scRM: A single-cell foundation model trained on scRNA-seq reads

To our knowledge, scRM is the first single-cell foundation model trained on sequencing reads, demonstrating that raw data pretraining is not only feasible but competitive at a fraction of the computational cost. We anticipate that scaling this framework and exploring alternative architectures will unlock biological information inaccessible to count models and extend the dataset-specific pretraining it already makes possible. The source code is available at https://github.com/altoslabs/scRM.