HazyResearch hyena-dna issues

HazyResearch / hyena-dna

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

https://arxiv.org/abs/2306.15794

Apache License 2.0

532 stars 74 forks source link

issues

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install problem

#72 agryji08 opened 4 days ago
0
transformers version forward compatibility

#71 bviggiano opened 2 weeks ago
1
Inquire about GWAS tasks

#70 1633347510 opened 1 month ago
0
Questions about pre-training with multiple sequences

#69 HelloWorldLTY opened 1 month ago
1
Training loss becomes NAN during pretraining

#68 larel5000 closed 1 month ago
1
Error when Resuming pre-training

#67 richardsun-voyager opened 2 months ago
0
Symbol lookup error

#66 buwanim opened 2 months ago
0
Failure to reproduce the hyenaDNA reported results on NT tasks. HURRY! HURRY HURRY

#65 multydoffer opened 2 months ago
0
How can I access the dataset--genomic_benchmark I got timeout issue

#64 qijishinidie opened 2 months ago
0
Question: How to generate DNA sequence or sequence embeddings based on own bed file

#63 HelloWorldLTY opened 3 months ago
0
Bugs when I try to access the embeddings

#62 HelloWorldLTY opened 3 months ago
3
The default for pretrained_model_path in config files is a personal directory

#61 leannmlindsey opened 3 months ago
0
Running with standard Huggingface config and trainer files does not give optimal results

#60 leannmlindsey opened 3 months ago
0
Reproducing the HyenaDNA results on NT Benchmarks

#59 leannmlindsey opened 3 months ago
0
Using Triton-based layer-norm

#58 ankitvgupta opened 3 months ago
0
need to swap layer norm op for triton-based layer norm?

#57 ankitvgupta opened 3 months ago
2
How to pre-train on custom dataset using hyena-dna

#56 OswaldoBornemann opened 3 months ago
0
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.

#55 Ontos46 opened 3 months ago
0
Delete this one, thanks.

#54 ardapekis closed 3 months ago
0
How to recreate the result of DNABERT in paper

#53 jimmylihui opened 4 months ago
1
Predicting probability vectors of equal length to input sequence

#52 CherWeiYuan opened 4 months ago
0
Updating Chromatin Profiling Based on Issue #43

#51 lhendre opened 4 months ago
0
The tokenizer's bug in Huggingface

#50 Horikitasaku opened 4 months ago
1
How to define which dataset to use in command?

#49 jimmylihui opened 4 months ago
0
BUG: Using Path.iterdir() for classification labels

#48 alancleary opened 4 months ago
0
hyenaDNA for regression?

#47 pierrj closed 4 months ago
1
Pretraining runtimes from the paper

#46 sgalkina opened 5 months ago
1
cannot run hg38_hyena_seqlen_warmup_reload

#45 sustcsonglin opened 5 months ago
2
Pre-training on local genome data

#44 richardsun-voyager closed 4 months ago
1
Chromatin Preprocessing

#43 lhendre opened 5 months ago
9
Sanity Checking DataLoader error

#42 DieTANG opened 6 months ago
3
Could this HyenaDNA model be used for a pure language task?

#41 jabogithub closed 4 months ago
1
CUFFT-type error when running huggingface.py to generate embeddings

#40 salvatoreloguercio closed 6 months ago
3
Clarifying the models available on HF

#39 yair-schiff closed 5 months ago
4
Trouble reproducing Nucleotide Transformer Benchmarks Result

#38 yair-schiff closed 6 months ago
2
Trouble reproducing Genomics Benchmark Result

#37 yair-schiff closed 6 months ago
2
How to correctly provide padding tokens to forward pass of pretrained model?

#36 josiahbjorgaard opened 6 months ago
1
Genome build versions are inconsistent in reference and chromatin profile (DeepSEA benchmark)

#35 kohanlee1995 closed 7 months ago
3
Error in Pretraining on Human Genome

#34 leannmlindsey closed 7 months ago
6
Updated to run hg38 experiment on newer pytorch lightning version.

#33 jondeaton opened 7 months ago
0
Update hg38 data download to use curl instead of gsutil.

#32 jondeaton closed 7 months ago
3
MCC value problem on Nucleotide Transformer

#31 WeiminWu2000 closed 7 months ago
7
Cuda out of memory for huggingface pre-trained model on A100-80GB

#30 AndreiBlindu closed 7 months ago
6
Model weights trained on the Genomics Benchmark Dataset

#29 abhinav-kashyap-asus closed 7 months ago
2
Question about HyenaDNA working

#28 varuntrivedi18 closed 7 months ago
2
Pre-trained model for genomic benchmarks

#27 alancleary closed 8 months ago
2
ImportError: Error loading 'src.models.sequence.dna_embedding.DNAEmbeddingModel':

#26 richardsun-voyager closed 8 months ago
2
Unable to download the Human Reference Genome data

#25 Geraldene closed 8 months ago
0
Questions on running as module

#24 zhguo9 closed 8 months ago
1
Human Reference Genome questions

#23 kirill-vishniakov closed 8 months ago
1