flash-genomics-model

Flash Genomics Model (FGM)

My own attempt at a long context genomics model, leveraging recent advances in long context attention modeling (Flash Attention + other hierarchical methods).

If you would like to collaborate and not averse to having the final model completely open sourced, get in touch. My goal is to simply figure out if long context is what holds us back from a new SOTA model.

Update: Question has been answered, but I'll probably still continue with the project.

Todo

• add ability to combine with hyena, or even hyena alone, to fully evaluate what is necessary

Citations

@inproceedings{dao2022flashattention,
    title   = {Flash{A}ttention: Fast and Memory-Efficient Exact Attention with {IO}-Awareness},
    author  = {Dao, Tri and Fu, Daniel Y. and Ermon, Stefano and Rudra, Atri and R{\'e}, Christopher},
    booktitle = {Advances in Neural Information Processing Systems},
    year    = {2022}
}

@article {Dalla-Torre2023.01.11.523679,
    author  = {Hugo Dalla-Torre and Liam Gonzalez and Javier Mendoza Revilla and Nicolas Lopez Carranza and Adam Henryk Grzywaczewski and Francesco Oteri and Christian Dallago and Evan Trop and Hassan Sirelkhatim and Guillaume Richard and Marcin Skwark and Karim Beguir and Marie Lopez and Thomas Pierrot},
    title   = {The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics},
    elocation-id = {2023.01.11.523679},
    year    = {2023},
    doi     = {10.1101/2023.01.11.523679},
    publisher = {Cold Spring Harbor Laboratory},
    URL     = {https://www.biorxiv.org/content/early/2023/01/15/2023.01.11.523679},
    eprint  = {https://www.biorxiv.org/content/early/2023/01/15/2023.01.11.523679.full.pdf},
    journal = {bioRxiv}
}

@article {Benegas2022.08.22.504706,
    author  = {Gonzalo Benegas and Sanjit Singh Batra and Yun S. Song},
    title   = {DNA language models are powerful zero-shot predictors of genome-wide variant effects},
    elocation-id = {2022.08.22.504706},
    year    = {2023},
    doi     = {10.1101/2022.08.22.504706},
    publisher = {Cold Spring Harbor Laboratory},
    URL     = {https://www.biorxiv.org/content/early/2023/04/12/2022.08.22.504706},
    eprint  = {https://www.biorxiv.org/content/early/2023/04/12/2022.08.22.504706.full.pdf},
    journal = {bioRxiv}
}

@article{Nguyen2023HyenaDNALG,
    title   = {HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution},
    author  = {Eric D Nguyen and Michael Poli and Marjan Faizi and Armin W. Thomas and Callum Jacob Birch-sykes and Michael Wornow and Aman Patel and Clayton M. Rabideau and Stefano Massaroli and Yoshua Bengio and Stefano Ermon and Stephen A. Baccus and Christopher R{\'e}},
    journal = {ArXiv},
    year    = {2023},
    volume  = {abs/2306.15794}
}