selectio

Selectio: Multi-Model Feature Importance Scoring and Auto Feature Selection.

This Python package provides multiple feature importance scores and automatically suggests a feature selection based on the majority vote of all models.

Models

Currently the following models for feature importance scoring are included:

• Spearman rank analysis (see 'selectio.models.spearman')
• Correlation coefficient significance of linear/log-scaled Bayesian Linear Regression (see 'selectio.models.blr')
• Random Forest Permutation test (see 'selectio.models.rf')
• Random Decision Trees on various subsamples of data (see 'selectio.models.rdt')
• Mutual Information Regression (see 'selectio.models.mi')
• General correlation coefficients (see 'selectio.models.xicor')

Feature Importance Scores and Cross-Correlations

The current feature importance models support numerical data only. Categorical data will need to be encoded to numerical features beforehand.

All model scores are normalized to unity, i.e., $\sum i^{N{features}} score_i = 1$

This package includes multiple functions for visualisation of the importance scores and automatic feature ranking.

Feature-to-feature correlations are automatically clustered using hierarchical clustering of the Spearman correlation coefficients (for more details see utils.plot_feature_correlation_spearman).

Installation

pip install selectio

or for development in a conda environment:

conda env update --file environment.yaml
conda activate selectio

Requirements

• numpy
• pandas
• scikit-learn
• scipy
• matplotlib
• pyyaml

See file environment.yaml for more details.

Usage

There are multiple options to compute feature selection scores

Option 1)

with a settings yaml file (template provided) that includes all processing and plotting functionality, e.g:

from selectio import selectio
# Read in data from file, generate feature importance plots and save results as csv:
selectio.main('settings_featureimportance.yaml')

This will automatically save all scores and selections in csv file and create multiple score plots.

Option 2)

computed directly using the class selectio.Fsel, e.g.

from selectio.selectio import Fsel
# Read in data X (nsample, nfeatures) and y (nsample)
fsel = Fsel(X, y)
# Score features and return results as dataframe:
dfres = fsel.score_models()

This returns a table with all scores and feature selections. See for more details and visualisation of scores "Option 2)" in the example notebook feature_selection.ipynb.

Option 3)

as standalone script with a settings file:

cd selectio
python selectio.py -s <FILENAME>.yaml

User settings such as input/output paths and all other options are set in the settings file (Default filename: settings_featureimportance.yaml) Alternatively, the settings file can be specified as a command line argument with: '-s', or '--settings' followed by PATH-TO-FILE/FILENAME.yaml (e.g. python selectio.py -s settings/settings_featureimportance.yaml).

Settings YAML file

For settings file template, see here

The main settings are:

# Input data path:
inpath: ...
# File name with soil data and corresponding covariates:
infname: ...
# Output results path:
outpath: ...
# Name of target for prediction (column name in dataframe):
name_target: ...
# Name or List of features (column names in infname):
# (covariates to be considered )
name_features: 
- ...
- ...

Simulation and Testing

The selectio package provides the option to generate simulated data (see selectio.simdata) and includes multiple test functions (see selectio.tests), e.g.

from selectio import tests
tests.test_select()

For more examples and how to create simulated via simdata.py, see the provided Jupyter notebooks feature_selection.ipynb.

Adding Custom Model Extensions

More models for feature scoring can be added in the folder 'models' following the existing scripts as example, which includes at least:

• a function with name 'factor_importance' that takes X and y as argument and one optional argument norm
• a __name__ and __fullname__ attribute
• adding the new module name to the __init_file__.py file in the folder models

Other models for feature selections have been considered, such as PCA or SVD-based methods or univariate screening methods (t-test, correlation, etc.). However, some of these models consider either only linear relationships, or do not take into account the potential multivariate nature of the data structure (e.g., higher order interaction between variables). Note that not all included models are completely generalizable, such as Bayesian regression and Spearman ranking given their dependence on monotonic functional behavior.

Since most models have some limitations or rely on certain data assumptions, it is important to consider a variety of techniques for feature selection and to apply model cross-validations.

License

LGPL-3.0 License

Copyright (c) 2022 Sebastian Haan