Sync latest GeneMamba docs and next-token training updates

README.md

@@ -26,7 +26,6 @@ A Hugging Face compatible implementation of GeneMamba, a foundational state-spac
 - [Datasets](#datasets)
 - [Usage Guide](#usage-guide)
 - [Citation](#citation)
-- [License](#license)
 
 ---
 
@@ -316,14 +315,14 @@ Task-Specific Heads:
 
 ### Key Design Choices
 
-- **Sequence Processing**: Bidirectional Mamba with multiple aggregation modes (mean/sum/concat/gate)
-- **Pooling Strategy**: Mean pooling over sequence (CLS token available as option)
+- **Bidirectional Mamba Block**: Bidirectional Mamba enables significant improvement in gene rank reconstruction task
+- **Pooling Strategy**: Bidirectional Mamba with multiple aggregation modes (mean/sum/concat/gate)
 - **Regularization**: Dropout on classification head
 - **Activation**: No explicit activation (Mamba uses internal gating)
 
 ---
 
-## Usage Guide
+<!-- ## Usage Guide
 
 ### Loading Models
 
@@ -387,7 +386,7 @@ config = model.config
 config.hidden_dropout_prob = 0.2
 ```
 
----
+--- -->
 
 ## Important Notes ⚠️
 
@@ -436,26 +435,20 @@ See the `examples/` directory for complete scripts:
 
 - `1_extract_embeddings.py` - Extract cell embeddings
 - `2_finetune_classification.py` - Cell type annotation
-- `4_pretrain_from_scratch.py` - Train from scratch (next-token + optional resume)
-
-Run any example:
-
-```bash
-python examples/01_extract_embeddings.py
-```
+- `3_pretrain_from_scratch.py` - Train from scratch (next-token + optional resume)
 
 ---
 
 ## Citation
 
-If you use GeneMamba in your research, please cite:
+If you find GeneMamba is useful in your research, please cite:
 
 ```bibtex
-@article{genemamba2024,
-  title={GeneMamba: A Foundation Model for Single-Cell Analysis},
-  author={Contributors...},
-  journal={bioRxiv},
-  year={2024}
+@article{qi2025genemamba,
+  title={GeneMamba: An Efficient and Effective Foundation Model on Single Cell Data},
+  author={Qi, Cong and Fang, Hanzhang and Jiang, Siqi and Song, Xun and Hu, Tianxing and Zhi, Wei},
+  journal={arXiv preprint arXiv:2504.16956},
+  year={2026}
 }
 ```
 
@@ -515,30 +508,4 @@ GeneMamba_repo/
 
 ---
 
-## Contributing
-
-Contributions welcome! Please:
-
-1. Fork the repository
-2. Create a feature branch
-3. Submit a pull request
-
----
-
-## License
-
-This project is licensed under the Apache 2.0 License - see [LICENSE](LICENSE) for details.
-
----
-
-## Support
-
-- 📖 **Documentation**: See `docs/` directory
-- 🐛 **Issues**: Report on GitHub
-- 💬 **Discussions**: Join our community forum
-- 📧 **Email**: Support contact (to be added)
-
----
-
-**Last Updated**: March 2026  
-**Maintained by**: GeneMamba Team
+**Last Updated**: March 2026