finepix/rebate

Relief Based Algorithms in Python

Relief Based Algorithms

This suite includes stand-alone Python code to run any of the included/available Relief-Based algorithms designed for attribute filtering/ranking. These algorithms are a quick way to identify attributes in the dataset that may be most important to predicting some phenotypic endpoint. These scripts output an ordered set of attribute names, along with respective scores (uniquely determined by the particular algorithm selected). Certain algorithms require key run parameters to be specified.

MDR

This code is largely based on the Relief-Based algorithms implemented in the Multifactor Dimensionality Reduction (MDR) software. However these implementations have been expanded to accomodate continuous attributes (and continuous attributes mixed with discrete attributes) as well as a continuous endpoint. This code also accomodates missing data points. Built into this code, is a strategy to automatically detect from the loaded data, these relevant characteristics.

Cython

Portions of this code has been optimized with Cython routines.

How to run

1. Compile cython file(s) ./make.sh
2. Run rebate.py -h for all the available options
3. No Windows support as yet.

To Do

1. Make this an installable package
2. Convert to Classes
3. Create GUI Interface