GeneMamba is introduced as a scalable and efficient foundation model for single-cell transcriptomics built on state space modeling.
It captures bidirectional gene context with linear-time complexity, offering substantial computational gains over transformer baselines.
GeneMamba is pretrained on nearly 30 million cells and incorporates biologically informed objectives, including pathway-aware contrastive loss and rank-based gene encoding.
Evaluation of GeneMamba showcases its strong performance, interpretability, and robustness, making it a practical and powerful alternative to transformer-based methods for single-cell data analysis.