To be a next-generation DL-based phenotype prediction from genome mutations.

Last update: Jan 11, 2022

Related tags

Overview

Sequence -----------+--> 3D_structure --> 3D_module --+                                      +--> ?
|                   |                                 |                                      +--> ?
|                   |                                 +--> Joint_module --> Hierarchical_CLF +--> ?
|                   |                                 |                                      +--> ?
+-> NLP_embeddings -+-------> Embedding_module -------+                                      +--> ?

ClynMut: Predicting the Clynical Relevance of Genome Mutations (wip)

To be a next-generation DL-based phenotype prediction from genome mutations. Will use sota NLP and structural techniques.

Planned modules will likely be:

3D learning module
NLP embeddings
Joint module + Hierarchical classification

The main idea is for the model to learn the prediction in an end-to-end fashion.

Install

$ pip install clynmut

Example Usage:

import torch
from clynmut import *

hier_graph = {"class": "all", 
              "children": [
                {"class": "effect_1", "children": [
                  {"class": "effect_12", "children": []},
                  {"class": "effect_13", "children": []}
                ]},
                {"class": "effect_2", "children": []},
                {"class": "effect_3", "children": []},
              ]}

model = MutPredict(
    seq_embedd_dim = 512,
    struct_embedd_dim = 256, 
    seq_reason_dim = 512, 
    struct_reason_dim = 256,
    hier_graph = hier_graph,
    dropout = 0.0,
    use_msa = False,
    device = None)

seqs = ["AFTQRWHDLKEIMNIDALTWER",
        "GHITSMNWILWVYGFLE"]

pred_dicts = model(seqs, pred_format="dict")

Important topics:

3D structure learning

There are a couple architectures that can be used here. I've been working on 2 of them, which are likely to be used here:

GVP
E(n)-gnn

Hierarchical classification

A simple custom helper class has been developed for it.

Testing

$ python setup.py test

Datasets:

This package will use the awesome work by Jonathan King at this repository.

To install

$ pip install git+https://github.com/jonathanking/sidechainnet.git

$ git clone https://github.com/jonathanking/sidechainnet.git
$ cd sidechainnet && pip install -e .

Citations:

@article{pejaver_urresti_lugo-martinez_pagel_lin_nam_mort_cooper_sebat_iakoucheva et al._2020,
    title={Inferring the molecular and phenotypic impact of amino acid variants with MutPred2},
    volume={11},
    DOI={10.1038/s41467-020-19669-x},
    number={1},
    journal={Nature Communications},
    author={Pejaver, Vikas and Urresti, Jorge and Lugo-Martinez, Jose and Pagel, Kymberleigh A. and Lin, Guan Ning and Nam, Hyun-Jun and Mort, Matthew and Cooper, David N. and Sebat, Jonathan and Iakoucheva, Lilia M. et al.},
    year={2020}

@article{rehmat_farooq_kumar_ul hussain_naveed_2020, 
    title={Predicting the pathogenicity of protein coding mutations using Natural Language Processing},
    DOI={10.1109/embc44109.2020.9175781},
    journal={2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)},
    author={Rehmat, Naeem and Farooq, Hammad and Kumar, Sanjay and ul Hussain, Sibt and Naveed, Hammad},
    year={2020}

@article{pagel_antaki_lian_mort_cooper_sebat_iakoucheva_mooney_radivojac_2019,
    title={Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome},
    volume={15},
    DOI={10.1371/journal.pcbi.1007112},
    number={6},
    journal={PLOS Computational Biology},
    author={Pagel, Kymberleigh A. and Antaki, Danny and Lian, AoJie and Mort, Matthew and Cooper, David N. and Sebat, Jonathan and Iakoucheva, Lilia M. and Mooney, Sean D. and Radivojac, Predrag},
    year={2019},
    pages={e1007112}

You might also like...

An Analysis Toolkit for Natural Language Generation (Translation, Captioning, Summarization, etc.)

VizSeq is a Python toolkit for visual analysis on text generation tasks like machine translation, summarization, image captioning, speech translation

409 Oct 28, 2022

Summarization, translation, sentiment-analysis, text-generation and more at blazing speed using a T5 version implemented in ONNX.

Summarization, translation, Q&A, text generation and more at blazing speed using a T5 version implemented in ONNX. This package is still in alpha stag

211 Dec 28, 2022

GAP-text2SQL: Learning Contextual Representations for Semantic Parsing with Generation-Augmented Pre-Training

GAP-text2SQL: Learning Contextual Representations for Semantic Parsing with Generation-Augmented Pre-Training Code and model from our AAAI 2021 paper

83 Jan 9, 2023

Toolkit for Machine Learning, Natural Language Processing, and Text Generation, in TensorFlow. This is part of the CASL project: http://casl-project.ai/

Texar is a toolkit aiming to support a broad set of machine learning, especially natural language processing and text generation tasks. Texar provides

2.1k Feb 17, 2021

An Analysis Toolkit for Natural Language Generation (Translation, Captioning, Summarization, etc.)

VizSeq is a Python toolkit for visual analysis on text generation tasks like machine translation, summarization, image captioning, speech translation

310 Feb 1, 2021

Summarization, translation, sentiment-analysis, text-generation and more at blazing speed using a T5 version implemented in ONNX.

Summarization, translation, Q&A, text generation and more at blazing speed using a T5 version implemented in ONNX. This package is still in alpha stag

137 Feb 1, 2021

Official code of our work, Unified Pre-training for Program Understanding and Generation [NAACL 2021].

PLBART Code pre-release of our work, Unified Pre-training for Program Understanding and Generation accepted at NAACL 2021. Note. A detailed documentat

138 Dec 30, 2022

Python generation script for BitBirds

BitBirds generation script Intro This is published under MIT license, which means you can do whatever you want with it - entirely at your own risk. Pl

286 Dec 6, 2022

TTS is a library for advanced Text-to-Speech generation.

TTS is a library for advanced Text-to-Speech generation. It's built on the latest research, was designed to achieve the best trade-off among ease-of-training, speed and quality. TTS comes with pretrained models, tools for measuring dataset quality and already used in 20+ languages for products and research projects.

6.5k Jan 8, 2023

Comments

TO DO LIST
[x] Add embeddings functionality

[ ] Add 3d structure module (likely-to-be GVP/... based)

[x] Add classifier

[x] Hierarchical classification helper based on differentiability

[x] End-to-end code

[ ] data collection

[ ] data formatting

[ ] Run featurization for all data points (esm1b + af2 structs)

[ ] Perform a sample training

[ ] Perform sample evaluation

[ ] Iterate - improve

[ ] ...

[ ] idk, will see as we go
opened by hypnopump 0

Releases(0.0.2)

0.0.2(Mar 16, 2021)
Adds main architecture

Adds main helper functions

After some tests and fixes, and trials, it should be ready.

Source code(tar.gz)
Source code(zip)
0.0.01(Mar 12, 2021)

Initial infra. Statement of purpose and wip
Source code(tar.gz)
Source code(zip)

To be a next-generation DL-based phenotype prediction from genome mutations.

Related tags

Overview

ClynMut: Predicting the Clynical Relevance of Genome Mutations (wip)

Install

Example Usage:

Important topics:

3D structure learning

Hierarchical classification

Testing

Datasets:

Citations:

You might also like...

An Analysis Toolkit for Natural Language Generation (Translation, Captioning, Summarization, etc.)

Summarization, translation, sentiment-analysis, text-generation and more at blazing speed using a T5 version implemented in ONNX.

GAP-text2SQL: Learning Contextual Representations for Semantic Parsing with Generation-Augmented Pre-Training

Toolkit for Machine Learning, Natural Language Processing, and Text Generation, in TensorFlow. This is part of the CASL project: http://casl-project.ai/

An Analysis Toolkit for Natural Language Generation (Translation, Captioning, Summarization, etc.)

Summarization, translation, sentiment-analysis, text-generation and more at blazing speed using a T5 version implemented in ONNX.

Official code of our work, Unified Pre-training for Program Understanding and Generation [NAACL 2021].

Python generation script for BitBirds

TTS is a library for advanced Text-to-Speech generation.

Comments

TO DO LIST

Releases(0.0.2)

0.0.2(Mar 16, 2021)

0.0.01(Mar 12, 2021)

Owner

Eric Alcaide

Code and checkpoints for training the transformer-based Table QA models introduced in the paper TAPAS: Weakly Supervised Table Parsing via Pre-training.

A simple visual front end to the Maya UE4 RBF plugin delivered with MetaHumans

Non-Autoregressive Translation with Layer-Wise Prediction and Deep Supervision

🤗 Transformers: State-of-the-art Natural Language Processing for Pytorch, TensorFlow, and JAX.

Asr abc - Automatic speech recognition(ASR),中文语音识别

Finding Label and Model Errors in Perception Data With Learned Observation Assertions

pkuseg多领域中文分词工具; The pkuseg toolkit for multi-domain Chinese word segmentation

华为商城抢购手机的Python脚本 Python script of Huawei Store snapping up mobile phones

Implementation of the Hybrid Perception Block and Dual-Pruned Self-Attention block from the ITTR paper for Image to Image Translation using Transformers

Unet-TTS: Improving Unseen Speaker and Style Transfer in One-shot Voice Cloning

This python module is an easy-to-use port of the text normalization used in the paper "Not low-resource anymore: Aligner ensembling, batch filtering, and new datasets for Bengali-English machine translation". It is intended to be used for normalizing / cleaning Bengali and English text.

Toolkit for Machine Learning, Natural Language Processing, and Text Generation, in TensorFlow. This is part of the CASL project: http://casl-project.ai/

Performance-Efficiency Trade-offs in Unsupervised Pre-training for Speech Recognition

PhoNLP: A BERT-based multi-task learning toolkit for part-of-speech tagging, named entity recognition and dependency parsing

Automatically search Stack Overflow for the command you want to run

DomainWordsDict, Chinese words dict that contains more than 68 domains, which can be used as text classification、knowledge enhance task

Stand-alone language identification system

This repository contains the code, data, and models of the paper titled "XL-Sum: Large-Scale Multilingual Abstractive Summarization for 44 Languages" published in Findings of the Association for Computational Linguistics: ACL 2021.

NLP-SentimentAnalysis - Coursera Course ( Duration : 5 weeks ) offered by DeepLearning.AI

Ceaser-Cipher - The Caesar Cipher technique is one of the earliest and simplest method of encryption technique