Preprint
Jul 2026
When Does Deep Representation Learning Help Single-Cell Clustering? A Sensitivity-Aware Diagnostic Benchmark for Biomedical AI Pipelines
Per-dataset analysis reveals three reproducible regimes: probabilistic variational autoencoder variants help on the smallest datasets, deep autoencoders win on mid-scale data with multi-batch or many-type structure, and classical PCA pipelines remain competitive when linear projection already captures the dominant variation.
Phong T. Nguyen, T. Vu, Thu Ha Nguyen et al.
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