Domain specific (dis-)similarity or proximity measures used e.g. in alignment algorithms of sequence data, are popular to analyze complex data objects and to cover domain specific data properties. Without an underlying vector space these data are given as pairwise (dis-)similarities only. The few available methods for such data focus widely on similarities and do not scale to large data sets. Kernel methods are very effective for metric similarity matrices, also at large scale, but costly transformations are necessary starting with non-metric (dis-) similarities. We propose an integrative combination of Nystroem approximation, potential double centering and eigenvalue correction to obtain valid kernel matrices at linear costs in the number of samples. By the proposed approach effective kernel approaches, become accessible. Experiments with several larger (dis-)similarity data sets show that the proposed method achieves much better runtime performance than the standard strategy while keeping competitive model accuracy. The main contribution is an efficient and accurate technique, to convert (potentially non-metric) large scale dissimilarity matrices into approximated positive semi-definite kernel matrices at linear costs.
A problem for many kernel-based methods is that the amount of computation required to find the solution scales as O(n3), where n is the number of training examples. We develop and analyze an algorithm to compute an easily-interpretable low-rank approximation to an n × n Gram matrix G such that computations of interest may be performed more rapidly. The approximation is of the form Gk = CWk+CT, where C is a matrix consisting of a small number c of columns of G and Wk is the best rank-k approximation to W, the matrix formed by the intersection between those c columns of G and the corresponding c rows of G. An important aspect of the algorithm is the probability distribution used to randomly sample the columns; we will use a judiciously-chosen and data-dependent nonuniform probability distribution. Let ||·||2 and ||·||F denote the spectral norm and the Frobenius norm, respectively, of a matrix, and let Gk be the best rank-k approximation to G. We prove that by choosing O(k e4) columns||G-CWk+CT||ξ ≤ ||G-Gk||ξ + e Σi=1n Gii2 ,both in expectation and with high probability, for both ξ = 2, F, and for all k: 0 ≤ k ≤ rank(W). This approximation can be computed using O(n) additional space and time, after making two passes over the data from external storage. The relationships between this algorithm, other related matrix decompositions, and the Nystrom method from integral equation theory are discussed.