Ecosyste.ms: Issues

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GitHub / hazyresearch/hyena-dna issues and pull requests

#82 - hyena equivalent to cross attention

Issue - State: open - Opened by MiqG 2 months ago

#81 - Train Evo in hyena-dna pytorch lighting framework

Issue - State: open - Opened by GUOSHU-COOL 3 months ago - 1 comment

#80 - For the dataset GenomicBenchmarks

Issue - State: open - Opened by Eyulaochen 3 months ago - 2 comments

#79 - added multispecies dataset class

Pull Request - State: closed - Opened by pmaldonado4 4 months ago

#78 - Pretrain hyenadna with more format support

Issue - State: open - Opened by HelloWorldLTY 5 months ago - 1 comment

#77 - Performance question regarding next token prediction task

Issue - State: open - Opened by HeMuling 5 months ago - 1 comment

#76 - not compatible with H100

Issue - State: open - Opened by takakoyama 5 months ago - 1 comment

#75 - RuntimeError: cuFFT error: CUFFT_INTERNAL_ERROR

Issue - State: open - Opened by ani11452 7 months ago - 3 comments

#72 - install problem

Issue - State: open - Opened by agryji08 8 months ago

#71 - transformers version forward compatibility

Pull Request - State: open - Opened by bviggiano 8 months ago - 1 comment

#70 - Inquire about GWAS tasks

Issue - State: open - Opened by 1633347510 9 months ago

#69 - Questions about pre-training with multiple sequences

Issue - State: open - Opened by HelloWorldLTY 9 months ago - 1 comment

#68 - Training loss becomes NAN during pretraining

Issue - State: closed - Opened by larel5000 9 months ago - 5 comments

#67 - Error when Resuming pre-training

Issue - State: open - Opened by richardsun-voyager 10 months ago

#66 - Symbol lookup error

Issue - State: open - Opened by buwanim 10 months ago

#62 - Bugs when I try to access the embeddings

Issue - State: open - Opened by HelloWorldLTY 11 months ago - 3 comments

#59 - Reproducing the HyenaDNA results on NT Benchmarks

Issue - State: open - Opened by leannmlindsey 11 months ago

#58 - Using Triton-based layer-norm

Pull Request - State: open - Opened by ankitvgupta 11 months ago

#57 - need to swap layer norm op for triton-based layer norm?

Issue - State: open - Opened by ankitvgupta 11 months ago - 2 comments

#54 - Delete this one, thanks.

Pull Request - State: closed - Opened by ardapekis 11 months ago

#53 - How to recreate the result of DNABERT in paper

Issue - State: open - Opened by jimmylihui 12 months ago - 1 comment

#51 - Updating Chromatin Profiling Based on Issue #43

Pull Request - State: open - Opened by lhendre 12 months ago

#50 - The tokenizer's bug in Huggingface

Issue - State: open - Opened by Horikitasaku about 1 year ago - 2 comments

#49 - How to define which dataset to use in command?

Issue - State: open - Opened by jimmylihui about 1 year ago

#48 - BUG: Using Path.iterdir() for classification labels

Pull Request - State: open - Opened by alancleary about 1 year ago

#47 - hyenaDNA for regression?

Issue - State: closed - Opened by pierrj about 1 year ago - 1 comment

#46 - Pretraining runtimes from the paper

Issue - State: open - Opened by sgalkina about 1 year ago - 1 comment

#45 - cannot run hg38_hyena_seqlen_warmup_reload

Issue - State: open - Opened by sustcsonglin about 1 year ago - 2 comments

#44 - Pre-training on local genome data

Issue - State: closed - Opened by richardsun-voyager about 1 year ago - 1 comment

#43 - Chromatin Preprocessing

Issue - State: open - Opened by lhendre about 1 year ago - 10 comments

#42 - Sanity Checking DataLoader error

Issue - State: open - Opened by DieTANG about 1 year ago - 3 comments

#41 - Could this HyenaDNA model be used for a pure language task?

Issue - State: closed - Opened by jabogithub about 1 year ago - 1 comment

#40 - CUFFT-type error when running huggingface.py to generate embeddings

Issue - State: closed - Opened by salvatoreloguercio about 1 year ago - 3 comments

#39 - Clarifying the models available on HF

Issue - State: closed - Opened by yair-schiff about 1 year ago - 4 comments

#38 - Trouble reproducing Nucleotide Transformer Benchmarks Result

Issue - State: closed - Opened by yair-schiff about 1 year ago - 2 comments

#37 - Trouble reproducing Genomics Benchmark Result

Issue - State: closed - Opened by yair-schiff about 1 year ago - 2 comments

#34 - Error in Pretraining on Human Genome

Issue - State: closed - Opened by leannmlindsey about 1 year ago - 6 comments

#33 - Updated to run hg38 experiment on newer pytorch lightning version.

Pull Request - State: open - Opened by jondeaton about 1 year ago

#32 - Update hg38 data download to use curl instead of gsutil.

Pull Request - State: closed - Opened by jondeaton about 1 year ago - 3 comments

#31 - MCC value problem on Nucleotide Transformer

Issue - State: closed - Opened by WeiminWu2000 about 1 year ago - 7 comments

#31 - MCC value problem on Nucleotide Transformer

Issue - State: closed - Opened by WeiminWu2000 about 1 year ago - 7 comments

#30 - Cuda out of memory for huggingface pre-trained model on A100-80GB

Issue - State: closed - Opened by AndreiBlindu over 1 year ago - 6 comments

#29 - Model weights trained on the Genomics Benchmark Dataset

Issue - State: closed - Opened by abhinav-kashyap-asus over 1 year ago - 2 comments

#28 - Question about HyenaDNA working

Issue - State: closed - Opened by varuntrivedi18 over 1 year ago - 2 comments

#27 - Pre-trained model for genomic benchmarks

Issue - State: closed - Opened by alancleary over 1 year ago - 2 comments

#25 - Unable to download the Human Reference Genome data

Issue - State: closed - Opened by Geraldene over 1 year ago

#24 - Questions on running as module

Issue - State: closed - Opened by zhguo9 over 1 year ago - 1 comment

#23 - Human Reference Genome questions

Issue - State: closed - Opened by kirill-vishniakov over 1 year ago - 1 comment

#22 - Some doubts about downstream tasks

Issue - State: closed - Opened by zhguo9 over 1 year ago - 4 comments

#21 - Next token prediction - head code location / config to pass

Issue - State: closed - Opened by HuangPZ over 1 year ago - 1 comment

#20 - Language model inference

Issue - State: closed - Opened by gonzalobenegas over 1 year ago - 9 comments

#19 - nucleotide finetuning

Issue - State: closed - Opened by wawpaopao over 1 year ago - 5 comments

#18 - Nucleotide vs codons

Issue - State: closed - Opened by KadirErturk4r over 1 year ago - 3 comments

#17 - pretrain model weights miss pos_emb

Issue - State: closed - Opened by WalkerSue over 1 year ago - 6 comments

#16 - tokenizer do not padding sequence to same length autoly.

Issue - State: closed - Opened by WalkerSue over 1 year ago - 4 comments

#15 - CUDA out of memory with hyena-1m on A100-80G

Issue - State: closed - Opened by pone7 over 1 year ago - 6 comments

#14 - git-lfs missing from container

Issue - State: closed - Opened by KatharinaHoff over 1 year ago - 12 comments

#13 - Fix moving torchmetrics to cuda device 0

Pull Request - State: closed - Opened by awaelchli over 1 year ago

#12 - ICL question

Issue - State: closed - Opened by annamykcode over 1 year ago - 1 comment

#11 - several updates

Pull Request - State: closed - Opened by exnx over 1 year ago

#10 - Speed-up Genomic Benchmarks dataloader

Pull Request - State: closed - Opened by cbirchsy over 1 year ago - 1 comment

#9 - Flash Attention 2

Issue - State: closed - Opened by dbrami over 1 year ago - 1 comment

#8 - Thank you for doing this, and thank you for open-sourcing it!

Issue - State: closed - Opened by Tylersuard over 1 year ago - 2 comments

#7 - flash-attention installment

Issue - State: closed - Opened by rohandavidg over 1 year ago - 3 comments

#6 - README update with species

Pull Request - State: closed - Opened by Miking98 over 1 year ago

#5 - ImportError: dropout_add_layer_norm is not installed

Issue - State: closed - Opened by kunjiefan over 1 year ago - 4 comments

#4 - Fix typo in encoders.py

Pull Request - State: closed - Opened by eltociear over 1 year ago

#3 - Addition to Transformers

Issue - State: closed - Opened by tanaymeh over 1 year ago - 3 comments

#2 - Model output changes randomly

Issue - State: closed - Opened by swertz over 1 year ago - 4 comments

#1 - fix huggingface links

Pull Request - State: closed - Opened by atgctg over 1 year ago - 1 comment