A Survey of Network Representation Learning Methods for Link Prediction in Biological Network

2020 ◽  
Vol 26 (26) ◽  
pp. 3076-3084 ◽  
Author(s):  
Jiajie Peng ◽  
Guilin Lu ◽  
Xuequn Shang
Keyword(s):  
Network Analysis ◽  
Biological Networks ◽  
Link Prediction ◽  
Biological Network ◽  
Representation Learning ◽  
Learning Methods ◽  
Future Directions ◽  
Value Network ◽  
Network Representation ◽  
Important Practical Application

Background: Networks are powerful resources for describing complex systems. Link prediction is an important issue in network analysis and has important practical application value. Network representation learning has proven to be useful for network analysis, especially for link prediction tasks. Objective: To review the application of network representation learning on link prediction in a biological network, we summarize recent methods for link prediction in a biological network and discuss the application and significance of network representation learning in link prediction task. Method & Results: We first introduce the widely used link prediction algorithms, then briefly introduce the development of network representation learning methods, focusing on a few widely used methods, and their application in biological network link prediction. Existing studies demonstrate that using network representation learning to predict links in biological networks can achieve better performance. In the end, some possible future directions have been discussed.

scholarly journals iMDA-BN: Identification of miRNA-Disease Associations based on the Biological Network and Graph Embedding Algorithm

2020 ◽  
Author(s):  
Kai Zheng ◽  
Zhu-Hong You ◽  
Lei Wang
Keyword(s):  
High Throughput ◽  
Biological Networks ◽  
Domain Knowledge ◽  
Biological Network ◽  
Representation Learning ◽  
Biological Properties ◽  
Disease Association ◽  
Sequence Information ◽  
Network Representation ◽  
Disease Associations

AbstractBenefiting from advances in high-throughput experimental techniques, important regulatory roles of miRNAs, lncRNAs, and proteins, as well as biological property information, are gradually being complemented. As the key data support to promote biomedical research, domain knowledge such as intermolecular relationships that are increasingly revealed by molecular genome-wide analysis is often used to guide the discovery of potential associations. However, the method of performing network representation learning from the perspective of the global biological network is scarce. These methods cover a very limited type of molecular associations and are therefore not suitable for more comprehensive analysis of molecular network representation information. In this study, we propose a computational model based on the Biological network for predicting potential associations between miRNAs and diseases called iMDA-BN. The iMDA-BN has three significant advantages: I) It uses a new method to describe disease and miRNA characteristics which analyzes node representation information for disease and miRNA from the perspective of biological networks. II) It can predict unproven associations even if miRNAs and diseases do not appear in the biological network. III) Accurate description of miRNA characteristics from biological properties based on high-throughput sequence information. The iMDA-BN predictor achieves an AUC of 0.9145 and an accuracy of 84.49% on the miRNA-disease association baseline dataset, and it can also achieve an AUC of 0.8765 and an accuracy of 80.96% when predicting unknown diseases and miRNAs in the biological network. Compared to existing miRNA-disease association prediction methods, iMDA-BN has higher accuracy and the advantage of predicting unknown associations. In addition, 45, 49, and 49 of the top 50 miRNA-disease associations with the highest predicted scores were confirmed in the case studies, respectively.

A Drug Target Interaction Prediction Based on LINE-RF Learning

2020 ◽  
Vol 15 (7) ◽  
pp. 750-757
Author(s):  
Jihong Wang ◽  
Yue Shi ◽  
Xiaodan Wang ◽  
Huiyou Chang
Keyword(s):  
Network Topology ◽  
Drug Target ◽  
Large Scale ◽  
Representation Learning ◽  
New Drugs ◽  
Combination Method ◽  
Learning Methods ◽  
Network Representation ◽  
On Line ◽  
Clinical Experiments

Background: At present, using computer methods to predict drug-target interactions (DTIs) is a very important step in the discovery of new drugs and drug relocation processes. The potential DTIs identified by machine learning methods can provide guidance in biochemical or clinical experiments. Objective: The goal of this article is to combine the latest network representation learning methods for drug-target prediction research, improve model prediction capabilities, and promote new drug development. Methods: We use large-scale information network embedding (LINE) method to extract network topology features of drugs, targets, diseases, etc., integrate features obtained from heterogeneous networks, construct binary classification samples, and use random forest (RF) method to predict DTIs. Results: The experiments in this paper compare the common classifiers of RF, LR, and SVM, as well as the typical network representation learning methods of LINE, Node2Vec, and DeepWalk. It can be seen that the combined method LINE-RF achieves the best results, reaching an AUC of 0.9349 and an AUPR of 0.9016. Conclusion: The learning method based on LINE network can effectively learn drugs, targets, diseases and other hidden features from the network topology. The combination of features learned through multiple networks can enhance the expression ability. RF is an effective method of supervised learning. Therefore, the Line-RF combination method is a widely applicable method.

Unifying Online and Offline Preference for Social Link Prediction

2021 ◽  
Author(s):  
Fan Zhou ◽  
Kunpeng Zhang ◽  
Bangying Wu ◽  
Yi Yang ◽  
Harry Jiannan Wang
Keyword(s):  
Neural Network ◽  
Social Relations ◽  
Link Prediction ◽  
Factor Model ◽  
Representation Learning ◽  
Machine Learning Algorithms ◽  
Locality Sensitive Hashing ◽  
Network Representation ◽  
Mobility Data ◽  
Social Link

Recent advances in network representation learning have enabled significant improvement in the link prediction task, which is at the core of many downstream applications. As an increasing amount of mobility data become available because of the development of location-based technologies, we argue that this resourceful mobility data can be used to improve link prediction tasks. In this paper, we propose a novel link prediction framework that utilizes user offline check-in behavior combined with user online social relations. We model user offline location preference via a probabilistic factor model and represent user social relations using neural network representation learning. To capture the interrelationship of these two sources, we develop an anchor link method to align these two different user latent representations. Furthermore, we employ locality-sensitive hashing to project the aggregated user representation into a binary matrix, which not only preserves the data structure but also improves the efficiency of convolutional network learning. By comparing with several baseline methods that solely rely on social networks or mobility data, we show that our unified approach significantly improves the link prediction performance. Summary of Contribution: This paper proposes a novel framework that utilizes both user offline and online behavior for social link prediction by developing several machine learning algorithms, such as probabilistic factor model, neural network embedding, anchor link model, and locality-sensitive hashing. The scope and mission has the following aspects: (1) We develop a data and knowledge modeling approach that demonstrates significant performance improvement. (2) Our method can efficiently manage large-scale data. (3) We conduct rigorous experiments on real-world data sets and empirically show the effectiveness and the efficiency of our proposed method. Overall, our paper can contribute to the advancement of social link prediction, which can spur many downstream applications in information systems and computer science.

scholarly journals Structural Hierarchy-Enhanced Network Representation Learning

2020 ◽  
Vol 10 (20) ◽  
pp. 7214
Author(s):  
Cheng-Te Li ◽  
Hong-Yu Lin
Keyword(s):  
Network Topology ◽  
Link Prediction ◽  
Main Idea ◽  
Representation Learning ◽  
Coarse Grained ◽  
Community Knowledge ◽  
Structural Hierarchy ◽  
Network Representation ◽  
Node Classification ◽  
Node Embeddings

Network representation learning (NRL) is crucial in generating effective node features for downstream tasks, such as node classification (NC) and link prediction (LP). However, existing NRL methods neither properly identify neighbor nodes that should be pushed together and away in the embedding space, nor model coarse-grained community knowledge hidden behind the network topology. In this paper, we propose a novel NRL framework, Structural Hierarchy Enhancement (SHE), to deal with such two issues. The main idea is to construct a structural hierarchy from the network based on community detection, and to utilize such a hierarchy to perform level-wise NRL. In addition, lower-level node embeddings are passed to higher-level ones so that community knowledge can be aware of in NRL. Experiments conducted on benchmark network datasets show that SHE can significantly boost the performance of NRL in both tasks of NC and LP, compared to other hierarchical NRL methods.

scholarly journals Feature Hashing for Network Representation Learning

2018 ◽  
Author(s):  
Qixiang Wang ◽  
Shanfeng Wang ◽  
Maoguo Gong ◽  
Yue Wu
Keyword(s):  
Link Prediction ◽  
Feature Space ◽  
Representation Learning ◽  
Learning Approaches ◽  
Network Representation ◽  
Proximity Matrix ◽  
Low Dimensional ◽  
Vector Representations ◽  
Feature Hashing ◽  
Node Embeddings

The goal of network representation learning is to embed nodes so as to encode the proximity structures of a graph into a continuous low-dimensional feature space. In this paper, we propose a novel algorithm called node2hash based on feature hashing for generating node embeddings. This approach follows the encoder-decoder framework. There are two main mapping functions in this framework. The first is an encoder to map each node into high-dimensional vectors. The second is a decoder to hash these vectors into a lower dimensional feature space. More specifically, we firstly derive a proximity measurement called expected distance as target which combines position distribution and co-occurrence statistics of nodes over random walks so as to build a proximity matrix, then introduce a set of T different hash functions into feature hashing to generate uniformly distributed vector representations of nodes from the proximity matrix. Compared with the existing state-of-the-art network representation learning approaches, node2hash shows a competitive performance on multi-class node classification and link prediction tasks on three real-world networks from various domains.

scholarly journals Biological network analysis and comparison: mining new biological knowledge

2011 ◽  
Vol 1 (2) ◽  
Author(s):  
Valeria Fionda
Keyword(s):  
Life Cycle ◽  
Network Analysis ◽  
Biological Networks ◽  
Biological Network ◽  
Biological Knowledge ◽  
Biological Network Analysis ◽  
Cell Life ◽  
The World ◽  
Automated Tools

AbstractThe mechanisms underlying life machinery are still not completely understood. Something is known, something is “probably” known, other things are still unknown. Scientists all over the world are working very hard to clarify the processes regulating the cell life cycle and bioinformaticians try to support them by developing specialized automated tools. Within the plethora of applications devoted to the study of life mechanisms, tools for the analysis and comparison of biological networks are catching the attention of many researchers. It is interesting to investigate why.

scholarly journals Link Prediction Based on Deep Convolutional Neural Network

Information ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 172
Author(s):  
Wentao Wang ◽  
Lintao Wu ◽  
Ye Huang ◽  
Hao Wang ◽  
Rongbo Zhu
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Link Prediction ◽  
Prediction Method ◽  
Representation Learning ◽  
Deep Convolutional Neural Network ◽  
Published Data ◽  
Neighborhood Structure ◽  
Structure Information ◽  
Network Representation

In recent years, endless link prediction algorithms based on network representation learning have emerged. Network representation learning mainly constructs feature vectors by capturing the neighborhood structure information of network nodes for link prediction. However, this type of algorithm only focuses on learning topology information from the simple neighbor network node. For example, DeepWalk takes a random walk path as the neighborhood of nodes. In addition, such algorithms only take advantage of the potential features of nodes, but the explicit features of nodes play a good role in link prediction. In this paper, a link prediction method based on deep convolutional neural network is proposed. It constructs a model of the residual attention network to capture the link structure features from the sub-graph. Further study finds that the information flow transmission efficiency of the residual attention mechanism was not high, so a densely convolutional neural network model was proposed for link prediction. We evaluate our proposed method on four published data sets. The results show that our method is better than several other benchmark algorithms on link prediction.

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