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  1. Code Supplement for "Multidimensional Scaling of Noisy High Dimensional Data"

    Peterfreund, Erez
    January 2018

    Multidimensional Scaling (MDS) is a classical technique for embedding data in low dimensions, still in widespread use today. Originally introduced in the 1950's, MDS was not designed with high-dimensional data in mind; while it remains popular with data analysis practitioners, no doubt it should be adapted to the high-dimensional data regime. In this paper we study MDS under modern setting, and specifically, high dimensions and ambient measurement noise. We show that, as the ambient noise level increase, MDS suffers a sharp breakdown that depends on the data dimension and noise level, and derive an explicit formula for this breakdown point in the case of white noise. We then introduce MDS+, an extremely simple variant of MDS, which applies a carefully derived shrinkage nonlinearity to the eigenvalues of the MDS similarity matrix. Under a loss function measuring the embedding quality, MDS+ is the unique asymptotically optimal shrinkage function. We prove that MDS+ offers improved embedding, sometimes significantly so, compared with classical MDS. Furthermore, MDS+ does not require external estimates of the embedding dimension (a famous difficulty in classical MDS), as it calculates the optimal dimension into which the data should be embedded.

  2. Code Supplement for "Local Conformal Autoencoder for standardized data coordinates"

    Peterfreund, Erez
    August 2020

    In this code supplement to the paper "LOCA: LOcal Conformal Autoencoder for standardized data coordinates" we offer a Python software library that includes: - Implementation of the LOCA algorithm - Scripts that generate each of the figures in this paper.

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