[Feature] Can I use bionemo framework to extract the embeddings of evo2_40b model？

[fengxy-03]

Problem & Motivation

Hi, I am a user of bionemo.

I noticed that in evo2's github webpage, they mention that people can use bionemo for embedding long sequences. I want to use evo2_40b to extract embeddings for long sequence which length is almost 1M. I am wonder that how can I achieve this purpose through bionemo framework.

Thank you.

BioNeMo Framework Version

v2.6.3

Category

Inference

Proposed Solution

Use bionemo to extract long sequences embeddings of evo2_40b

Expected Benefits

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Code Example

[Oblynx]

Trying to do the same, I'm running into some shape mismatches when I try to run a long context model (both 7b and 40b) across 2 H200 GPUs.

[fengxy-03]

@Oblynx
I checked out the Evo2 code in BioNeMo, and it doesn't seem to support extract embeddings directly. To handle long sequences (128k), I implemented a chunking strategy for inference, and the results on my downstream tasks look promising. Hope this helps.