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In manifold learning, algorithms based on graph Laplacian constructed from data have received considerable attention both in practical applications and theoretical analysis. Much of the existing work has been done under the assumption that the data is sampled from a manifold without boundaries and singularities or that the functions of interest are evaluated away from such points. At the same time, it can be argued that singularities and boundaries are an important aspect of the geometry of realistic data. Boundaries occur whenever the process generating data has a bounding constraint; while singularities appear when two different manifolds intersect or if a process undergoes a "phase transition", changing non-smoothly as a function of a parameter. In this paper we consider the behavior of graph Laplacians at points at or near boundaries and two main types of other singularities: intersections, where different manifolds come together and sharp "edges", where a manifold sharply changes direction. We show that the behavior of graph Laplacian near these singularities is quite different from that in the interior of the manifolds. In fact, a phenomenon somewhat reminiscent of the Gibbs effect in the analysis of Fourier series, can be observed in the behavior of graph Laplacian near such points. Unlike in the interior of the domain, where graph Laplacian converges to the Laplace-Beltrami operator, near singularities graph Laplacian tends to a first-order differential operator, which exhibits different scaling behavior as a function of the kernel width. One important implication is that while points near the singularities occupy only a small part of the total volume, the difference in scaling results in a disproportionately large contribution to the total behavior. Another significant finding is that while the scaling behavior of the operator is the same near different types of singularities, they are very distinct at a more refined level of analysis. We believe that a comprehensive understanding of these structures in addition to the standard case of a smooth manifold can take us a long way toward better methods for analysis of complex non-linear data and can lead to significant progress in algorithm design. Keywords: Graph Laplacian, singularities, limit analysis
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