Comments (18)
random forests have been used for gene sequencing classification. you can find
those refs. online.
if you can represent your input data as a matrix and targets as a vector for a
supervised classification/regression framework, then refer to the tutorial
files in the package. and also take a look at variable importance
http://www.stat.berkeley.edu/~breiman/RandomForests/cc_home.htm#varimp which
gives feature importance.
Original comment by abhirana
on 1 Feb 2012 at 8:13
from randomforest-matlab.
Yes, I can represent input as a matrix. The features are the positions of
A,C,T,G in the sequence.So I need to specify categorical attributes. The input
matrix will be in the form of 1's and 0's.It represents the presence or absence
of features.For eg.
If the input sequence is ACTGCCCGTCATCCC, then the matrix will be in the form
(1,0,1), (1,0,0,1),(1,0,0,0),(0,0,1,1,0) etc..
Original comment by [email protected]
on 1 Feb 2012 at 8:19
from randomforest-matlab.
yup, that would work
this package doesnot do categorical splits for the trees but splits the
features considering it as a continous value.i think, it wont affect the
results unless you have many many categories. if R works out better for you and
you need categorical splits then use this
http://cran.r-project.org/web/packages/randomForest/index.html from which i
derived the matlab package.
do tell if you have any questions.
Original comment by abhirana
on 1 Feb 2012 at 8:31
from randomforest-matlab.
Thank you for the information.this is for my pg project, and i am totally new
in classification field.And also I am new to R and i just downloaded it. Let me
go through cran.r-project.If I have queries i will post it.
Original comment by [email protected]
on 1 Feb 2012 at 8:43
from randomforest-matlab.
Is there any restriction in number of fetures?
Original comment by [email protected]
on 1 Feb 2012 at 2:41
from randomforest-matlab.
usually none. i have run datasets with upto 50k features and 1000 examples.
Original comment by abhirana
on 1 Feb 2012 at 2:48
from randomforest-matlab.
I am trying this code for my classification. I downloaded the precompiled
windows file. Then i tried to run the compile_windows.m file and got the the
following error.
I am going to use the precompiled fortran file
If it doesnt work then use cygwin+g77 (or gfortran) to recompile rfsub.f
Error
C:\USERS\RAKSHMI\DOCUME~1\MATLAB\MAINPR~1\RF_MEX~1.02-\RANDOM~1\RF_CLA~1\SRC\cla
ssRF.cpp: 83 empty declaration
Error
C:\USERS\RAKSHMI\DOCUME~1\MATLAB\MAINPR~1\RF_MEX~1.02-\RANDOM~1\RF_CLA~1\SRC\cla
ssRF.cpp: 83 syntax error; found "C" expecting `;'
Error
C:\USERS\RAKSHMI\DOCUME~1\MATLAB\MAINPR~1\RF_MEX~1.02-\RANDOM~1\RF_CLA~1\SRC\cla
ssRF.cpp: 83 unrecognized declaration
Error
C:\USERS\RAKSHMI\DOCUME~1\MATLAB\MAINPR~1\RF_MEX~1.02-\RANDOM~1\RF_CLA~1\SRC\cla
ssRF.cpp: 83 unrecognized declaration
Error
C:\USERS\RAKSHMI\DOCUME~1\MATLAB\MAINPR~1\RF_MEX~1.02-\RANDOM~1\RF_CLA~1\SRC\cla
ssRF.cpp: 100 unrecognized declaration
Error
C:\USERS\RAKSHMI\DOCUME~1\MATLAB\MAINPR~1\RF_MEX~1.02-\RANDOM~1\RF_CLA~1\SRC\cla
ssRF.cpp: 102 empty declaration
Error
C:\USERS\RAKSHMI\DOCUME~1\MATLAB\MAINPR~1\RF_MEX~1.02-\RANDOM~1\RF_CLA~1\SRC\cla
ssRF.cpp: 102 syntax error; found "C" expecting `;'
Error
C:\USERS\RAKSHMI\DOCUME~1\MATLAB\MAINPR~1\RF_MEX~1.02-\RANDOM~1\RF_CLA~1\SRC\cla
ssRF.cpp: 102 unrecognized declaration
Error
C:\USERS\RAKSHMI\DOCUME~1\MATLAB\MAINPR~1\RF_MEX~1.02-\RANDOM~1\RF_CLA~1\SRC\cla
ssRF.cpp: 102 unrecognized declaration
Error
C:\USERS\RAKSHMI\DOCUME~1\MATLAB\MAINPR~1\RF_MEX~1.02-\RANDOM~1\RF_CLA~1\SRC\cla
ssRF.cpp: 110 unrecognized declaration
Warning
C:\USERS\RAKSHMI\DOCUME~1\MATLAB\MAINPR~1\RF_MEX~1.02-\RANDOM~1\RF_CLA~1\SRC\cla
ssRF.cpp: 121 empty declaration
Warning
C:\USERS\RAKSHMI\DOCUME~1\MATLAB\MAINPR~1\RF_MEX~1.02-\RANDOM~1\RF_CLA~1\SRC\cla
ssRF.cpp: 122 empty declaration
10 errors, 2 warnings
C:\PROGRA~2\MATLAB\R2008B\BIN\MEX.PL: Error: Compile of 'SRC\classRF.cpp' failed.
??? Error using ==> mex at 213
Unable to complete successfully.
Error in ==> compile_windows at 19
mex -DMATLAB -output mexClassRF_train src/classRF.cpp src/classTree.cpp src/cokus.cpp precompiled_rfsub/win32/rfsub.o
src/mex_ClassificationRF_train.cpp src/rfutils.cpp
Original comment by [email protected]
on 2 Feb 2012 at 6:35
from randomforest-matlab.
hi
if you are using the precompiled version, dont use the compile_windows.m file.
the compiled mex files are already present in the precompiled package(they
might be removed if compile_windows.m was ru, so re-extract the files if needed)
just take a look into tutorial_*.m files
Original comment by abhirana
on 2 Feb 2012 at 6:39
from randomforest-matlab.
[deleted comment]
from randomforest-matlab.
i got an earlier message of it looking like taking a long time.
you might want to print out the trace while the trees are being created
extra_options.do_trace = 1; %(Default = 0)
model = regRF_train(X_trn,Y_trn, 100, 0, extra_options);
Original comment by abhirana
on 3 Feb 2012 at 9:47
from randomforest-matlab.
Is it possible to do clustering with this code?
Original comment by [email protected]
on 13 Feb 2012 at 9:06
from randomforest-matlab.
hi
the code for clustering is not within the download but you can get the code
within the svn repository
http://code.google.com/p/randomforest-matlab/source/checkout
http://code.google.com/p/randomforest-matlab/source/browse/trunk/RF_Class_C/tuto
rial_ClusterRF.m
is a tutorial file. and if you pass in without any labels you can use the
proximity matrix between examples
http://www.stat.berkeley.edu/~breiman/RandomForests/cc_home.htm#prox
what i am then doing is plotting the first 2 principal components via cmdscale
also take a look at how to interpret proximities for clustering
http://www.stat.berkeley.edu/~breiman/RandomForests/cc_home.htm#cluster
its not straightforward clustering but a way of dimensionality reduction. though some have used the proximity matrix in conjunction with other clustering methods (mediod) http://www.iai.uni-bonn.de/~jz/RFclusteringRenalCancer.pdf
Original comment by abhirana
on 15 Feb 2012 at 5:22
from randomforest-matlab.
I get the following error when running this tutorial file tutorial_ClusterRF.m
??? Error using ==> classRF_train at 192
have to fill stuff here
Original comment by [email protected]
on 17 Feb 2012 at 9:17
from randomforest-matlab.
Hi Flemming
the code for clustering is in the svn and not in the downloads.
you will have to compile the code from the svn to get clustering working
Original comment by abhirana
on 17 Feb 2012 at 9:19
from randomforest-matlab.
Is it possible to find out which all features were used for classification?
Original comment by [email protected]
on 24 Feb 2012 at 9:15
from randomforest-matlab.
hi
usually all features will be used for classification
if you want to know what are the most important features (and sometimes the top
some number of features are all what is required for good accuracy), take a
look into importance (which should be in the tutorial file)
Original comment by abhirana
on 25 Feb 2012 at 1:05
from randomforest-matlab.
Original comment by abhirana
on 8 Apr 2012 at 11:57
- Changed state: Done
from randomforest-matlab.
hai abhirana. i want to explore random forest in feature selection process, to
know how affective this method. have u tried it? do you got the matlab source
codes for random forest in feature selection? TQ
Original comment by [email protected]
on 18 Jun 2012 at 7:42
from randomforest-matlab.
Related Issues (20)
- weak learner HOT 1
- Compiling on Mac Lion HOT 6
- Compiled mexmaci64 for OSX 10.8.2 (Mountain Lion) HOT 2
- about the unbalanced data HOT 32
- Segmentation violation problem HOT 2
- Hierarchical sampling of data? HOT 3
- memory leak in HOT 1
- probability of classes for highly skewed dataset HOT 2
- Feature Normalization HOT 1
- sampsize problem
- score values from random forest HOT 1
- MATLAB crashes after tens of thousands runs !! HOT 3
- Compilation Problems with Matlab 2014a on Mac HOT 7
- How to get individual tree predictions for regression HOT 2
- use library (gcc) in matlab and error with compile of mex HOT 1
- NaN data HOT 4
- multivariate label output in regression analysis
- Matlab (randomly) crash after a number of runs HOT 5
- Directions for Bagging Regression HOT 2
- Quantifying Fractal Dimension HOT 1
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