/maxjoshua.svg?logo=lgtm&logoWidth=18
   :target: https://lgtm.com/projects/g/ulf1/maxjoshua/context:python
.. |Total alerts| image:: https://img.shields.io/lgtm/alerts/g/ulf1/maxjoshua.svg?logo=lgtm&logoWidth=18
   :target: https://lgtm.com/projects/g/ulf1/maxjoshua/alerts/