math domain error while using PCA

Question

I am using python\'s scikit-learn package to implement PCA .I am getting math

domain error :
C:\\Users\\Akshenndra\\Anaconda2\\lib\\site-packages\\sklearn\\deco         


        

Answer 1

I don't know whether i am right or not, but I truly find a way to solve it.

I just print some error information(The value of spectrum_[i] and spectrum_[j]), and I find :

sometimes, they are same!!!

(Maybe they are not same but they are too close, I guess)

so , here

pa += log((spectrum[i] - spectrum[j]) *
                  (1. / spectrum_[j] - 1. / spectrum_[i])) + log(n_samples)

it will report error when calculate log(0).

My way to solve it is to add a very small number 1e-99 to 0, so it become log(0 + 1e-99)

so you can just change it to:

            pa += log((spectrum[i] - spectrum[j]) *
                  (1. / spectrum_[j] - 1. / spectrum_[i]) + 1e-99) + log(n_samples)

Answer 2

I think you should add 1 instead, as the numpy log1p description page. Since log(p+1) = 0 when p = 0 (while log(e-99) = -99), and as the quote in the link

For real-valued input, log1p is accurate also for x so small that 1 + x == 1 in floating-point accuracy

The code can be modified as follows to make what you trying to resolve more reasonable:

for i in range(rank):
    for j in range(i + 1, len(spectrum)):
        pa += log((spectrum[i] - spectrum[j]) *
        (1. / spectrum_[j] - 1. / spectrum_[i]) + 1) + log(n_samples + 1)
    ll = pu + pl + pv + pp - pa / 2. - rank * log(n_samples + 1) / 2