Graph clustering methods such as spectral clustering are defined for general weighted graphs. In machine learning, however, data often is not given in form of a graph, but in terms of similarity (or distance) values between points. In this case, first a neighborhood graph is constructed using the similarities between the points and then a graph clustering algorithm is applied to this graph. In this paper we investigate the influence of the construction of the similarity graph on the clustering results. We first study the convergence of graph clustering criteria such as the normalized cut (Ncut) as the sample size tends to infinity. We find that the limit expressions are different for different types of graph, for example the r-neighborhood graph or the k -nearest neighbor graph. In plain words: Ncut on a kNN graph does something systematically different than Ncut on an r-neighborhood graph! This finding shows that graph clustering criteria cannot be studied independently of the kind of graph they are applied to. We also provide examples which show that these differences can be observed for toy and real data already for rather small sample sizes.

We consider the problem of denoising a noisily sampled submanifold M in Rd, where the submanifold M is a priori unknown and we are only given a noisy point sample. The presented denoising algorithm is based on a graph-based diffusion process of the point sample. We analyze this diffusion process using recent re- sults about the convergence of graph Laplacians. In the experiments we show that our method is capable of dealing with non-trivial high-dimensional noise. More- over using the denoising algorithm as pre-processing method we can improve the results of a semi-supervised learning algorithm.