Implementation of ProteinBERT in Pytorch

Last update: Dec 25, 2022

Overview

ProteinBERT - Pytorch (wip)

Implementation of ProteinBERT in Pytorch.

Install

$ pip install protein-bert-pytorch

Usage

import torch
from protein_bert_pytorch import ProteinBERT

model = ProteinBERT(
    num_tokens = 21,
    num_annotation = 8943,
    dim = 512,
    dim_global = 256,
    depth = 6,
    narrow_conv_kernel = 9,
    wide_conv_kernel = 9,
    wide_conv_dilation = 5,
    attn_heads = 8,
    attn_dim_head = 64
)

seq = torch.randint(0, 21, (2, 2048))
mask = torch.ones(2, 2048).bool()
annotation = torch.randint(0, 1, (2, 8943)).float()

seq_logits, annotation_logits = model(seq, annotation, mask = mask) # (2, 2048, 21), (2, 8943)

Citations

@article {Brandes2021.05.24.445464,
    author      = {Brandes, Nadav and Ofer, Dan and Peleg, Yam and Rappoport, Nadav and Linial, Michal},
    title       = {ProteinBERT: A universal deep-learning model of protein sequence and function},
    year        = {2021},
    doi         = {10.1101/2021.05.24.445464},
    publisher   = {Cold Spring Harbor Laboratory},
    URL         = {https://www.biorxiv.org/content/early/2021/05/25/2021.05.24.445464},
    eprint      = {https://www.biorxiv.org/content/early/2021/05/25/2021.05.24.445464.full.pdf},
    journal     = {bioRxiv}
}

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Comments

bugFix: x and y not on the same device when Learner is trained on GPU

When

seq        = torch.randint(0, 21, (2, 2048)).cuda()
annotation = torch.randint(0, 1, (2, 8943)).float().cuda()
mask       = torch.ones(2, 2048).bool().cuda()

learner.cuda()

loss = learner(seq, annotation, mask = mask) # (2, 2048, 21), (2, 8943)

OUTPUT

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-2-60892e498570> in <module>
      4 learner.cuda()
      5 
----> 6 loss = learner(seq, annotation, mask = mask) # (2, 2048, 21), (2, 8943)

~/data/.conda/envs/torch/lib/python3.8/site-packages/torch/nn/modules/module.py in _call_impl(self, *input, **kwargs)
    887             result = self._slow_forward(*input, **kwargs)
    888         else:
--> 889             result = self.forward(*input, **kwargs)
    890         for hook in itertools.chain(
    891                 _global_forward_hooks.values(),

/mnt/5280b/wwang/proteinbert/protein_bert_pytorch.py in forward(self, seq, annotation, mask)
    365 
    366         for token_id in self.exclude_token_ids:
--> 367             random_replace_token_prob_mask = random_replace_token_prob_mask & (random_tokens != token_id)  # make sure you never substitute a token with an excluded token type (pad, start, end)
    368 
    369         # noise sequence

RuntimeError: Expected all tensors to be on the same device, but found at least two devices, cuda:0 and cpu!

opened by wilmerwang 0

How to use this bert version to use the pretrianed model?

Hi guys, thanks for great work. I'm trying to use this pytorch version protein-bert to use the pre-trained model 'ftp://ftp.cs.huji.ac.il/users/nadavb/protein_bert/epoch_92400_sample_23500000.pkl', but have no clues at all. Could you please give some suggestions? Thank you so much!

opened by Y-H-Joe 1

Implementation of ProteinBERT in Pytorch

Related tags

Overview

ProteinBERT - Pytorch (wip)

Install

Usage

Citations

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How to use this bert version to use the pretrianed model?

Releases(0.1.0)

0.1.0(Aug 10, 2021)

0.0.11(Aug 6, 2021)

0.0.10(Jun 11, 2021)

0.0.9(Jun 11, 2021)

0.0.8(Jun 11, 2021)

0.0.7(Jun 10, 2021)

0.0.6(May 29, 2021)

0.0.5(May 28, 2021)

0.0.4(May 28, 2021)

0.0.3a(May 28, 2021)

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Owner

Phil Wang

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