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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. Hy
by robwwilliams 3y 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.
- ssn 3y agoI am interested in this. Can you point to a reference about the application of LLMs to sequence secreening? Thanks.
- robwwilliams 3y agoScaling 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://hazyresearch.stanford.edu/blog/2023-06-29-hyena-dna https://github.com/instadeepai/nucleotide-transformer https://github.com/instadeepai/nucleotide-transformer https://dl.acm.org/doi/pdf/10.1145/3535508.3545512 https://dl.acm.org/doi/pdf/10.1145/3535508.3545512 https://github.com/dnbaker/bioseq https://github.com/dnbaker/bioseq https://huggingface.co/AIRI-Institute/gena-lm-bert-base https://huggingface.co/AIRI-Institute/gena-lm-bert-base https://discuss.huggingface.co/t/dna-long-sequence-tokenization/16154 https://discuss.huggingface.co/t/dna-long-sequence-tokenizat...