HazyResearch / hyena-dna

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

https://arxiv.org/abs/2306.15794

HazyResearch/hyena-dna Issues

Where are genomic_bench_dataloader.py and nucleotide_transformer_dataloader.py located?
Closed 17 days ago
CUDA out of memory occurs when the training length reaches 450k on a100
Updated 19 days ago1
install problem
Updated 2 months ago
Inquire about GWAS tasks
Updated 2 months ago
Training loss becomes NAN during pretraining
Closed 3 months ago1
Bugs when I try to access the embeddings
Updated 3 months ago3
Questions about pre-training with multiple sequences
Updated 3 months ago1
Chromatin Preprocessing
Updated 3 months ago9
Error when Resuming pre-training
Updated 3 months ago
Symbol lookup error
Updated 4 months ago
Failure to reproduce the hyenaDNA reported results on NT tasks. HURRY! HURRY HURRY
Updated 4 months ago
How can I access the dataset--genomic_benchmark I got timeout issue
Updated 4 months ago
Question: How to generate DNA sequence or sequence embeddings based on own bed file
Updated 4 months ago
The default for pretrained_model_path in config files is a personal directory
Updated 5 months ago
Running with standard Huggingface config and trainer files does not give optimal results
Updated 5 months ago
Reproducing the HyenaDNA results on NT Benchmarks
Updated 5 months ago
need to swap layer norm op for triton-based layer norm?
Updated 5 months ago2
How to pre-train on custom dataset using hyena-dna
Updated 5 months ago
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.
Updated 5 months ago
Sanity Checking DataLoader error
Updated 5 months ago3
How to recreate the result of DNABERT in paper
Updated 5 months ago1
Predicting probability vectors of equal length to input sequence
Updated 6 months ago
CUFFT-type error when running huggingface.py to generate embeddings
Closed 8 months ago3
The tokenizer's bug in Huggingface
Updated 6 months ago1
hyenaDNA for regression?
Closed 6 months ago1
Pre-training on local genome data
Closed 6 months ago1
How to correctly provide padding tokens to forward pass of pretrained model?
Updated 6 months ago1
Could this HyenaDNA model be used for a pure language task?
Closed 6 months ago1
Pretraining runtimes from the paper
Updated 6 months ago1
How to define which dataset to use in command?
Updated 6 months ago
Clarifying the models available on HF
Closed 7 months ago4
cannot run hg38_hyena_seqlen_warmup_reload
Updated 7 months ago2
Trouble reproducing Genomics Benchmark Result
Closed 8 months ago2
Trouble reproducing Nucleotide Transformer Benchmarks Result
Closed 8 months ago2
Genome build versions are inconsistent in reference and chromatin profile (DeepSEA benchmark)
Closed 8 months ago3
Error in Pretraining on Human Genome
Closed 8 months ago6
MCC value problem on Nucleotide Transformer
Closed 9 months ago7
Language model inference
Closed 10 months ago9
Cuda out of memory for huggingface pre-trained model on A100-80GB
Closed 9 months ago6
Model weights trained on the Genomics Benchmark Dataset
Closed 9 months ago2
Question about HyenaDNA working
Closed 9 months ago2
ImportError: Error loading 'src.models.sequence.dna_embedding.DNAEmbeddingModel':
Closed 9 months ago2
Pre-trained model for genomic benchmarks
Closed 9 months ago2
Unable to download the Human Reference Genome data
Closed 10 months ago
Human Reference Genome questions
Closed 10 months ago1
Questions on running as module
Closed 10 months ago1
Some doubts about downstream tasks
Closed 10 months ago4
Next token prediction - head code location / config to pass
Closed 10 months ago1
nucleotide finetuning
Closed 10 months ago5
Nucleotide vs codons
Closed a year ago3