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Life sciences · Preprint
arXiv · November 4, 2026
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Dimensionality reduction (DR) techniques are fundamental to the analysis of high-dimensional data, yet their substantial computational cost limits their use in interactive settings. To address this limitation, we present GPU-accelerated Progressive Uniform Manifold Approximation and Projection (GPUMAP), an efficient progressive DR algorithm designed for interactive use. We identify three atomic operations within UMAP and restructure them into a progressive pipeline. As part of this adaptation, we introduce modifications to UMAP, including operation queues, instance-wise local join, and scheduling strategies. We further accelerate computation by leveraging GPU parallelism, enabling interactive analysis of million-scale datasets on commodity GPU hardware. Finally, we employ our implementation to systematically study the behavior of progressive DR, investigating how projections evolve over time relative to the ground-truth projection and how biased data streams influence the quality and stability of the resulting projections.