scholarly journals Application of Deep Learning in Plant–Microbiota Association Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhiyu Deng ◽  
Jinming Zhang ◽  
Junya Li ◽  
Xiujun Zhang
Keyword(s):  
Deep Learning ◽  
Data Analysis ◽  
Data Processing ◽  
Association Analysis ◽  
Learning Models ◽  
Plant Host ◽  
Learning Methods ◽  
Microbiome Data ◽  
Plant Microbiome ◽  
Microbiome Data Analysis

Unraveling the association between microbiome and plant phenotype can illustrate the effect of microbiome on host and then guide the agriculture management. Adequate identification of species and appropriate choice of models are two challenges in microbiome data analysis. Computational models of microbiome data could help in association analysis between the microbiome and plant host. The deep learning methods have been widely used to learn the microbiome data due to their powerful strength of handling the complex, sparse, noisy, and high-dimensional data. Here, we review the analytic strategies in the microbiome data analysis and describe the applications of deep learning models for plant–microbiome correlation studies. We also introduce the application cases of different models in plant–microbiome correlation analysis and discuss how to adapt the models on the critical steps in data processing. From the aspect of data processing manner, model structure, and operating principle, most deep learning models are suitable for the plant microbiome data analysis. The ability of feature representation and pattern recognition is the advantage of deep learning methods in modeling and interpretation for association analysis. Based on published computational experiments, the convolutional neural network and graph neural networks could be recommended for plant microbiome analysis.

scholarly journals Validating Deep Neural Networks for Online Decoding of Motor Imagery Movements from EEG Signals

Sensors ◽  
2019 ◽  
Vol 19 (1) ◽  
pp. 210 ◽  
Author(s):  
Zied Tayeb ◽  
Juri Fedjaev ◽  
Nejla Ghaboosi ◽  
Christoph Richter ◽  
Lukas Everding ◽  
...  
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Motor Imagery ◽  
Classification Performance ◽  
Feature Engineering ◽  
Learning Models ◽  
Eeg Signals ◽  
Learning Methods

Non-invasive, electroencephalography (EEG)-based brain-computer interfaces (BCIs) on motor imagery movements translate the subject’s motor intention into control signals through classifying the EEG patterns caused by different imagination tasks, e.g., hand movements. This type of BCI has been widely studied and used as an alternative mode of communication and environmental control for disabled patients, such as those suffering from a brainstem stroke or a spinal cord injury (SCI). Notwithstanding the success of traditional machine learning methods in classifying EEG signals, these methods still rely on hand-crafted features. The extraction of such features is a difficult task due to the high non-stationarity of EEG signals, which is a major cause by the stagnating progress in classification performance. Remarkable advances in deep learning methods allow end-to-end learning without any feature engineering, which could benefit BCI motor imagery applications. We developed three deep learning models: (1) A long short-term memory (LSTM); (2) a spectrogram-based convolutional neural network model (CNN); and (3) a recurrent convolutional neural network (RCNN), for decoding motor imagery movements directly from raw EEG signals without (any manual) feature engineering. Results were evaluated on our own publicly available, EEG data collected from 20 subjects and on an existing dataset known as 2b EEG dataset from “BCI Competition IV”. Overall, better classification performance was achieved with deep learning models compared to state-of-the art machine learning techniques, which could chart a route ahead for developing new robust techniques for EEG signal decoding. We underpin this point by demonstrating the successful real-time control of a robotic arm using our CNN based BCI.

scholarly journals Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis

2017 ◽  
Vol 34 (8) ◽  
pp. 1411-1413 ◽  
Author(s):  
Nick Weber ◽  
David Liou ◽  
Jennifer Dommer ◽  
Philip MacMenamin ◽  
Mariam Quiñones ◽  
...  
Keyword(s):  
Data Analysis ◽  
Cloud Platform ◽  
Microbiome Data ◽  
Microbiome Data Analysis

scholarly journals MHSNMF: multi-view hessian regularization based symmetric nonnegative matrix factorization for microbiome data analysis

2020 ◽  
Vol 21 (S6) ◽  
Author(s):  
Yuanyuan Ma ◽  
Junmin Zhao ◽  
Yingjun Ma
Keyword(s):  
Data Analysis ◽  
Matrix Factorization ◽  
Nonnegative Matrix Factorization ◽  
Rapid Development ◽  
Nonnegative Matrix ◽  
Metabolomics Data ◽  
Normalized Mutual Information ◽  
Microbiome Data ◽  
Symmetric Nonnegative Matrix Factorization ◽  
Microbiome Data Analysis

Abstract Background With the rapid development of high-throughput technique, multiple heterogeneous omics data have been accumulated vastly (e.g., genomics, proteomics and metabolomics data). Integrating information from multiple sources or views is challenging to obtain a profound insight into the complicated relations among micro-organisms, nutrients and host environment. In this paper we propose a multi-view Hessian regularization based symmetric nonnegative matrix factorization algorithm (MHSNMF) for clustering heterogeneous microbiome data. Compared with many existing approaches, the advantages of MHSNMF lie in: (1) MHSNMF combines multiple Hessian regularization to leverage the high-order information from the same cohort of instances with multiple representations; (2) MHSNMF utilities the advantages of SNMF and naturally handles the complex relationship among microbiome samples; (3) uses the consensus matrix obtained by MHSNMF, we also design a novel approach to predict the classification of new microbiome samples. Results We conduct extensive experiments on two real-word datasets (Three-source dataset and Human Microbiome Plan dataset), the experimental results show that the proposed MHSNMF algorithm outperforms other baseline and state-of-the-art methods. Compared with other methods, MHSNMF achieves the best performance (accuracy: 95.28%, normalized mutual information: 91.79%) on microbiome data. It suggests the potential application of MHSNMF in microbiome data analysis. Conclusions Results show that the proposed MHSNMF algorithm can effectively combine the phylogenetic, transporter, and metabolic profiles into a unified paradigm to analyze the relationships among different microbiome samples. Furthermore, the proposed prediction method based on MHSNMF has been shown to be effective in judging the types of new microbiome samples.

scholarly journals An Investigation of Deep Learning Models for EEG-Based Emotion Recognition

2020 ◽  
Vol 14 ◽  
Author(s):  
Yaqing Zhang ◽  
Jinling Chen ◽  
Jen Hong Tan ◽  
Yuxuan Chen ◽  
Yunyi Chen ◽  
...  
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Emotion Recognition ◽  
Real Life ◽  
Learning Rate ◽  
Learning Models ◽  
Learning Methods ◽  
Time Frequency ◽  
Comparison Results

Emotion is the human brain reacting to objective things. In real life, human emotions are complex and changeable, so research into emotion recognition is of great significance in real life applications. Recently, many deep learning and machine learning methods have been widely applied in emotion recognition based on EEG signals. However, the traditional machine learning method has a major disadvantage in that the feature extraction process is usually cumbersome, which relies heavily on human experts. Then, end-to-end deep learning methods emerged as an effective method to address this disadvantage with the help of raw signal features and time-frequency spectrums. Here, we investigated the application of several deep learning models to the research field of EEG-based emotion recognition, including deep neural networks (DNN), convolutional neural networks (CNN), long short-term memory (LSTM), and a hybrid model of CNN and LSTM (CNN-LSTM). The experiments were carried on the well-known DEAP dataset. Experimental results show that the CNN and CNN-LSTM models had high classification performance in EEG-based emotion recognition, and their accurate extraction rate of RAW data reached 90.12 and 94.17%, respectively. The performance of the DNN model was not as accurate as other models, but the training speed was fast. The LSTM model was not as stable as the CNN and CNN-LSTM models. Moreover, with the same number of parameters, the training speed of the LSTM was much slower and it was difficult to achieve convergence. Additional parameter comparison experiments with other models, including epoch, learning rate, and dropout probability, were also conducted in the paper. Comparison results prove that the DNN model converged to optimal with fewer epochs and a higher learning rate. In contrast, the CNN model needed more epochs to learn. As for dropout probability, reducing the parameters by ~50% each time was appropriate.

scholarly journals Short-Term Forecasting of Photovoltaic Solar Power Production Using Variational Auto-Encoder Driven Deep Learning Approach

2020 ◽  
Vol 10 (23) ◽  
pp. 8400 ◽  
Author(s):  
Abdelkader Dairi ◽  
Fouzi Harrou ◽  
Ying Sun ◽  
Sofiane Khadraoui
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Solar Power ◽  
Power Production ◽  
Superior Performance ◽  
Support Vector ◽  
Learning Models ◽  
Short Term ◽  
Learning Methods ◽  
Short Term Forecasting

The accurate modeling and forecasting of the power output of photovoltaic (PV) systems are critical to efficiently managing their integration in smart grids, delivery, and storage. This paper intends to provide efficient short-term forecasting of solar power production using Variational AutoEncoder (VAE) model. Adopting the VAE-driven deep learning model is expected to improve forecasting accuracy because of its suitable performance in time-series modeling and flexible nonlinear approximation. Both single- and multi-step-ahead forecasts are investigated in this work. Data from two grid-connected plants (a 243 kW parking lot canopy array in the US and a 9 MW PV system in Algeria) are employed to show the investigated deep learning models’ performance. Specifically, the forecasting outputs of the proposed VAE-based forecasting method have been compared with seven deep learning methods, namely recurrent neural network, Long short-term memory (LSTM), Bidirectional LSTM, Convolutional LSTM network, Gated recurrent units, stacked autoencoder, and restricted Boltzmann machine, and two commonly used machine learning methods, namely logistic regression and support vector regression. The results of this investigation demonstrate the satisfying performance of deep learning techniques to forecast solar power and point out that the VAE consistently performed better than the other methods. Also, results confirmed the superior performance of deep learning models compared to the two considered baseline machine learning models.

scholarly journals Deep Learning for Recommender Systems: A Netflix Case Study

AI Magazine ◽  
2022 ◽  
Vol 42 (3) ◽  
pp. 7-18
Author(s):  
Harald Steck ◽  
Linas Baltrunas ◽  
Ehtsham Elahi ◽  
Dawen Liang ◽  
Yves Raimond ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Recommender Systems ◽  
Input Data ◽  
Lessons Learned ◽  
Learning Approaches ◽  
Learning Models ◽  
Learning Methods ◽  
Recommendation Algorithms

Deep learning has profoundly impacted many areas of machine learning. However, it took a while for its impact to be felt in the field of recommender systems. In this article, we outline some of the challenges encountered and lessons learned in using deep learning for recommender systems at Netflix. We first provide an overview of the various recommendation tasks on the Netflix service. We found that different model architectures excel at different tasks. Even though many deep-learning models can be understood as extensions of existing (simple) recommendation algorithms, we initially did not observe significant improvements in performance over well-tuned non-deep-learning approaches. Only when we added numerous features of heterogeneous types to the input data, deep-learning models did start to shine in our setting. We also observed that deep-learning methods can exacerbate the problem of offline–online metric (mis-)alignment. After addressing these challenges, deep learning has ultimately resulted in large improvements to our recommendations as measured by both offline and online metrics. On the practical side, integrating deep-learning toolboxes in our system has made it faster and easier to implement and experiment with both deep-learning and non-deep-learning approaches for various recommendation tasks. We conclude this article by summarizing our take-aways that may generalize to other applications beyond Netflix.

scholarly journals Deep Learning-Based Models for Pain Recognition: A Systematic Review

2020 ◽  
Author(s):  
Rasha M. Al-Eidan ◽  
Hend Al-Khalifa ◽  
AbdulMalik Alsalman
Keyword(s):  
Systematic Review ◽  
Deep Learning ◽  
Data Sets ◽  
Observer Variability ◽  
Learning Models ◽  
Learning Methods ◽  
Inter Observer Variability ◽  
Recognition Systems ◽  
Pain Recognition ◽  
Open Issues

The traditional standards employed for pain assessment have many limitations. One such limitation is reliability because of inter-observer variability. Therefore, there have been many approaches to automate the task of pain recognition. Recently, deep-learning methods have appeared to solve many challenges, such as feature selection and cases with a small number of data sets. This study provides a systematic review of pain-recognition systems that are based on deep-learning models for the last two years only. Furthermore, it presents the major deep-learning methods that were used in review papers. Finally, it provides a discussion of the challenges and open issues.

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