Author

Oliver Wardhana

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Open access Oct 2026

Dataset structure outweighs method choice in single-cell cell-type annotation

Automated cell-type annotation is a prerequisite for nearly all single-cell RNA-sequencing (scRNA-seq) analysis, and the proliferation of annotation tools — spanning marker-based, similarity-based, classical machine-learning, deep-learning, semi-supervised, large language model (LLM), and transformer foundation-model f...

Oliver Wardhana · bioRxiv · 0 citations

#small language model Open access Sep 2026

Cell-type separability predicts annotation accuracy and outweighs algorithm choice: a factorial benchmark across seven scRNA paradigms

Using standardized oracle inputs and Cohen’s κ, it is found that, within the ranges tested, the major paradigms achieved comparable accuracy, and the field’s near-term gains lie in strengthening infrastructure—prioritizing tool accessibility, standardized evaluation, and robustness to pipeline variation.

Oliver Wardhana, Zi-Yu Zeng, Xin Lu · bioRxiv · 0 citations