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by robwwilliams 797 days ago
This approach is already useful in functional genomics. A common type of question requires analysis of hundreds of potentially functional sequence variants.

Hybrid LLM+ approaches are beginning to improve efficiency of ranking candidates and even proposing tests and soon I hope—higher order non-linear interactions among DNA variants.
1 comments
ssn 796 days ago
I am interested in this. Can you point to a reference about the application of LLMs to sequence secreening? Thanks.
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robwwilliams 792 days ago
Scaling if context window size has been a problem but now good potential of solutions using mamba.

HyenaDNA is one to look at wrt DNA.

And here are some other interesting links from Erik Garrison—a leader in pangenomics.

https://hazyresearch.stanford.edu/blog/2023-06-29-hyena-dna

https://github.com/instadeepai/nucleotide-transformer

https://dl.acm.org/doi/pdf/10.1145/3535508.3545512

https://github.com/dnbaker/bioseq

https://huggingface.co/AIRI-Institute/gena-lm-bert-base

https://discuss.huggingface.co/t/dna-long-sequence-tokenizat...

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