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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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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