scholarly journals iMLP, a predictor for internal matrix targeting-like sequences in mitochondrial proteins

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Kevin Schneider ◽  
David Zimmer ◽  
Henrik Nielsen ◽  
Johannes M. Herrmann ◽  
Timo Mühlhaus
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Recurrent Neural Network ◽  
Protein Sequences ◽  
Structural Features ◽  
Mitochondrial Proteins ◽  
Learning Approach ◽  
Command Line ◽  
Link Type ◽  
Command Line Tool

Abstract Matrix targeting sequences (MTSs) direct proteins from the cytosol into mitochondria. Efficient targeting often relies on internal matrix targeting-like sequences (iMTS-Ls) which share structural features with MTSs. Predicting iMTS-Ls was tedious and required multiple tools and webservices. We present iMLP, a deep learning approach for the prediction of iMTS-Ls in protein sequences. A recurrent neural network has been trained to predict iMTS-L propensity profiles for protein sequences of interest. The iMLP predictor considerably exceeds the speed of existing approaches. Expanding on our previous work on iMTS-L prediction, we now serve an intuitive iMLP webservice available at http://iMLP.bio.uni-kl.de and a stand-alone command line tool for power user in addition.

scholarly journals Reimplementing Unirep in JAX

2020 ◽  
Author(s):  
Eric J. Ma ◽  
Arkadij Kummer
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Protein Engineering ◽  
Network Model ◽  
Recurrent Neural Network ◽  
Neural Network Model ◽  
Protein Sequences ◽  
Original Model ◽  
Ease Of Use ◽  
Deep Learning Model

AbstractUniRep is a recurrent neural network model trained on 24 million protein sequences, and has shown utility in protein engineering. The original model, however, has rough spots in its implementation, and a convenient API is not available for certain tasks. To rectify this, we reimplemented the model in JAX/NumPy, achieving near-100X speedups in forward pass performance, and implemented a convenient API for specialized tasks. In this article, we wish to document our model reimplementation process with the goal of educating others interested in learning how to dissect a deep learning model, and engineer it for robustness and ease of use.

A deep learning approach to identify association of disease–gene using information of disease symptoms and protein sequences

2020 ◽  
Vol 12 (15) ◽  
pp. 2016-2026
Author(s):  
Xingyu Chen ◽  
Qixing Huang ◽  
Yang Wang ◽  
Jinlong Li ◽  
Haiyan Liu ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Disease Gene ◽  
Protein Sequences ◽  
Deep Convolutional Neural Network ◽  
Learning Approach ◽  
Disease Symptoms ◽  
Gene Association

Prediction of disease–gene association based on a deep convolutional neural network.

scholarly journals Audio-Based Drone Detection and Identification Using Deep Learning Techniques with Dataset Enhancement through Generative Adversarial Networks

Sensors ◽  
2021 ◽  
Vol 21 (15) ◽  
pp. 4953
Author(s):  
Sara Al-Emadi ◽  
Abdulla Al-Ali ◽  
Abdulaziz Al-Ali
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Recurrent Neural Network ◽  
Learning Algorithms ◽  
Generative Adversarial Networks ◽  
Generative Adversarial Network ◽  
Adversarial Networks ◽  
Detection And Identification ◽  
Learning Techniques ◽  
The Impact

Drones are becoming increasingly popular not only for recreational purposes but in day-to-day applications in engineering, medicine, logistics, security and others. In addition to their useful applications, an alarming concern in regard to the physical infrastructure security, safety and privacy has arisen due to the potential of their use in malicious activities. To address this problem, we propose a novel solution that automates the drone detection and identification processes using a drone’s acoustic features with different deep learning algorithms. However, the lack of acoustic drone datasets hinders the ability to implement an effective solution. In this paper, we aim to fill this gap by introducing a hybrid drone acoustic dataset composed of recorded drone audio clips and artificially generated drone audio samples using a state-of-the-art deep learning technique known as the Generative Adversarial Network. Furthermore, we examine the effectiveness of using drone audio with different deep learning algorithms, namely, the Convolutional Neural Network, the Recurrent Neural Network and the Convolutional Recurrent Neural Network in drone detection and identification. Moreover, we investigate the impact of our proposed hybrid dataset in drone detection. Our findings prove the advantage of using deep learning techniques for drone detection and identification while confirming our hypothesis on the benefits of using the Generative Adversarial Networks to generate real-like drone audio clips with an aim of enhancing the detection of new and unfamiliar drones.

scholarly journals A Review of Plant Phenotypic Image Recognition Technology Based on Deep Learning

Electronics ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 81
Author(s):  
Jianbin Xiong ◽  
Dezheng Yu ◽  
Shuangyin Liu ◽  
Lei Shu ◽  
Xiaochan Wang ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Plant Species ◽  
Image Recognition ◽  
Recurrent Neural Network ◽  
Plant Diseases ◽  
Learning Methods ◽  
Smart Agriculture ◽  
Important Branch

Plant phenotypic image recognition (PPIR) is an important branch of smart agriculture. In recent years, deep learning has achieved significant breakthroughs in image recognition. Consequently, PPIR technology that is based on deep learning is becoming increasingly popular. First, this paper introduces the development and application of PPIR technology, followed by its classification and analysis. Second, it presents the theory of four types of deep learning methods and their applications in PPIR. These methods include the convolutional neural network, deep belief network, recurrent neural network, and stacked autoencoder, and they are applied to identify plant species, diagnose plant diseases, etc. Finally, the difficulties and challenges of deep learning in PPIR are discussed.

scholarly journals Ensemble Empirical Mode Decomposition with Adaptive Noise with Convolution Based Gated Recurrent Neural Network: A New Deep Learning Model for South Asian High Intensity Forecasting

Symmetry ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 931
Author(s):  
Kecheng Peng ◽  
Xiaoqun Cao ◽  
Bainian Liu ◽  
Yanan Guo ◽  
Wenlong Tian
Keyword(s):  
Neural Network ◽  
Time Series ◽  
Deep Learning ◽  
South Asian ◽  
Recurrent Neural Network ◽  
Ensemble Empirical Mode Decomposition ◽  
South Asian High ◽  
Mode Decomposition ◽  
Adaptive Noise ◽  
Deep Learning Model

The intensity variation of the South Asian high (SAH) plays an important role in the formation and extinction of many kinds of mesoscale systems, including tropical cyclones, southwest vortices in the Asian summer monsoon (ASM) region, and the precipitation in the whole Asia Europe region, and the SAH has a vortex symmetrical structure; its dynamic field also has the symmetry form. Not enough previous studies focus on the variation of SAH daily intensity. The purpose of this study is to establish a day-to-day prediction model of the SAH intensity, which can accurately predict not only the interannual variation but also the day-to-day variation of the SAH. Focusing on the summer period when the SAH is the strongest, this paper selects the geopotential height data between 1948 and 2020 from NCEP to construct the SAH intensity datasets. Compared with the classical deep learning methods of various kinds of efficient time series prediction model, we ultimately combine the Ensemble Empirical Mode Decomposition with Adaptive Noise (CEEMDAN) method, which has the ability to deal with the nonlinear and unstable single system, with the Permutation Entropy (PE) method, which can extract the SAH intensity feature of IMF decomposed by CEEMDAN, and the Convolution-based Gated Recurrent Neural Network (ConvGRU) model is used to train, test, and predict the intensity of the SAH. The prediction results show that the combination of CEEMDAN and ConvGRU can have a higher accuracy and more stable prediction ability than the traditional deep learning model. After removing the redundant features in the time series, the prediction accuracy of the SAH intensity is higher than that of the classical model, which proves that the method has good applicability for the prediction of nonlinear systems in the atmosphere.

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