progen

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Weird behavior with memory usage within samply.py

1

So for some reason `progen2-base` starts to use an ungodly amount of VRAM the more I increase the value for `--num-samples`. If I set the value of `--num-samples` to 50...

GrayWasTaken

Wonderful paper, a great experimental exposition of where/why the natural sequence models will cap out to support Weinsteins theoretical work. Could you provide the dataset used from Koenig? > Lastly,...

oliverdutton

correlation with Facebook ESM's log_likelihood

8

Hi all, I've tested progen2 on an antibody Fv for which we've also calculated Facebook's ESM log_likelihood stability values, and we see very little correlation between the two. I've tested...

avilella

Add a sequence classification head to ProtGen2

2

I'm trying to put a sequence prediction head(= sequence classification with 1 output) on top of the ProGen2 model and am experiencing some problems. For this one usually needs to...

franzigeiger

Sampling conditional token distribution

1

It would be super valuable to have an example script to sample conditional token probabilities for a target index given sequence context. There seem to be some technical details that...

aiXander

How can we extract embedding for a protein sequence?

1

Is there a way to extract the embedding from the pretrained model using the input protein sequence?

suresh-pokharel

Greetings, really impressive work!. However, I came accross a problem when I run the command below: python3 sample.py --model ${model} --t 0.8 --p 0.9 --max-length 1500 --num-samples 10 --context "1MDKKY...

ZeroKeng

Generate sequence based on natural one

4

Hi, First of all, thank you for sharing ProGen2 code. I read the article as part of my thesis, and started playing with the model. My questions: 1) How may...

avivlazar

How to specify a control tag in the sample script?

3

In the paper it was mentioned that one can sample sequences based on a control tag. Could you provide an example for using a control tag with the ```sample.py ```...

LiorZ

Control tags not in tokenizer

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Curious how we can prepend control tags for conditional generation. I noticed the control tags are not in the tokenizer, so how could we input them to the model?

lhallee