SpaceMAP: Visualizing High-Dimensional Data by Space Expansion

Xinrui Zu · Qian Tao

Hall E #623

Keywords: [ DL: Algorithms ] [ APP: Genetics, Cell Biology, etc ] [ DL: Other Representation Learning ] [ MISC: Representation Learning ] [ DL: Self-Supervised Learning ] [ MISC: Unsupervised and Semi-supervised Learning ]


Dimensionality reduction (DR) of high-dimensional data is of theoretical and practical interest in machine learning. However, there exist intriguing, non-intuitive discrepancies between the geometry of high- and low-dimensional space. We look into such discrepancies and propose a novel visualization method called Space-based Manifold Approximation and Projection (SpaceMAP). Our method establishes an analytical transformation on distance metrics between spaces to address the ``crowding problem" in DR. With the proposed equivalent extended distance (EED), we are able to match the capacity of high- and low-dimensional space in a principled manner. To handle complex data with different manifold properties, we propose hierarchical manifold approximation to model the similarity function in a data-specific manner. We evaluated SpaceMAP on a range of synthetic and real datasets with varying manifold properties, and demonstrated its excellent performance in comparison with classical and state-of-the-art DR methods. In particular, the concept of space expansion provides a generic framework for understanding nonlinear DR methods including the popular t-distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation and Projection

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