Implementation of ProteinBERT in Pytorch

Related tags

Text Data & NLPdeep-learningartificial-intelligenceprotein-sequencesunsupervised-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 Repository
端到端的长本文摘要模型（法研杯2020司法摘要赛道）

端到端的长文本摘要模型（法研杯2020司法摘要赛道）

苏剑林(Jianlin Su) 334 Jan 08, 2023
Simple text to phones converter for multiple languages

Phonemizer -- foʊnmaɪzɚ The phonemizer allows simple phonemization of words and texts in many languages. Provides both the phonemize command-line tool

CoML 762 Dec 29, 2022
A high-level Python library for Quantum Natural Language Processing

lambeq About lambeq is a toolkit for quantum natural language processing (QNLP). Documentation: https://cqcl.github.io/lambeq/ Getting started Prerequ

Cambridge Quantum 315 Jan 01, 2023
In this repository we have tested 3 VQA models on the ImageCLEF-2019 dataset.

Med-VQA In this repository we have tested 3 VQA models on the ImageCLEF-2019 dataset. Two of these are made on top of Facebook AI Reasearch's Multi-Mo

Kshitij Ambilduke 8 Apr 14, 2022
This is the library for the Unbounded Interleaved-State Recurrent Neural Network (UIS-RNN) algorithm, corresponding to the paper Fully Supervised Speaker Diarization.

UIS-RNN Overview This is the library for the Unbounded Interleaved-State Recurrent Neural Network (UIS-RNN) algorithm. UIS-RNN solves the problem of s

Google 1.4k Dec 28, 2022
CodeBERT: A Pre-Trained Model for Programming and Natural Languages.

CodeBERT This repo provides the code for reproducing the experiments in CodeBERT: A Pre-Trained Model for Programming and Natural Languages. CodeBERT

Microsoft 1k Jan 03, 2023
Official implementation of MLP Singer: Towards Rapid Parallel Korean Singing Voice Synthesis

MLP Singer Official implementation of MLP Singer: Towards Rapid Parallel Korean Singing Voice Synthesis. Audio samples are available on our demo page.

Neosapience 103 Dec 23, 2022
Visual Automata is a Python 3 library built as a wrapper for Caleb Evans' Automata library to add more visualization features.

Visual Automata Copyright 2021 Lewi Lie Uberg Released under the MIT license Visual Automata is a Python 3 library built as a wrapper for Caleb Evans'

Lewi Uberg 55 Nov 17, 2022
Natural Language Processing for Adverse Drug Reaction (ADR) Detection

Natural Language Processing for Adverse Drug Reaction (ADR) Detection This repo contains code from a project to identify ADRs in discharge summaries a

Medicines Optimisation Service - Austin Health 21 Aug 05, 2022
Just Another Telegram Ai Chat Bot Written In Python With Pyrogram.

OkaeriChatBot Just another Telegram AI chat bot written in Python using Pyrogram. Requirements Python 3.7 or higher.

Wahyusaputra 2 Dec 23, 2021
Creating a python chatbot that Starbucks users can text to place an order + help cut wait time of a normal coffee.

Creating a python chatbot that Starbucks users can text to place an order + help cut wait time of a normal coffee.

2 Jan 20, 2022
DziriBERT: a Pre-trained Language Model for the Algerian Dialect

DziriBERT is the first Transformer-based Language Model that has been pre-trained specifically for the Algerian Dialect.

117 Jan 07, 2023
This is a NLP based project to extract effective date of the contract from their text files.

Date-Extraction-from-Contracts This is a NLP based project to extract effective date of the contract from their text files. Problem statement This is

Sambhav Garg 1 Jan 26, 2022
TunBERT is the first release of a pre-trained BERT model for the Tunisian dialect using a Tunisian Common-Crawl-based dataset.

TunBERT is the first release of a pre-trained BERT model for the Tunisian dialect using a Tunisian Common-Crawl-based dataset. TunBERT was applied to three NLP downstream tasks: Sentiment Analysis (S

InstaDeep Ltd 72 Dec 09, 2022
Pervasive Attention: 2D Convolutional Networks for Sequence-to-Sequence Prediction

This is a fork of Fairseq(-py) with implementations of the following models: Pervasive Attention - 2D Convolutional Neural Networks for Sequence-to-Se

Maha 490 Dec 15, 2022
BERTAC (BERT-style transformer-based language model with Adversarially pretrained Convolutional neural network)

BERTAC (BERT-style transformer-based language model with Adversarially pretrained Convolutional neural network) BERTAC is a framework that combines a

6 Jan 24, 2022
This is the 25 + 1 year anniversary version of the 1995 Rachford-Rice contest

Rachford-Rice Contest This is the 25 + 1 year anniversary version of the 1995 Rachford-Rice contest. Can you solve the Rachford-Rice problem for all t

13 Sep 20, 2022
Python api wrapper for JellyFish Lights

Python api wrapper for JellyFish Lights The hope is to make this a pip installable package Current capabalilities: Connects to a local JellyFish Light

10 Dec 18, 2022
Yet Another Sequence Encoder - Encode sequences to vector of vector in python !

Yase Yet Another Sequence Encoder - encode sequences to vector of vectors in python ! Why Yase ? Yase enable you to encode any sequence which can be r

Pierre PACI 12 Aug 19, 2021
Document processing using transformers

Doc Transformers Document processing using transformers. This is still in developmental phase, currently supports only extraction of form data i.e (ke

Vishnu Nandakumar 13 Dec 21, 2022