DNABERT VS transformers

If I want to get started, they said it's optional to pre-train (so you can skip to step 3). This is where I got tripped up: "Note that the sequences are in kmer format, so you will need to convert your sequences into that." From what I understand, you need to do this so that all of the sequences are the same length? So kmer=6 means all of the sequences are length 6? Someone suggested that I take the first nucleotide in the promoter and grab 3 nucleotides before and 3 nucleotides after (+/-3 bases). I don't think that's how the kmer thing works though? I tried replicating how I think it works down below (I got confused on the last row of the 'after' df). Please correct me if I'm wrong!

Fascinating work, very promising.

Can you summarise how the model in your paper differs from this one ?

https://github.com/huggingface/transformers/issues/27011

transformers is a package by Hugging Face, that helps you interact with models on HF Hub (GitHub)

Is t5x an encoder/decoder architecture?

Some more general options.

The Flax ecosystem

https://github.com/google/flax?tab=readme-ov-file

or dm-haiku

https://github.com/google-deepmind/dm-haiku

were some of the best developed communities in the Jax AI field

Perhaps the “trax” repo? https://github.com/google/trax

Some HF examples https://github.com/huggingface/transformers/tree/main/exampl...

Sadly it seems much of the work is proprietary these days, but one example could be Grok-1, if you customize the details. https://github.com/xai-org/grok-1/blob/main/run.py

The HuggingFace transformers library already has support for a similar method called prompt lookup decoding that uses the existing context to generate an ngram model: https://github.com/huggingface/transformers/issues/27722

I don't think it would be that hard to switch it out for a pretrained ngram model.

Most of this tutorial is based on Hugging Face course about Transformers and on Niels Rogge's Transformers tutorials: make sure to check their work and give them a star on GitHub, if you please ❤️

* Superconvergence + LR range finder + Fast AI's Ranger21 optimizer was the goto optimizer for CNNs, and worked fabulously well, but on transformers, the learning rate range finder sadi 1e-3 was the best, whilst 1e-5 was better. However, the 1 cycle learning rate stuck. https://github.com/huggingface/transformers/issues/16013

Thanks! :) I'm pushing them into transformers, pytorch-gemma and collabing with the Gemma team to resolve all the issues :)

The RoPE fix should already be in transformers 4.38.2: https://github.com/huggingface/transformers/pull/29285

My main PR for transformers which fixes most of the issues (some still left): https://github.com/huggingface/transformers/pull/29402