README updated

README.md

@@ -9,7 +9,7 @@ To appear in Proceedings of WABI 2017.
 bioRxiv DOI: https://doi.org/10.1101/139618
 
 ## Requirements:
-- MATLAB 9.0.0.341360 (R2016a) [We developed _CoMIK_ using this version of MATLAB (R2016a). Compatbility checked with version R2015b]
+- MATLAB 9.0.0.341360 (R2016a) [We developed _CoMIK_ using this version of MATLAB (R2016a). Compatbility checked with version 8.6 (R2015b)]
 - Python 2.7 or higher
 - SHOGUN Release version 3.2.0 [See issue #7 (issues/7) in this regard. _CoMIK_ also works with the latest SHOGUN version 6.0.0]
 
@@ -20,7 +20,7 @@ For the visualizations, the following R (R version 3.4.0) packages are needed
 This repository contains Matlab code for the project *CoMIK*. The various ".m" files define corresponding Matlab functions.
 We use MKL implementation from Shogun's modular interface for Python. The Python script mkl.py handles solving of the MKL problem.
 
-If you have MATLAB installed, you can run _CoMIK_ from inside MATLAB. But, in case you do not have MATLAB installed, we provide an executable version for which you would additionally need the MATLAB Runtime. MATLAB Runtime can be downloaded from https://mathworks.com/products/compiler/mcr.html . We recommend getting version 9.0 (R2016a) installed.
+If you have MATLAB installed, you can run _CoMIK_ from inside MATLAB. But, in case you do not have MATLAB installed, we provide an executable version for which you would additionally need the MATLAB Runtime. MATLAB Runtime can be downloaded from https://mathworks.com/products/compiler/mcr.html . We recommend getting version 9.0 (R2016a) installed. If that does not work, 8.6 (R2015) would also work.
 
 ## Installation:
 ```
@@ -29,7 +29,7 @@ cd comik
 sh install.sh
 ```
 - Install SHOGUN
-- Install MATLAB Runtime. Follow the instructions for installation of the MATLAB Runtime; install at any location of your choice on the disk.
+- Only if you are planning to use the executable, install MATLAB Runtime. Follow the instructions for installation of the MATLAB Runtime; install at any location of your choice on the disk.
 Once the dependencies are handled, e.g., SHOGUN, MATLAB runtime etc., and the paths are set, you can test _CoMIK_ as follows
 ```
 a) sh test_install.sh matlab
@@ -53,10 +53,12 @@ comik_wrapper('config-comik.txt');
 If not, you can use the executable as follows:
 
 ```
-./run_CoMIK_v90.sh <MATLAB_Runtime_location> <config_file>
-./run_CoMIK_v90.sh /usr/lib/matlab-9.0 config-comik.txt #for version 9.0 (R2016a)
+# ./run_CoMIK_v90.sh <MATLAB_Runtime_location> <config_file>
+# for version 9.0 (R2016a)
+./run_CoMIK_v90.sh /usr/lib/matlab-9.0 config-comik.txt
  OR
-./run_CoMIK_v86.sh /usr/lib/matlab-8.6 config-comik.txt #for version 8.6 (R2015b)
+# for version 8.6 (R2015b)
+./run_CoMIK_v86.sh /usr/lib/matlab-8.6 config-comik.txt
 ```
 where `/usr/lib/matlab-9.0` could be replaced with the location of the MATLAB Runtime on your machine. Additionally, when required, you can add your own paths to the `LD_LIBRARY_PATH` environment variable in the file `run_CoMIK_v86.sh` or `run_CoMIK_v90.sh` (for example, the path for shogun can be added here).
 

config-comik.txt

@@ -22,7 +22,7 @@ COST_VALUES=10.^[-3:1:3]
 ## Above are params which are required
 ## Further, params with otherwise default values
 MKL_NORM=2.0
-NUMBER_OF_INNER_FOLDS=10
+NUMBER_OF_INNER_FOLDS=5
 NUMBER_OF_OUTER_FOLDS=5
 WHETHER_TO_PLOT_HEATMAP=No
 WHETHER_TO_VISUALIZE_WEIGHT_VECTOR=Yes