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.
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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.
I am interested in this. Can you point to a reference about the application of LLMs to sequence secreening? Thanks.
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...