Implementation of ProteinBERT in Pytorch

Related tags

Text Data & NLP deep-learning artificial-intelligence protein-sequences unsupervised-learning
Overview

ProteinBERT - Pytorch (wip)

Implementation of ProteinBERT in Pytorch.

Original Repository

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}
}
You might also like...
A PyTorch implementation of paper
A PyTorch implementation of paper "Learning Shared Semantic Space for Speech-to-Text Translation", ACL (Findings) 2021

Chimera: Learning Shared Semantic Space for Speech-to-Text Translation This is a Pytorch implementation for the "Chimera" paper Learning Shared Semant

Chi Han 43 Dec 28, 2022
PyTorch Implementation of Meta-StyleSpeech : Multi-Speaker Adaptive Text-to-Speech Generation
PyTorch Implementation of Meta-StyleSpeech : Multi-Speaker Adaptive Text-to-Speech Generation

StyleSpeech - PyTorch Implementation PyTorch Implementation of Meta-StyleSpeech : Multi-Speaker Adaptive Text-to-Speech Generation. Status (2021.06.09

Keon Lee 142 Jan 6, 2023
PyTorch implementation and pretrained models for XCiT models. See XCiT: Cross-Covariance Image Transformer
PyTorch implementation and pretrained models for XCiT models. See XCiT: Cross-Covariance Image Transformer

Cross-Covariance Image Transformer (XCiT) PyTorch implementation and pretrained models for XCiT models. See XCiT: Cross-Covariance Image Transformer L

Facebook Research 605 Jan 2, 2023
A pytorch implementation of the ACL2019 paper
A pytorch implementation of the ACL2019 paper "Simple and Effective Text Matching with Richer Alignment Features".

RE2 This is a pytorch implementation of the ACL 2019 paper "Simple and Effective Text Matching with Richer Alignment Features". The original Tensorflo

null 286 Jan 2, 2023
PyTorch Implementation of VAENAR-TTS: Variational Auto-Encoder based Non-AutoRegressive Text-to-Speech Synthesis.
PyTorch Implementation of VAENAR-TTS: Variational Auto-Encoder based Non-AutoRegressive Text-to-Speech Synthesis.

VAENAR-TTS - PyTorch Implementation PyTorch Implementation of VAENAR-TTS: Variational Auto-Encoder based Non-AutoRegressive Text-to-Speech Synthesis.

Keon Lee 67 Nov 14, 2022
A Pytorch implementation of
A Pytorch implementation of "Splitter: Learning Node Representations that Capture Multiple Social Contexts" (WWW 2019).

Splitter ⠀⠀ A PyTorch implementation of Splitter: Learning Node Representations that Capture Multiple Social Contexts (WWW 2019). Abstract Recent inte

Benedek Rozemberczki 201 Nov 9, 2022
Simple Text-Generator with OpenAI gpt-2 Pytorch Implementation

GPT2-Pytorch with Text-Generator Better Language Models and Their Implications Our model, called GPT-2 (a successor to GPT), was trained simply to pre

Tae-Hwan Jung 775 Jan 8, 2023
PyTorch original implementation of Cross-lingual Language Model Pretraining.
PyTorch original implementation of Cross-lingual Language Model Pretraining.

XLM NEW: Added XLM-R model. PyTorch original implementation of Cross-lingual Language Model Pretraining. Includes: Monolingual language model pretrain

Facebook Research 2.7k Dec 27, 2022
A PyTorch implementation of the WaveGlow: A Flow-based Generative Network for Speech Synthesis

WaveGlow A PyTorch implementation of the WaveGlow: A Flow-based Generative Network for Speech Synthesis Quick Start: Install requirements: pip install

Yuchao Zhang 204 Jul 14, 2022
Comments
  • bugFix: x and y not on the same device when Learner is trained on GPU

    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?

    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
Owner
Phil Wang
Working with Attention
Phil Wang
GitHub
pytorch-kaldi is a project for developing state-of-the-art DNN/RNN hybrid speech recognition systems. The DNN part is managed by pytorch, while feature extraction, label computation, and decoding are performed with the kaldi toolkit.

The PyTorch-Kaldi Speech Recognition Toolkit PyTorch-Kaldi is an open-source repository for developing state-of-the-art DNN/HMM speech recognition sys

Mirco Ravanelli 2.3k Dec 27, 2022
Pytorch-version BERT-flow: One can apply BERT-flow to any PLM within Pytorch framework.

Pytorch-version BERT-flow: One can apply BERT-flow to any PLM within Pytorch framework.

Ubiquitous Knowledge Processing Lab 59 Dec 1, 2022
SAINT PyTorch implementation

SAINT-pytorch A Simple pyTorch implementation of "Towards an Appropriate Query, Key, and Value Computation for Knowledge Tracing" based on https://arx

Arshad Shaikh 63 Dec 25, 2022
Implementation of COCO-LM, Correcting and Contrasting Text Sequences for Language Model Pretraining, in Pytorch

COCO LM Pretraining (wip) Implementation of COCO-LM, Correcting and Contrasting Text Sequences for Language Model Pretraining, in Pytorch. They were a

Phil Wang 44 Jul 28, 2022
Implementation / replication of DALL-E, OpenAI's Text to Image Transformer, in Pytorch

Implementation / replication of DALL-E, OpenAI's Text to Image Transformer, in Pytorch

Phil Wang 5k Jan 2, 2023
A fast and easy implementation of Transformer with PyTorch.

FasySeq FasySeq is a shorthand as a Fast and easy sequential modeling toolkit. It aims to provide a seq2seq model to researchers and developers, which

宁羽 7 Jul 18, 2022
A PyTorch Implementation of End-to-End Models for Speech-to-Text

speech Speech is an open-source package to build end-to-end models for automatic speech recognition. Sequence-to-sequence models with attention, Conne

Awni Hannun 647 Dec 25, 2022
Pytorch implementation of Tacotron

Tacotron-pytorch A pytorch implementation of Tacotron: A Fully End-to-End Text-To-Speech Synthesis Model. Requirements Install python 3 Install pytorc

soobin seo 203 Dec 2, 2022
Google AI 2018 BERT pytorch implementation

BERT-pytorch Pytorch implementation of Google AI's 2018 BERT, with simple annotation BERT 2018 BERT: Pre-training of Deep Bidirectional Transformers f

Junseong Kim 5.3k Jan 7, 2023
Unofficial PyTorch implementation of Google AI's VoiceFilter system

VoiceFilter Note from Seung-won (2020.10.25) Hi everyone! It's Seung-won from MINDs Lab, Inc. It's been a long time since I've released this open-sour

MINDs Lab 881 Jan 3, 2023