Fig. 6

Scalability of DeDaL for large networks. The figure shows the number of seconds needed for DeDaL to compute network smoothing (red line, circles), first ten principal components (blue line, rhombes) and the principal manifold (brown line, crosses) for a set of 100 ovarian cancer transcriptomes and a series of networks with increasing number of nodes (up to 10000 nodes in the whole HPRD PPI database). Network smoothing scaling is separately shown for the case of de-novo computation of the eigenvector decomposition of the network Laplacian (red line, circles) and for the case of using the pre-computed eigenvector decomposition (green line, squares). The benchmarking was done in the command line mode of DeDaL