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Image Credit: Arxiv

Bidirectional Mamba for Single-Cell Data: Efficient Context Learning with Biological Fidelity

  • 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.

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