Comments (3)
exnx
commented on August 13, 2024
That's a fine idea! Though we did not for this work, we were also interested in regulatory regions of the genome.
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KadirErturk4r
commented on August 13, 2024
it may be more make sense, since there are only 22 amino acid in proteins and 20 of them in universal genetic code.
Like alphabet letters vs words.
Also codon series may make regions more visible. (Think it as a words in a sentence)
if you have a new sequence are you able to make it chemically?
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exnx
commented on August 13, 2024
We certainly encourage folks to experiment with the model for their use cases. As mentioned above, we're interested in regulatory regions too, which do not have a codon vocab.
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Related Issues (20)
- Predicting probability vectors of equal length to input sequence
- How to recreate the result of DNABERT in paper HOT 1
- How to convert the batch cell from the GenomicBenchmarks data to user data? CUDA memory overload if running "Single example" cell multiple times to produce embeddings.
- How to pre-train on custom dataset using hyena-dna
- need to swap layer norm op for triton-based layer norm? HOT 2
- Reproducing the HyenaDNA results on NT Benchmarks
- Running with standard Huggingface config and trainer files does not give optimal results
- The default for pretrained_model_path in config files is a personal directory
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- Question: How to generate DNA sequence or sequence embeddings based on own bed file
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- Failure to reproduce the hyenaDNA reported results on NT tasks. HURRY! HURRY HURRY
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- Questions about pre-training with multiple sequences HOT 1
- Inquire about GWAS tasks
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- Where are genomic_bench_dataloader.py and nucleotide_transformer_dataloader.py located?
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