The MCFS-ID Algorithm for Feature Selection and Interdependency Discovery

MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data. M.Draminski, A.Rada-Iglesias, S.Enroth, C.Wadelius, J. Koronacki, J.Komorowski (2008) .


*** R rmcfs ***

1.1.2 MCFS-ID works on numeric target (new classifier M5 (regression tree) is implemented in MCFS-ID) replaces value '?' by NA fix in write.arff dmLab.jar version 2.1.2
1.1.1 function info() is now showme() minor fixes 1.1.0 first official CRAN release functionality of the package is highly simplified - available 12 basic functions new names of functions: save.result()/read.result() are now export.result()/import.result(); build.ID.graph() is now build.idgraph() removed useles prefix 'mcfs.' from input params in function mcfs() function combines all functionality of:, and function mcfc() returns 'mcfs' object - one plot() function (parameter 'type') and one print() function for 'mcfs' object function build.idgraph() returns 'idgraph' object - new plot() function for 'idgraph' object function plot(type="ri") implements plot.permutations functionality - now it shows maxRI values(if 'plot_permutations' = TRUE) fixed margins in plot.idgraph() - now idgraph uses entire plot space removed curved_edges param from plot.idgraph() - curved_edges are always on plot.idgraph() has new parameter label.dist() that defines distance of labels to corresponding nodes build.idgraph() implements get.min.ID() functionality - get.min.ID() is not visible new function '' that creates artificial example many minor fixes to meet CRAN rules RD files updated by example function mcfc() has new seed parameter - now it is possible to replicate the result dmLab.jar version 2.1.0 1.0.6 function write.adx is reiplemented and now it uses a smart exporting (chunk based) for huge datasets function write.arff is reiplemented and now it uses a smart exporting (chunk based) for huge datasets function info() extended and changed - better for huge data.frames function added (colNames are cleaned from various unwanted chars e.g. "|", "#", ",") and works much faster on huge data fixed plot.distances (x axis shows correct values projections(s)) dmLab.jar version 2.0.6
1.0.5 useless parameter 'iType' is removed from plot.ID.graph function in mcfs function removed parameter 'splitSetSizeLimit' splitSetSize does the job new parameter in mcfs function 'cutoffMethod' fix of helps (mcfs, build.ID.graph, plot.ID.graph) running mcfs on one class data is not allowed function 'model.frame' replaced by faster and more stable own implementation updated and improved help *.rd files dmLab.jar version 2.0.5 1.0.4 new parameter in plot.permutations (parameter 'type') cleaning of temporary files after reading result by mcfs function dmLab.jar version 2.0.4 1.0.3 parameters u & v are available in mcfs function 1.0.2 new parameter in plot.ID.graph (curved.edges=T) refactoring: importances -> RI, interactions -> ID [plot.ID.graph, build.ID.graph, plot.RI, plot.ID] 1.0.1 new function build.rules updated help *.rd files (in mcfs introduced parameters s,t according to official papers about MCFS-ID)
1.0.0 first version of rmcfs

*** Java dmLab ***

2.1.2 regression tree M5 added - MCFS-ID works on numeric target in the case of regression task the following quality measures are calculated: "pearson","MAE","RMSE","SMAPE" (cmatrix is not calculated) distance is calculated on minimum 30 top attributes - better presentation of progress for small number of columns
adx file does not require "decision(all)" use "decision" instead (backward compatible) 2.1.1 minor fixes 2.1.0 huge source code refactoring and cleaning ADXClassifier works on nominal and numeric data (discretization is built-in now) removed useless 'discretizeData' parameter that control discretization in MCFS (never used) cleaning in Params and in all inherit classes cleaning in Classification & removed useless discretization from there removed useless parameters 'split', 'project', 'testFileName' fixed AttributesRI fixed measures projecions, freq (and changed its name to classifiers) now _RI.csv file is more readable
removed cloudgarden Layouts new seed parameter - it helps to repeat MCFS-ID results random reordering of input columns before the split - decision tree bias removed 2.0.6 huge source code refactoring and cleaning reimplementation of base Array classes and functions (Container replaced by Array, FArray, SArray) cleaning in classes Attribute, Domain (ADXDomain, SDomain, FDomain), Discretization cleaning in DiscFunctions, ExtFunctions, SelectFunctions that operate on Array/FArray/SArray Array/FArray/SArray need less memory
parameter splitSetSizeLimit removed parameter balanceClasses removed, balancing is turned off as default fix in print information parameter mcfs.topRankingMethod replaced by mcfs.cutoffMethod 2.0.4 shapiro replaced by anderson darling during permutations experiment normality of each attribute (pval) is calc as well as student_t (pval) refactoring of parameters mcfs.progressShow and mcfs.progressInterval added distlib-0.4.1-bin.jar fix in main panel set inputFiles as well as inputFileName
2.0.3 final rules are created on full data but there is cross validation result added instead as re classification of training dataset confMatrix printing change rename of result files: importances -> ri, connections -> id 2.0.2 all headers updated in source code fix in finding number of attributes to feed CV experiment (now getCutoffValues always returns 5 values) 2.0.1 mcfs works on multiple input files it runs experiments one by one on the same parameters 2.0.0 final cv is based on all determined cutoff values. Additionally [0.25,0.5,0.75] * min(cutoff) and [1.25,1.5,2]*max(cutoff) JRIP added to CV JRIP rules created on topRankingMethod(cutoff) attributes and entire input dataset attribute name in ADX can contain any character but must be quoted
minor improvements and fixes 1.9.9 Stability improvements WekaClassifier in memory mode is default - speed up for about 30% for some data and configurations New rewritten AttributesConnection
1 result from all cut off methods Contrast Attributes as permutation of originals parameter topRankingSize=projectionSize final CV experiment is added. Now you may test classification accuracy based on top ranking features. Classifiers: c4.5, nb, svm, knn, logistic regression.

    cutpoint -> cutoff experiment now it is integrated with MCFS. If cutoffPermutations=0 then 
        classic MCFS without permutation will be run.
    plenty minor changes
    graph viewer upgraded to v 2.0 now it presents directed graphs

1.9.4 new cutoff methods 1.9.3 fix in matrix saving 1.9.2 refactoring and source code cleaning confusion matrix added 1.9.1 ID grapph ignores contrast features 1.9.0 parameter useInfoGain=false replaced by useGainRatio=true new method addConnectionsDirected() parameter maxConnectionLevel replaced by maxConnectionDepth

*** Known Problems ***

    contrastAttributes functionality is not fully implemented and tested (keep mcfs.contrastAttr = false)           
XML import and export in graphViewer does not work correctly
ADXClassifier does not perform very well as it used years ago it needs review

Reference manual

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1.2.8 by Michal Draminski, a month ago

Browse source code at

Authors: Michal Draminski [aut, cre], Jacek Koronacki [aut], Julian Zubek [ctb]

Documentation:   PDF Manual  

GPL-3 license

Imports yaml, ggplot2, reshape2, dplyr, igraph

Depends on rJava

Suggests testthat, R.rsp

System requirements: Java (>= 6.0)

Imported by BASiNET.

See at CRAN