ArticlebioRxiv : the preprint server for biology2025
Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance.
Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
The success of transformer-based foundation models on natural language and images has motivated their use in single-cell biology. Single-cell foundation models have been trained on increasingly larger transcriptomic datasets, scaling from initial studies with 1 million cells to newer atlases with over 100 million cells. This study investigates the role of pre-training dataset size and diversity on the performance of single-cell foundation models on both zero-shot and fine-tuned tasks. Using a large corpus of 22.2 million cells, we pre-train a total of 400 models, which we evaluate by conducting 6,400 experiments. Our results show that current methods tend to plateau in performance with pre-training datasets that are only a fraction of the size of current training corpora.
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