scholarly journals Integrating multi-network topology for gene function prediction using deep neural networks

2019 ◽  
Author(s):  
Hansheng Xue ◽  
Jiajie Peng ◽  
Xuequn Shang
Keyword(s):  
Neural Network ◽  
Gene Function ◽  
State Of The Art ◽  
Feature Learning ◽  
Function Prediction ◽  
Feature Representation ◽  
Superior Performance ◽  
Gene Function Prediction ◽  
Multiple Networks ◽  
Low Dimensional

AbstractMotivationThe emerging of abundant biological networks, which benefit from the development of advanced high-throughput techniques, contribute to describing and modeling complex internal interactions among biological entities such as genes and proteins. Multiple networks provide rich information for inferring the function of genes or proteins. To extract functional patterns of genes based on multiple heterogeneous networks, network embedding-based methods, aiming to capture non-linear and low-dimensional feature representation based on network biology, have recently achieved remarkable performance in gene function prediction. However, existing methods mainly do not consider the shared information among different networks during the feature learning process. Thus, we propose a novel multi-networks embedding-based function prediction method based on semi-supervised autoencoder and feature convolution neural network, named DeepMNE-CNN, which captures complex topological structures of multi-networks and takes the correlation among multi-networks into account.ResultsWe design a novel semi-supervised autoencoder method to integrate multiple networks and generate a low-dimensional feature representation. Then we utilize a convolutional neural network based on the integrated feature embedding to annotate unlabeled gene functions. We test our method on both yeast and human dataset and compare with four state-of-the-art methods. The results demonstrate the superior performance of our method over four state-of-the-art algorithms. From the future explorations, we find that semi-supervised autoencoder based multi-networks integration method and CNN-based feature learning methods both contribute to the task of function prediction.AvailabilityDeepMNE-CNN is freely available at https://github.com/xuehansheng/DeepMNE-CNN

scholarly journals Integrating multi-network topology for gene function prediction using deep neural networks

2020 ◽  
Author(s):  
Jiajie Peng ◽  
Hansheng Xue ◽  
Zhongyu Wei ◽  
Idil Tuncali ◽  
Jianye Hao ◽  
...  
Keyword(s):  
Gene Function ◽  
Biological Networks ◽  
Feature Learning ◽  
Learning Task ◽  
Function Prediction ◽  
Feature Representation ◽  
Superior Performance ◽  
Gene Function Prediction ◽  
Multiple Networks ◽  
Low Dimensional

Abstract Motivation The emergence of abundant biological networks, which benefit from the development of advanced high-throughput techniques, contributes to describing and modeling complex internal interactions among biological entities such as genes and proteins. Multiple networks provide rich information for inferring the function of genes or proteins. To extract functional patterns of genes based on multiple heterogeneous networks, network embedding-based methods, aiming to capture non-linear and low-dimensional feature representation based on network biology, have recently achieved remarkable performance in gene function prediction. However, existing methods do not consider the shared information among different networks during the feature learning process. Results Taking the correlation among the networks into account, we design a novel semi-supervised autoencoder method to integrate multiple networks and generate a low-dimensional feature representation. Then we utilize a convolutional neural network based on the integrated feature embedding to annotate unlabeled gene functions. We test our method on both yeast and human datasets and compare with three state-of-the-art methods. The results demonstrate the superior performance of our method. We not only provide a comprehensive analysis of the performance of the newly proposed algorithm but also provide a tool for extracting features of genes based on multiple networks, which can be used in the downstream machine learning task. Availability DeepMNE-CNN is freely available at https://github.com/xuehansheng/DeepMNE-CNN Contact [email protected]; [email protected]; [email protected]

scholarly journals Towards Gene Function Prediction via Multi-Networks Representation Learning

2019 ◽  
Vol 33 ◽  
pp. 10069-10070 ◽  
Author(s):  
Hansheng Xue ◽  
Jiajie Peng ◽  
Xuequn Shang
Keyword(s):  
Gene Function ◽  
State Of The Art ◽  
Representation Learning ◽  
Information Loss ◽  
Function Prediction ◽  
Experimental Results ◽  
Learning Method ◽  
Gene Function Prediction ◽  
Networks Integration ◽  
Information Loss Problem

Multi-networks integration methods have achieved prominent performance on many network-based tasks, but these approaches often incur information loss problem. In this paper, we propose a novel multi-networks representation learning method based on semi-supervised autoencoder, termed as DeepMNE, which captures complex topological structures of each network and takes the correlation among multinetworks into account. The experimental results on two realworld datasets indicate that DeepMNE outperforms the existing state-of-the-art algorithms.

scholarly journals Integrating Multiple Interaction Networks for Gene Function Inference

Molecules ◽  
2018 ◽  
Vol 24 (1) ◽  
pp. 30 ◽  
Author(s):  
Jingpu Zhang ◽  
Lei Deng
Keyword(s):  
State Of The Art ◽  
Interaction Networks ◽  
Dimensional Representation ◽  
Functional Interaction ◽  
High Throughput Data ◽  
Multiple Networks ◽  
The Past ◽  
Proteomic Data ◽  
Multiple Interaction ◽  
Low Dimensional

In the past few decades, the number and variety of genomic and proteomic data available have increased dramatically. Molecular or functional interaction networks are usually constructed according to high-throughput data and the topological structure of these interaction networks provide a wealth of information for inferring the function of genes or proteins. It is a widely used way to mine functional information of genes or proteins by analyzing the association networks. However, it remains still an urgent but unresolved challenge how to combine multiple heterogeneous networks to achieve more accurate predictions. In this paper, we present a method named ReprsentConcat to improve function inference by integrating multiple interaction networks. The low-dimensional representation of each node in each network is extracted, then these representations from multiple networks are concatenated and fed to gcForest, which augment feature vectors by cascading and automatically determines the number of cascade levels. We experimentally compare ReprsentConcat with a state-of-the-art method, showing that it achieves competitive results on the datasets of yeast and human. Moreover, it is robust to the hyperparameters including the number of dimensions.

scholarly journals Disentangled Feature Learning Network for Vehicle Re-Identification

2020 ◽  
Author(s):  
Yan Bai ◽  
Yihang Lou ◽  
Yongxing Dai ◽  
Jun Liu ◽  
Ziqian Chen ◽  
...  
Keyword(s):  
State Of The Art ◽  
Feature Learning ◽  
Feature Representation ◽  
Public Security ◽  
The Public ◽  
Common Features ◽  
Learning Network ◽  
Single Feature ◽  
Art Performance

Vehicle Re-Identification (ReID) has attracted lots of research efforts due to its great significance to the public security. In vehicle ReID, we aim to learn features that are powerful in discriminating subtle differences between vehicles which are visually similar, and also robust against different orientations of the same vehicle. However, these two characteristics are hard to be encapsulated into a single feature representation simultaneously with unified supervision. Here we propose a Disentangled Feature Learning Network (DFLNet) to learn orientation specific and common features concurrently, which are discriminative at details and invariant to orientations, respectively. Moreover, to effectively use these two types of features for ReID, we further design a feature metric alignment scheme to ensure the consistency of the metric scales. The experiments show the effectiveness of our method that achieves state-of-the-art performance on three challenging datasets.

WTRPNet: An Explainable Graph Feature Convolutional Neural Network for Epileptic EEG Classification

2021 ◽  
Vol 17 (3s) ◽  
pp. 1-18
Author(s):  
Qi Xin ◽  
Shaohao Hu ◽  
Shuaiqi Liu ◽  
Ling Zhao ◽  
Shuihua Wang
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
State Of The Art ◽  
Traumatic Injury ◽  
Recurrence Plot ◽  
Superior Performance ◽  
Eeg Classification ◽  
Epilepsy Diagnosis ◽  
Electroencephalogram Eeg

As one of the important tools of epilepsy diagnosis, the electroencephalogram (EEG) is noninvasive and presents no traumatic injury to patients. It contains a lot of physiological and pathological information that is easy to obtain. The automatic classification of epileptic EEG is important in the diagnosis and therapeutic efficacy of epileptics. In this article, an explainable graph feature convolutional neural network named WTRPNet is proposed for epileptic EEG classification. Since WTRPNet is constructed by a recurrence plot in the wavelet domain, it can fully obtain the graph feature of the EEG signal, which is established by an explainable graph features extracted layer called WTRP block . The proposed method shows superior performance over state-of-the-art methods. Experimental results show that our algorithm has achieved an accuracy of 99.67% in classification of focal and nonfocal epileptic EEG, which proves the effectiveness of the classification and detection of epileptic EEG.

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