Diversified feature representation via deep auto-encoder ensemble through multiple activation functions

2022 ◽  
Author(s):  
Na Qiang ◽  
Xiang-Jun Shen ◽  
Chang-Bin Huang ◽  
Shengli Wu ◽  
Timothy Apasiba Abeo ◽  
...  
Keyword(s):  
Feature Representation ◽  
Activation Functions

Comparison of various Activation Functions A Deep Learning Approach

2018 ◽  
Vol 6 (3) ◽  
pp. 122-126
Author(s):  
Mohammed Ibrahim Khan ◽  
◽  
Akansha Singh ◽  
Anand Handa ◽  
◽  
...  
Keyword(s):  
Deep Learning ◽  
Learning Approach ◽  
Activation Functions

Feature Representation of Pathophysiology of Parkinsonian Dysarthria

2019 ◽  
Author(s):  
Alice Rueda ◽  
J.C. Vásquez-Correa ◽  
Cristian David Rios-Urrego ◽  
Juan Rafael Orozco-Arroyave ◽  
Sridhar Krishnan ◽  
...  
Keyword(s):  
Feature Representation

Towards Computational Models of Identifying Protein Ubiquitination Sites

2019 ◽  
Vol 20 (5) ◽  
pp. 565-578 ◽  
Author(s):  
Lidong Wang ◽  
Ruijun Zhang
Keyword(s):  
Computational Methods ◽  
Computational Models ◽  
Feature Representation ◽  
Biological Sequence ◽  
Post Translational Modification ◽  
Test Dataset ◽  
Protein Ubiquitination ◽  
Protein Functions ◽  
Independent Test Dataset ◽  
Benchmark Datasets

Ubiquitination is an important post-translational modification (PTM) process for the regulation of protein functions, which is associated with cancer, cardiovascular and other diseases. Recent initiatives have focused on the detection of potential ubiquitination sites with the aid of physicochemical test approaches in conjunction with the application of computational methods. The identification of ubiquitination sites using laboratory tests is especially susceptible to the temporality and reversibility of the ubiquitination processes, and is also costly and time-consuming. It has been demonstrated that computational methods are effective in extracting potential rules or inferences from biological sequence collections. Up to the present, the computational strategy has been one of the critical research approaches that have been applied for the identification of ubiquitination sites, and currently, there are numerous state-of-the-art computational methods that have been developed from machine learning and statistical analysis to undertake such work. In the present study, the construction of benchmark datasets is summarized, together with feature representation methods, feature selection approaches and the classifiers involved in several previous publications. In an attempt to explore pertinent development trends for the identification of ubiquitination sites, an independent test dataset was constructed and the predicting results obtained from five prediction tools are reported here, together with some related discussions.

An Integrated Prediction Method for Identifying Protein-Protein Interactions

2020 ◽  
Vol 17 (4) ◽  
pp. 271-286
Author(s):  
Chang Xu ◽  
Limin Jiang ◽  
Zehua Zhang ◽  
Xuyao Yu ◽  
Renhai Chen ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Feature Vector ◽  
Prediction Method ◽  
Feature Representation ◽  
Protein Interaction Networks ◽  
Learning Approach ◽  
Biological Processes ◽  
Integrated Learning ◽  
Protein Protein Interactions ◽  
Training Process

Background: Protein-Protein Interactions (PPIs) play a key role in various biological processes. Many methods have been developed to predict protein-protein interactions and protein interaction networks. However, many existing applications are limited, because of relying on a large number of homology proteins and interaction marks. Methods: In this paper, we propose a novel integrated learning approach (RF-Ada-DF) with the sequence-based feature representation, for identifying protein-protein interactions. Our method firstly constructs a sequence-based feature vector to represent each pair of proteins, viaMultivariate Mutual Information (MMI) and Normalized Moreau-Broto Autocorrelation (NMBAC). Then, we feed the 638- dimentional features into an integrated learning model for judging interaction pairs and non-interaction pairs. Furthermore, this integrated model embeds Random Forest in AdaBoost framework and turns weak classifiers into a single strong classifier. Meanwhile, we also employ double fault detection in order to suppress over-adaptation during the training process. Results: To evaluate the performance of our method, we conduct several comprehensive tests for PPIs prediction. On the H. pyloridataset, our method achieves 88.16% accuracy and 87.68% sensitivity, the accuracy of our method is increased by 0.57%. On the S. cerevisiaedataset, our method achieves 95.77% accuracy and 93.36% sensitivity, the accuracy of our method is increased by 0.76%. On the Humandataset, our method achieves 98.16% accuracy and 96.80% sensitivity, the accuracy of our method is increased by 0.6%. Experiments show that our method achieves better results than other outstanding methods for sequence-based PPIs prediction. The datasets and codes are available at https://github.com/guofei-tju/RF-Ada-DF.git.

A New Approach for Predicting the Value of Gene Expression: Two-way Collaborative Filtering

2019 ◽  
Vol 14 (6) ◽  
pp. 480-490 ◽  
Author(s):  
Tuncay Bayrak ◽  
Hasan Oğul
Keyword(s):  
Gene Expression ◽  
Regression Model ◽  
Collaborative Filtering ◽  
High Throughput Sequencing ◽  
Mean Squared Error ◽  
Experimental Studies ◽  
Kernel Functions ◽  
Feature Representation ◽  
Sequencing Analysis ◽  
Computational Systems Biology

Background: Predicting the value of gene expression in a given condition is a challenging topic in computational systems biology. Only a limited number of studies in this area have provided solutions to predict the expression in a particular pattern, whether or not it can be done effectively. However, the value of expression for the measurement is usually needed for further meta-data analysis. Methods: Because the problem is considered as a regression task where a feature representation of the gene under consideration is fed into a trained model to predict a continuous variable that refers to its exact expression level, we introduced a novel feature representation scheme to support work on such a task based on two-way collaborative filtering. At this point, our main argument is that the expressions of other genes in the current condition are as important as the expression of the current gene in other conditions. For regression analysis, linear regression and a recently popularized method, called Relevance Vector Machine (RVM), are used. Pearson and Spearman correlation coefficients and Root Mean Squared Error are used for evaluation. The effects of regression model type, RVM kernel functions, and parameters have been analysed in our study in a gene expression profiling data comprising a set of prostate cancer samples. Results: According to the findings of this study, in addition to promising results from the experimental studies, integrating data from another disease type, such as colon cancer in our case, can significantly improve the prediction performance of the regression model. Conclusion: The results also showed that the performed new feature representation approach and RVM regression model are promising for many machine learning problems in microarray and high throughput sequencing analysis.

Advances in the Prediction of Protein Subcellular Locations with Machine Learning

2019 ◽  
Vol 14 (5) ◽  
pp. 406-421 ◽  
Author(s):  
Ting-He Zhang ◽  
Shao-Wu Zhang
Keyword(s):  
Machine Learning ◽  
Feature Fusion ◽  
Protein Sequences ◽  
Subcellular Location ◽  
Automated Analysis ◽  
Cellular Level ◽  
Machine Learning Algorithms ◽  
Feature Representation ◽  
Protein Subcellular Location ◽  
Protein Subcellular Locations

Background: Revealing the subcellular location of a newly discovered protein can bring insight into their function and guide research at the cellular level. The experimental methods currently used to identify the protein subcellular locations are both time-consuming and expensive. Thus, it is highly desired to develop computational methods for efficiently and effectively identifying the protein subcellular locations. Especially, the rapidly increasing number of protein sequences entering the genome databases has called for the development of automated analysis methods. Methods: In this review, we will describe the recent advances in predicting the protein subcellular locations with machine learning from the following aspects: i) Protein subcellular location benchmark dataset construction, ii) Protein feature representation and feature descriptors, iii) Common machine learning algorithms, iv) Cross-validation test methods and assessment metrics, v) Web servers. Result & Conclusion: Concomitant with a large number of protein sequences generated by highthroughput technologies, four future directions for predicting protein subcellular locations with machine learning should be paid attention. One direction is the selection of novel and effective features (e.g., statistics, physical-chemical, evolutional) from the sequences and structures of proteins. Another is the feature fusion strategy. The third is the design of a powerful predictor and the fourth one is the protein multiple location sites prediction.

Analysis of Non-Linear Activation Functions for Classification Tasks Using Convolutional Neural Networks

2019 ◽  
Vol 12 (3) ◽  
pp. 156-161 ◽  
Author(s):  
Aman Dureja ◽  
Payal Pahwa
Keyword(s):  
Neural Networks ◽  
Deep Neural Networks ◽  
Activation Function ◽  
Primary Objective ◽  
Experimental Comparison ◽  
Activation Functions ◽  
Practical Applications ◽  
Network Activation ◽  
Non Linear ◽  
Hidden Layer

Background: In making the deep neural network, activation functions play an important role. But the choice of activation functions also affects the network in term of optimization and to retrieve the better results. Several activation functions have been introduced in machine learning for many practical applications. But which activation function should use at hidden layer of deep neural networks was not identified. Objective: The primary objective of this analysis was to describe which activation function must be used at hidden layers for deep neural networks to solve complex non-linear problems. Methods: The configuration for this comparative model was used by using the datasets of 2 classes (Cat/Dog). The number of Convolutional layer used in this network was 3 and the pooling layer was also introduced after each layer of CNN layer. The total of the dataset was divided into the two parts. The first 8000 images were mainly used for training the network and the next 2000 images were used for testing the network. Results: The experimental comparison was done by analyzing the network by taking different activation functions on each layer of CNN network. The validation error and accuracy on Cat/Dog dataset were analyzed using activation functions (ReLU, Tanh, Selu, PRelu, Elu) at number of hidden layers. Overall the Relu gave best performance with the validation loss at 25th Epoch 0.3912 and validation accuracy at 25th Epoch 0.8320. Conclusion: It is found that a CNN model with ReLU hidden layers (3 hidden layers here) gives best results and improve overall performance better in term of accuracy and speed. These advantages of ReLU in CNN at number of hidden layers are helpful to effectively and fast retrieval of images from the databases.

Hierarchical Quality-Relevant Feature Representation for Soft Sensor Modeling: A Novel Deep Learning Strategy

2020 ◽  
Vol 16 (6) ◽  
pp. 3721-3730 ◽  
Author(s):  
Xiaofeng Yuan ◽  
Jiao Zhou ◽  
Biao Huang ◽  
Yalin Wang ◽  
Chunhua Yang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Learning Strategy ◽  
Soft Sensor ◽  
Feature Representation ◽  
Relevant Feature ◽  
Sensor Modeling

scholarly journals Hardware implementation of radial-basis neural networks with Gaussian activation functions on FPGA

2021 ◽  
Author(s):  
Volodymyr Shymkovych ◽  
Sergii Telenyk ◽  
Petro Kravets
Keyword(s):  
Neural Networks ◽  
Hardware Implementation ◽  
Gaussian Function ◽  
Activation Function ◽  
Rbf Neural Networks ◽  
Activation Functions ◽  
Rbf Network ◽  
Combination Scheme ◽  
Radial Basis ◽  
Hidden Layer

AbstractThis article introduces a method for realizing the Gaussian activation function of radial-basis (RBF) neural networks with their hardware implementation on field-programmable gaits area (FPGAs). The results of modeling of the Gaussian function on FPGA chips of different families have been presented. RBF neural networks of various topologies have been synthesized and investigated. The hardware component implemented by this algorithm is an RBF neural network with four neurons of the latent layer and one neuron with a sigmoid activation function on an FPGA using 16-bit numbers with a fixed point, which took 1193 logic matrix gate (LUTs—LookUpTable). Each hidden layer neuron of the RBF network is designed on an FPGA as a separate computing unit. The speed as a total delay of the combination scheme of the block RBF network was 101.579 ns. The implementation of the Gaussian activation functions of the hidden layer of the RBF network occupies 106 LUTs, and the speed of the Gaussian activation functions is 29.33 ns. The absolute error is ± 0.005. The Spartan 3 family of chips for modeling has been used to get these results. Modeling on chips of other series has been also introduced in the article. RBF neural networks of various topologies have been synthesized and investigated. Hardware implementation of RBF neural networks with such speed allows them to be used in real-time control systems for high-speed objects.

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