Minor edits to function help messages.

snikumbh · Jul 28, 2017 · 1ae57b9 · 1ae57b9
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diff --git a/comik_main_with_weight_vector.m b/comik_main_with_weight_vector.m
@@ -1,9 +1,97 @@
 function [allSeqsAsBags, allSeqsConformedSetKernel, subkernelWeights, thetaVals, instanceWeightsInEachBag, resultString, bestParamComb, test_teAUROC, test_teAUPRC, predictions] = comik_main_with_weight_vector(givenPosFastaFilename, givenNegFastaFilename, givenNPos, givenNNeg, oligoLen, maxDist, segmentSizeInBps, nClusterVals, sigmaVals, Cs, mklNorm, nFolds, testIndices, debugLevel, debugMsgLocation, outputFolder, runSummaryFilename, whetherToPlotHeatmap, computationVersion, whetherToVisualizeWVector)
 
-% Author: snikumbh 
+% COMIK_MAIN_WITH_WITH_WEIHT_VECTOR
+% Main function for CoMIK
+%
+% INPUT PARAMS
+% Param 'givenPosFastaFilename'
+% Name of FASTA file with positive examples
+% 
+% Param 'givenNegFastaFilename'
+% Name of FASTA file with negative examples
+%
+% Param 'givenNPos'
+% Number of positive examples to use (can be less than those provided in file)
+%
+% Param 'givenNNeg'
+% Number of negative examples to use (can be less than those provided in file)
+%
+% Param 'oligoLen' and 'maxDist'
+% Specify the oligomer length and the maximum distance for the ODH 
+% representation. Caution: A combination of large values can be memory intensive!
+%
+% Param 'segmentSizeInBps'
+% Specify the segment-size in basepairs for CoMIK
+%
+% Param 'nClusterVals' (vector)
+% Specify the number of clusters for CoMIK
+%
+% Param 'sigmaVals' (vector)
+% Specify the sigma values for the Gaussian transformation
+%
+% Param 'Cs' (vector)
+% Cost values for SVM
+%
+% Param 'mklNorm'
+% Specify p-norm value for MKL
+%
+% Param 'nFolds' 
+% Specify number of inner cross-validation folds
+%
+% Param 'testIndices' (vector)
+% Indices of the sequences in the FASTA file which are to be considered as unseen 
+% test examples. For example, with a FASTA file containing a total of 100 
+% positive sequences followed by 100 negative sequences, the test indices 
+% are given as
+%       testIndices = [81:100 181:200]
+% for the corresponding 20 positives and 20 negatives to be treated as test 
+% examples.
+%
+% Param 'debugLevel' (0/1/2)
 %
-% All segments, shifted and non-shifted in one bag; Order of segments: non-shifted segments followed by shifted segments.
-% This results in #kernels = #clusterCentres
+% Param 'debugMsgLocation' (1/fileID)
+%
+% Param 'outputFolder'
+% Specify name of folder to write output results to
+%
+% OUTPUT PARAMS
+% Param 'allSeqsAsBags'
+% All sequences represented as bags
+% 
+% Param 'allSeqsConformedSetKernel' (matrix)
+% The conformally transformed MI kernel
+%
+% Param 'subkernelWeights' (vector)
+% Weights assigned to each sub-kernel upon solving MKL
+%
+% Param 'thetaVals' (vector)
+% Theta values used for obtaining the instance weights
+% 
+% Param 'instanceWeightsInEachBag'
+% Weights assigned to instances in each bag using the final model
+% 
+% Param 'resultString'
+% A combined string of per iteration results (as printed in the resultSummary file)
+% 
+% Param 'bestParamComb' (Struct)
+% Best performing values for various params
+%
+% Param 'test_teAUROC'
+% AUROC value for the test sequences
+%
+% Param 'test_teAUPRC'
+% AUPRC value for the test sequences
+%
+% Param 'predictions'
+% Prediction vector
+%
+% ADDITIONAL NOTES
+% -- Segmentation
+%    . All segments, shifted and non-shifted in one bag; Order of segments: non-shifted segments followed by shifted segments.
+%      This results in #kernels = #clusterCentres
+% -- 
+%
+% Author: snikumbh 
 %
 % debugLevel 2	prints all messages
 % debugLevel 1	place holder level, may be used in the future

diff --git a/comik_wrapper.m b/comik_wrapper.m
@@ -22,37 +22,46 @@
 % 
 % Required params:
 % ----------------
+% INPUT PARAMS
+% Param 'givenFastFilename' (string)
+% The input FASTA file should contain all sequences together, positives 
+% followed by negatives.
 %
-% Param 'givenFastFilename: The input FASTA file should contain all sequences 
-%     together -- positives followed by negatives.
+% Params 'nPosSequences' and 'nNegSequences'
+% Used to specify the number of positive and negative sequences in the dataset.
 %
-% Params 'nPosSequences' and 'nNegSequences' are used to specify the number of 
-%     positive and negative sequences in the dataset.
-%
-% Param 'testIndices' is a Matlab vector specifying the indices of the 
-%     sequences in athe FASTA file which are to be considered as unseen 
-%     test examples. For example, with a FASTA file containing a total of 100 
-%     positive sequences followed by 100 negative sequences, the test indices 
-%     are given as
+% Param 'testIndices' (vector)
+% Indices of the sequences in the FASTA file which are to be considered as unseen 
+% test examples. For example, with a FASTA file containing a total of 100 
+% positive sequences followed by 100 negative sequences, the test indices 
+% are given as
 %       testIndices = [81:100 181:200]
-%     for the corresponding 20 positives and 20 negatives to be treated as 
-%     test examples.
+% for the corresponding 20 positives and 20 negatives to be treated as test 
+% examples.
 % 
-% Param 'outputFolder': Specifies the path on disk where output can be written
+% Param 'outputFolder' (string)
+% Specifies the path on disk where output can be written
 % 
-% Params 'oligoLen' and 'maxDist': Specify the oligomer length and the maximum 
-%     distance for the ODH representation. Caution: A combination of large 
-%     values can be memory intensive!
+% Params 'oligoLen' and 'maxDist'
+% Specify the oligomer length and the maximum distance for the ODH 
+% representation. Caution: A combination of large values can be memory intensive!
 %
-% Param 'SegmentSizeInBps': Specify the segment-size in basepairs for CoMIKL
+% Param 'segmentSizeInBps'
+% Specify the segment-size in basepairs for CoMIK
 % 
-% Param 'nClusterVals': Specify the number of clusters for CoMIKL
+% Param 'nClusterVals'
+% Specify the number of clusters for CoMIK
 %
-% Param 'sigmaVals': Specify the sigma values for the Gaussian transformation
+% Param 'sigmaVals'
+% Specify the sigma values for the Gaussian transformation
+% 
+% Param 'Cs'
+% Cost values for SVM
 % 
-% Param 'Cs': Cost values for SVM
+% ADDITIONAL NOTES
+%
 % 
-% Author: snikumbh
+% Author: snikumbh@mpi-inf.mpg.de
 
 totalArguments = 20;
 if nargin < totalArguments

diff --git a/computeConformedMultiInstanceKernel.m b/computeConformedMultiInstanceKernel.m
@@ -4,59 +4,59 @@
 % Computes the conformally transformed multi-instance kernel
 
 % INPUT PARAMS
-% param 'instanceStarts' (vector)
+% Param 'instanceStarts' (vector)
 % Indices where instances (segments) of any sequence begin
 %
-% param 'instanceEnds' (vector)
+% Param 'instanceEnds' (vector)
 % Indices where instances (segments) of any sequence end
 % 
-% param 'instanceWideKernel' (matrix)
+% Param 'instanceWideKernel' (matrix)
 % The instance-wide kernel matrix of dimension #Instances x #Instances
 %
-% param 'trainIndices' (vector)
+% Param 'trainIndices' (vector)
 % Indices of the training sequences
 %
-% param 'allSeqsAsBags' (cell array)
+% Param 'allSeqsAsBags' (cell array)
 % Collection of all segments per sequence
 % 
-% param 'nClusters'
+% Param 'nClusters'
 % number of clusters for k-means
 %
-% param 'sig' 
+% Param 'sig' 
 % Gaussian bandwidth (sigma) value for the Gaussian transformation
 %
-% param 'Y' (vector)
+% Param 'Y' (vector)
 % Vector of labels
 %
-% param 'computationVersion' ('AccumArray'/'Looping')
+% Param 'computationVersion' ('AccumArray'/'Looping')
 % Flag specifying what approach to use for computing the kernel
 %
-% param 'debugLevel' (0/1/2)
+% Param 'debugLevel' (0/1/2)
 %
-% param 'debugMsgLocation' (1/fileID)
+% Param 'debugMsgLocation' (1/fileID)
 %
 %
 % OUTPUT PARAMS
-% param 'conformedMultiInstanceKernel' (matrix)
+% Param 'conformedMultiInstanceKernel' (matrix)
 % Normalized conformally transformed MI kernel
 % 
-% param 'rawConformedMultiInstanceKernel' (matrix)
+% Param 'rawConformedMultiInstanceKernel' (matrix)
 % Unnormalized conformally transformed MI kernel
 %
-% param 'instancesTransformationKernel' (matrix)
+% Param 'instancesTransformationKernel' (matrix)
 % Transformation of the training instances
 %
-% param 'clusterCentres' (matrix)
+% Param 'clusterCentres' (matrix)
 % Cluster centres obtained upon k-means
 %
-% ADDITIONAL NOTES:
+% ADDITIONAL NOTES
 % -- Stratification
 %    . If stratification is required, see below, set stratified = 1
 % -- Replicates for k-means
 %    . currently set to 1
 %    . can be increased
 %
-% author: snikumbh@mpi-inf.mpg.de
+% Author: snikumbh@mpi-inf.mpg.de
 
 
 % 1.1 Obtain expansion points

diff --git a/computeInstanceWideKernel.m b/computeInstanceWideKernel.m
@@ -4,33 +4,33 @@
 % Computes the instance-wide kernel matrix given a bag of instances
 %
 % INPUT PARAMS
-% param 'allSeqsAsBags' (cell array)
+% Param 'allSeqsAsBags' (cell array)
 % Collection of all segments per sequence
 %
-% param 'thisInstances' (vector)
+% Param 'thisInstances' (vector)
 % #instances in each bag (in other words, #segments per sequence) 
 %
-% param 'sparseComputation' (0/1)
+% Param 'sparseComputation' (0/1)
 % Flag specifying whether sparseComputation is to be performed (0/1)
 %
-% param 'debugLevel' (0/1/2)
+% Param 'debugLevel' (0/1/2)
 %
-% param 'debugMsgLocation' (1/fileID)
+% Param 'debugMsgLocation' (1/fileID)
 %
 %
 % OUTPUT PARAMS
-% param 'instanceStarts' (vector)
+% Param 'instanceStarts' (vector)
 % Indexes in the vector where instances (segments) of any sequence begin
 %
-% param 'instanceEnds' (vector)
+% Param 'instanceEnds' (vector)
 % Indexes in the vector where istances (segments) of any sequence end
 %
-% param 'instanceWideKernel' (matrix)
+% Param 'instanceWideKernel' (matrix)
 % The instance-wide kernel matrix of dimension #Instances x #Instances
 %
-% ADDITIONAL NOTES:
+% ADDITIONAL NOTES
 %
-% author: snikumbh@mpi-inf.mpg.de
+% Author: snikumbh@mpi-inf.mpg.de
 
 if nargin < 3
     debugMsgLocation = 1;