Two-class classification with naive baysian classifier

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see the COPYING file distributed with CoSMoMVPA. #

Contents

Define data
set the targets and chunks
Slice the dataset
train on even, test on odd
train on odd, test on even

Define data

config=cosmo_config();
data_path=fullfile(config.tutorial_data_path,'ak6','s01');

% Load the dataset with VT mask
ds = cosmo_fmri_dataset([data_path '/glm_T_stats_perrun.nii'], ...
                     'mask', [data_path '/vt_mask.nii']);

% remove constant features
ds=cosmo_remove_useless_data(ds);

set the targets and chunks

ds.sa.targets = repmat((1:6)',10,1);
ds.sa.chunks = floor(((1:60)-1)/6)'+1;

% Add labels as sample attributes
labels = {'monkey','lemur','mallard','warbler','ladybug','lunamoth'};
ds.sa.labels = repmat(labels,1,10)';

% get indices for monkeys and mallards
idx = strcmp(ds.sa.labels,'monkey') | strcmp(ds.sa.labels,'mallard');

Slice the dataset

Use sample attrubutes slicer to slice dataset

ds2 = cosmo_slice(ds,idx);

% slice into odd and even runs using chunks attribute
even_idx = mod(ds2.sa.chunks,2)==0;
odd_idx = mod(ds2.sa.chunks,2)==1;

evens = cosmo_slice(ds2,even_idx);
odds = cosmo_slice(ds2, odd_idx);

train on even, test on odd

pred = cosmo_classify_naive_bayes(evens.samples, evens.sa.targets, odds.samples);
accuracy = mean(odds.sa.targets == pred);
fprintf('Train on even, test on odd: accuracy %.3f\n', accuracy);
% Answer: accuracy should be .70

Train on even, test on odd: accuracy 0.800

train on odd, test on even

pred = cosmo_classify_naive_bayes(odds.samples, odds.sa.targets,evens.samples);
accuracy = mean(evens.sa.targets == pred);
fprintf('Train on odd, test on even: accuracy %.3f\n', accuracy);
% Answer: accuracy = .60

Train on odd, test on even: accuracy 0.600