MEDALLION: Manifold Embedding Distillation and Attributions for Low-dimensional Latent InterpretatiON

Vicky Jung, Claire M. He, Irene Chang, Genevera I. Allen

Dimensionality reduction is widely used to visualize high-dimensional data and guide scientific discovery, yet interpreting which original features contribute to low-dimensional representations remains challenging, particularly for black-box methods such as t-SNE and UMAP. We introduce \textbf{MEDALLION} (Manifold Embedding Distillation and Attributions for Low-dimensional Latent InterpretatiON), a novel framework for interpreting low-dimensional embeddings through knowledge distillation and neural feature attribution. MEDALLION distills any given embedding with a neural encoder which we explain via a broad range of existing neural feature attribution methods. Through experiments on MNIST and applications in single-cell transcriptomics, we show MEDALLION provides informative feature attributions that cast additional insights into the underlying embedding and compare its performance with existing interpretability approaches.