I'm using kernlab package

Here are two examples:

x <- runif(1020, 1, 5000)
y <- sqrt(x)
model.vanilla <- rvm(x, y, kernel='vanilladot')

Got error:

Error in chol.default(crossprod(Kr)/var + diag(1/thetatmp)) :
the leading minor of order 2 is not positive definite


x <- runif(1020, 1, 5000)
y <- sqrt(x)
model.rbf <- rvm(x[1:1000], y[1:1000], kernel='rbfdot')
py.rbf <- predict(model.rbf, x[1001:1020])
print(paste("MSE: ", sum((py.rbf - y[1001:1020]) ^ 2) / length(py.rbf)))


Using automatic sigma estimation (sigest) for RBF or laplace kernel 
Relevance Vector Machine object of class "rvm" 
Problem type: regression 

Gaussian Radial Basis kernel function. 
 Hyperparameter : sigma =  5.44268665122008e-06 

Number of Relevance Vectors : 247 
Variance :  4.368e-06
Training error : 3.418e-06 
[1] "MSE:  4.921706631013e-05"

Why doesn't using linear kernel work here? polydot (polynomial kernel function) doesn't work either.

Can this be fixed?

  • $\begingroup$ @NickCox Thanks for your answer. I don't think that it's bug in software. And i have no problems with programming here. I suppose it has something to do with the algorithm(rvm) and data type. But anything is possible... Second example work fine. $\endgroup$
    – luckyi
    Commented Aug 15, 2013 at 12:06
  • $\begingroup$ Does it make any difference if you add a small amount of noise to your y? $\endgroup$
    – Wayne
    Commented Aug 15, 2013 at 12:37
  • $\begingroup$ @Wayne slightly worse prediction with rbfdot kernel(MSE ~ 6) and still error with vanilladot $\endgroup$
    – luckyi
    Commented Aug 15, 2013 at 12:57
  • $\begingroup$ @NickCox I thought that this could be due to preprocessing data... $\endgroup$
    – luckyi
    Commented Aug 15, 2013 at 12:58

1 Answer 1


Evidently, your data is too sparse for that combination of method and kernel. If you change your

x <- runif(1020, 1, 5000)

to either of

x <- runif(10200, 1, 5000)
x <- runif(1020, 1, 100)

it works. For me.


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