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BMFM-RNA: An Open Framework for Building and Evaluating Transcriptomic Foundation Models
Bharath Dandala, Michael M. Danziger, Ella Barkan, Tanwi Biswas, Viatcheslav Gurev, Jianying Hu, Matthew Madgwick, Akira Koseki, Tal Kozlovski, Michal Rosen-Zvi, Yishai Shimoni, Ching-Huei Tsou
https://arxiv.org/abs/2506.14861

BMFM-RNA: An Open Framework for Building and Evaluating Transcriptomic Foundation Models
Transcriptomic foundation models (TFMs) have recently emerged as powerful tools for analyzing gene expression in cells and tissues, supporting key tasks such as cell-type annotation, batch correction, and perturbation prediction. However, the diversity of model implementations and training strategies across recent TFMs, though promising, makes it challenging to isolate the contribution of individual design choices or evaluate their potential synergies. This hinders the field's ability to conver…

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