wangjiaqi-lab-SYSU
wangjiaqi-lab-SYSU
> Biotrainer is using [bio_embeddings](https://github.com/sacdallago/bio_embeddings) to calculate embeddings for the provided sequences. Currently, this does not allow for fine-tuning existing protein language models (pLMs) such as [ProtTrans](https://github.com/agemagician/ProtTrans/tree/master) for specific tasks,...
> In the meantime, I would recommend using the notebooks provided here: https://github.com/RSchmirler/data-repo_plm-finetune-eval/tree/main/notebooks/finetune Cool. Thank you. Congratulation for the work! JQ
> Hi, typically this is a regression task, i.e. inputting a protein sequence to the model and getting the output value about the fitness effect. If your 500,000 protein sequences...
> Hi, you could refer to this issue #16 for some details. Thanks for the timely reply. Good day!
Thank you very much for the timely reply. JQ
> Hello and thanks for your question! I'd suggest you take a look at [biotrainer](https://github.com/sacdallago/biotrainer), a framework that allows to train standardized models on embeddings from any pLM (or even...
> Thanks for asking, I checked it today and only had to implement a small change ([sacdallago/biotrainer#105](https://github.com/sacdallago/biotrainer/pull/105)) to make the model work. While `tokenizer.tokenize(seq)` works as expected within the biotrainer...
> Hi JQ, > > Have you installed the environment successfully before running the script `run.sh`? I run the $bash install.sh, and it runs normally. I then have to go...
when I run $bash run.sh in local_server, it complains the same thing. -------------------------------------------------- The version is not the latest. Updating... HEAD is now at 23a69ad No public description Already up...
Ok, I have tried to install from scratch. I have first modify the install.sh to make a directory for cache in /home/dc/.cache/SaprotHub instead of /root/.cache/SaprotHub, the modified install.sh script is...