using precomputed kernels with libsvm

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You seem to already have figured out the problem… According to the README file included in the MATLAB package:

To use precomputed kernel, you must include sample serial number as
the first column of the training and testing data.

Let me illustrate with an example:

%# read dataset
[dataClass, data] = libsvmread('./heart_scale');

%# split into train/test datasets
trainData = data(1:150,:);
testData = data(151:270,:);
trainClass = dataClass(1:150,:);
testClass = dataClass(151:270,:);
numTrain = size(trainData,1);
numTest = size(testData,1);

%# radial basis function: exp(-gamma*|u-v|^2)
sigma = 2e-3;
rbfKernel = @(X,Y) exp(-sigma .* pdist2(X,Y,'euclidean').^2);

%# compute kernel matrices between every pairs of (train,train) and
%# (test,train) instances and include sample serial number as first column
K =  [ (1:numTrain)' , rbfKernel(trainData,trainData) ];
KK = [ (1:numTest)'  , rbfKernel(testData,trainData)  ];

%# train and test
model = svmtrain(trainClass, K, '-t 4');
[predClass, acc, decVals] = svmpredict(testClass, KK, model);

%# confusion matrix
C = confusionmat(testClass,predClass)

The output:

*
optimization finished, #iter = 70
nu = 0.933333
obj = -117.027620, rho = 0.183062
nSV = 140, nBSV = 140
Total nSV = 140
Accuracy = 85.8333% (103/120) (classification)

C =
    65     5
    12    38

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