Relevance and Redundancy ranking: Code and Supplementary material
dataGenerator.zip: Synthetic data generator inspired from
NIPS: Workshop on variable and feature selection (2001), http://www.clopinet.com/isabelle/Projects/NIPS2001/
rar-mfs-master.zip: Relevance and Redundancy Framework containing overview diagram, example datasets, source code and metadata. Details on installing and running are provided below.
Background. Feature ranking is benfiecial to gain knowledge and to identify the relevant features from a high-dimensional dataset. However, in several datasets, few features by themselves might have small correlation with the target classes, but by combining these features with some other features, they can be strongly correlated with the target. This means that multiple features exhibit interactions among themselves. It is necessary to rank the features based on these interactions for better analysis and classifier performance. However, evaluating these interactions on large datasets is computationally challenging. Furthermore, datasets often have features with redundant information. Using such redundant features hinders both efficiency and generalization capability of the classifier. The major challenge is to efficiently rank the features based on relevance and redundancy on mixed datasets. In the related publication, we propose a filter-based framework based on Relevance and Redundancy (RaR), RaR computes a single score that quantifies the feature relevance by considering interactions between features and redundancy. The top ranked features of RaR are characterized by maximum relevance and non-redundancy. The evaluation on synthetic and real world datasets demonstrates that our approach outperforms several state of-the-art feature selection techniques.
# Relevance and Redundancy Framework (rar-mfs) [![Build Status](https://travis-ci.org/tmbo/rar-mfs.svg?branch=master)](https://travis-ci.org/tmbo/rar-mfs)
rar-mfs is an algorithm for feature selection and can be employed to select features from labelled data sets.
The Relevance and Redundancy Framework (RaR), which is the theory behind the implementation, is a novel feature selection algorithm that
- works on large data sets (polynomial runtime),
- can handle differently typed features (e.g. nominal features and continuous features), and
- handles multivariate correlations.
The tool is written in scala and uses the weka framework to load and handle data sets. You can either run it independently providing the data as an `.arff` or `.csv` file or you can include the algorithm as a (maven / ivy) dependency in your project. As an example data set we use [heart-c](http://www.cs.umb.edu/~rickb/files/UCI/heart-c.arff).
### Project dependency
The project is published to maven central ([link](http://search.maven.org/#search|ga|1|a:"rar-mfs")). To depend on the project use:
libraryDependencies += "de.hpi.kddm" %% "rar-mfs" % "1.0.2"
To run the algorithm use
val dataSet = de.hpi.kddm.rar.Runner.loadCSVDataSet(new File("heart-c.csv", isNormalized = false, "")
val algorithm = new RaRSearch(
HicsContrastPramsFA(numIterations = config.samples, maxRetries = 1, alphaFixed = config.alpha, maxInstances = 1000),
RaRParamsFixed(k = 5, numberOfMonteCarlosFixed = 5000, parallelismFactor = 4))
### Command line tool
- EITHER download the prebuild binary which requires only an installation of a recent java version (>= 6)
1. download the prebuild jar from the releases tab ([latest](https://github.com/tmbo/rar-mfs/releases/download/v1.0.2/rar-mfs-1.0.2.jar))
2. run `java -jar rar-mfs-1.0.2.jar--help`
Using the prebuild jar, here is an example usage:
rar-mfs > java -jar rar-mfs-1.0.2.jar arff --samples 100 --subsetSize 5 --nonorm heart-c.arff
1 - age (12)
2 - sex (8)
3 - cp (11)
- OR build the repository on your own:
1. make sure [sbt](http://www.scala-sbt.org/) is installed
2. clone repository
3. run `sbt run`
Simple example using sbt directly after cloning the repository:
rar-mfs > sbt "run arff --samples 100 --subsetSize 5 --nonorm heart-c.arff"
1 - age (12)
2 - sex (8)
3 - cp (11)
To speed up the algorithm, consider using a fast solver such as Gurobi (http://www.gurobi.com/). Install the solver and put the provided `gurobi.jar` into the java classpath.
Abstract overview of the different steps of the proposed feature selection algorithm:
The Relevance and Redundancy ranking framework (RaR) is a method able to handle large scale data sets and data sets with mixed features. Instead of directly selecting a subset, a feature ranking gives a more detailed overview into the relevance of the features.
The method consists of a multistep approach where we
1. repeatedly sample subsets from the whole feature space and examine their relevance and redundancy: exploration of the search space to gather more and more knowledge about the relevance and redundancy of features
2. decude scores for features based on the scores of the subsets
3. create the best possible ranking given the sampled insights.
| Parameter | Default value | Description |
| ---------- | ------------- | ------------|
| *m* - contrast iterations | 100 | Number of different slices to evaluate while comparing marginal and conditional probabilities |
| *alpha* - subspace slice size | 0.01 | Percentage of all instances to use as part of a slice which is used to compare distributions |
| *n* - sampling itertations | 1000 | Number of different subsets to select in the sampling phase|
| *k* - sample set size | 5 | Maximum size of the subsets to be selected in the sampling phase|