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HazyResearch / hyena-dna

Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

Home Page:https://arxiv.org/abs/2306.15794

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Pre-trained model for genomic benchmarks

alancleary opened this issue · comments

commented

Hello. We've been working through replicating the results from your arXiv paper to better understand HyenaDNA and how we can use it for our own purposes. Using the hyena-dna-nt6 Docker image, we were able to successfully replicate the "Nucleotide Transformer" experiments. However, we've been unable to replicate the "Genomic Benchmark" experiments because the pretrained_model_path in the configs/experiment/hg38/genomic_benchmark.yaml file is set to a path that doesn't exist in the container: /local-scratch/nigam/projects/mwornow/projects/safari-internal/outputs/2023-04-14/2_128_1024.ckpt.

Is this file available somewhere that we can access it? This appears to be the file that's generated by the Quick Entry point experiment, but we would like to use a pre-trained model if possible before generating our own for this first round of validation.

Thanks!

commented

Sure, checkout the public weights here. It's the tiny-1k model.

commented

Thanks for the quick response @exnx. I had a suspicion we could use the pre-trained models on Hugging Face but didn't want to assume. Cheers!