On 11 December 2013 23:30, José Pablo González <[email protected]> wrote: > Hello, > > I am new in sklearn, but so far I'm impressed. I think it is a great > library! > > I think I found a little bug in the Multidimensional Scaling Function. It > expects "perfect" similarity matrices, which it's often not possible with > real data. Moreover, sklearn's functions are unable to get the expected > precision. > > For example if I use sklearn to computea similarity matrix of euclidean > distances: > > similarities = euclidean_distances(data) > print np.abs(similarities - similarities.T).max() > # this outputs 5.26835606386e-09, which I'd it's precise enough > > > Unfortunately, when I try to calculate MDS: > mds = manifold.MDS(n_components=2, dissimilarity="precomputed", n_jobs=1) > pos = mds.fit(similarities) > > I get a precision error. I have already tried casting to float64 as > suggested here, but it doesn't work either. There's no way to change the > precision of this, only the convergence precision. > > Am I overlooking at something?
Nope, this is indeed a problem from the MDS code. You can provide a fix for this by raising the precision required. Also, depending on the algorithm used to solve the MDS, a symmetric matrix should or shouldn't be required. I think in the case of the SMACOF algorithm (currently used in sklearn), it isn't even required. Someone should have a look at the litterature to check this (I should be able to in a couple of weeks). Cheers, N > > Thanks, > Jose > > > -- > José P. González-Brenes, Ph.D. > www.josepablogonzalez.com > > > > ------------------------------------------------------------------------------ > Rapidly troubleshoot problems before they affect your business. Most IT > organizations don't have a clear picture of how application performance > affects their revenue. With AppDynamics, you get 100% visibility into your > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics > Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk > _______________________________________________ > Scikit-learn-general mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/scikit-learn-general > ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Scikit-learn-general mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/scikit-learn-general
