scholarly journals Multi-View Network Representation Learning Algorithm Research

Algorithms ◽  
2019 ◽  
Vol 12 (3) ◽  
pp. 62 ◽  
Author(s):  
Zhonglin Ye ◽  
Haixing Zhao ◽  
Ke Zhang ◽  
Yu Zhu
Keyword(s):  
Learning Algorithm ◽  
Representation Learning ◽  
Research Field ◽  
Dimensional Representation ◽  
Multi Scale ◽  
Network Representation ◽  
Excellent Research ◽  
Network Feature ◽  
The Matrix ◽  
Low Dimensional

Network representation learning is a key research field in network data mining. In this paper, we propose a novel multi-view network representation algorithm (MVNR), which embeds multi-scale relations of network vertices into the low dimensional representation space. In contrast to existing approaches, MVNR explicitly encodes higher order information using k-step networks. In addition, we introduce the matrix forest index as a kind of network feature, which can be applied to balance the representation weights of different network views. We also research the relevance amongst MVNR and several excellent research achievements, including DeepWalk, node2vec and GraRep and so forth. We conduct our experiment on several real-world citation datasets and demonstrate that MVNR outperforms some new approaches using neural matrix factorization. Specifically, we demonstrate the efficiency of MVNR on network classification, visualization and link prediction tasks.

scholarly journals An Optimized Network Representation Learning Algorithm Using Multi-Relational Data

Mathematics ◽  
2019 ◽  
Vol 7 (5) ◽  
pp. 460
Author(s):  
Zhonglin Ye ◽  
Haixing Zhao ◽  
Ke Zhang ◽  
Yu Zhu ◽  
Zhaoyang Wang
Keyword(s):  
Knowledge Representation ◽  
Learning Algorithm ◽  
Representation Learning ◽  
Knowledge Bases ◽  
Relational Data ◽  
New Approach ◽  
Network Representation ◽  
Structural Relationships ◽  
Low Dimensional

Representation learning aims to encode the relationships of research objects into low-dimensional, compressible, and distributed representation vectors. The purpose of network representation learning is to learn the structural relationships between network vertices. Knowledge representation learning is oriented to model the entities and relationships in knowledge bases. In this paper, we first introduce the idea of knowledge representation learning into network representation learning, namely, we propose a new approach to model the vertex triplet relationships based on DeepWalk without TransE. Consequently, we propose an optimized network representation learning algorithm using multi-relational data, MRNR, which introduces the multi-relational data between vertices into the procedures of network representation learning. Importantly, we adopted a kind of higher order transformation strategy to optimize the learnt network representation vectors. The purpose of MRNR is that multi-relational data (triplets) can effectively guide and constrain the procedures of network representation learning. The experimental results demonstrate that the proposed MRNR can learn the discriminative network representations, which show better performance on network classification, visualization, and case study tasks compared to the proposed baseline algorithms in this paper.

scholarly journals The Network Representation Learning Algorithm Based on Semi-Supervised Random Walk

IEEE Access ◽  
2020 ◽  
Vol 8 ◽  
pp. 222956-222965
Author(s):  
Dong Liu ◽  
Qinpeng Li ◽  
Yan Ru ◽  
Jun Zhang
Keyword(s):  
Random Walk ◽  
Learning Algorithm ◽  
Representation Learning ◽  
Network Representation

scholarly journals Exponential Family Graph Embeddings

2020 ◽  
Vol 34 (04) ◽  
pp. 3357-3364
Author(s):  
Abdulkadir Celikkanat ◽  
Fragkiskos D. Malliaros
Keyword(s):  
Random Walk ◽  
Exponential Family ◽  
Representation Learning ◽  
Learning Problems ◽  
Interaction Patterns ◽  
Network Representation ◽  
Learning Tasks ◽  
Learning Techniques ◽  
Real World Datasets ◽  
Low Dimensional

Representing networks in a low dimensional latent space is a crucial task with many interesting applications in graph learning problems, such as link prediction and node classification. A widely applied network representation learning paradigm is based on the combination of random walks for sampling context nodes and the traditional Skip-Gram model to capture center-context node relationships. In this paper, we emphasize on exponential family distributions to capture rich interaction patterns between nodes in random walk sequences. We introduce the generic exponential family graph embedding model, that generalizes random walk-based network representation learning techniques to exponential family conditional distributions. We study three particular instances of this model, analyzing their properties and showing their relationship to existing unsupervised learning models. Our experimental evaluation on real-world datasets demonstrates that the proposed techniques outperform well-known baseline methods in two downstream machine learning tasks.

scholarly journals Representation learning of RNA velocity reveals robust cell transitions

2021 ◽  
Author(s):  
Chen Qiao ◽  
Yuanhua Huang
Keyword(s):  
Cellular Differentiation ◽  
Representation Learning ◽  
Biological Processes ◽  
Dimensional Representation ◽  
Promising Technique ◽  
Technical Noise ◽  
Wide Range ◽  
Cell Transcriptome ◽  
Low Dimensional ◽  
Single Cell Transcriptome

RNA velocity is a promising technique to reveal transient cellular dynamics among a heterogeneous cell population and quantify their transitions from single-cell transcriptome experiments. However, the cell transitions estimated from high dimensional RNA velocity are often unstable or inaccurate, partly due to the high technical noise and less informative projection. Here, we present VeloAE, a tailored representation learning method to learn a low-dimensional representation of RNA velocity on which cell transitions can be robustly estimated. From various experimental datasets, we show that VeloAE can both accurately identify stimulation dynamics in time-series designs and effectively capture the expected cellular differentiation in different biological systems. VeloAE therefore enhances the usefulness of RNA velocity for studying a wide range of biological processes.

scholarly journals Network Representation Learning-Based Drug Mechanism Discovery and Anti-Inflammatory Response Against COVID-19

2021 ◽  
Author(s):  
Wang Xiaoqi ◽  
Bin Xin ◽  
Zhijian Xu ◽  
Kenli LI ◽  
Fei Li ◽  
...  
Keyword(s):  
Inflammatory Response ◽  
Inflammatory Responses ◽  
Representation Learning ◽  
Binding Modes ◽  
Network Representation ◽  
Drug Mechanism ◽  
Docking Program ◽  
Therapeutic Development ◽  
Anti Inflammatory ◽  
Low Dimensional

<p>Recent studies have been demonstrated that the excessive inflammatory response is an important factor of death in COVID-19 patients. In this study, we proposed a network representation learning-based methodology, termed AIdrug2cov, to discover drug mechanism and anti-inflammatory response for patients with COVID-19. This work explores the multi-hub characteristic of a heterogeneous drug network integrating 8 unique networks. Inspired by the multi-hub characteristic, we design three billion special meta paths to train a deep representation model for learning low-dimensional vectors that integrate long-range structure dependency and complex semantic relation among network nodes. Using the representation vectors, AIdrug2cov identifies 40 potential targets and 22 high-confidence drugs that bind to tumor necrosis factor(TNF)-α or interleukin(IL)-6 to prevent excessive inflammatory responses in COVID-19 patients. Finally, we analyze mechanisms of action based on PubMed publications and ongoing clinical trials, and explore the possible binding modes between the new predicted drugs and targets via docking program. In addition, the results in 5 pharmacological application suggested that AIdrug2cov significantly outperforms 5 other state-of-the-art network representation approaches, future demonstrating the availability of AIdrug2cov in drug development field. In summary, AIdrug2cov is practically useful for accelerating COVID-19 therapeutic development. The source code and data can be downloaded from https://github.com/pengsl-lab/AIdrug2cov.git.</p>

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 An Information-Explainable Random Walk Based Unsupervised Network Representation Learning Framework on Node Classification Tasks

Mathematics ◽  
2021 ◽  
Vol 9 (15) ◽  
pp. 1767
Author(s):  
Xin Xu ◽  
Yang Lu ◽  
Yupeng Zhou ◽  
Zhiguo Fu ◽  
Yanjie Fu ◽  
...  
Keyword(s):  
Random Walk ◽  
Representation Learning ◽  
Local Information ◽  
Learning Framework ◽  
Network Representation ◽  
Label Node ◽  
Label Information ◽  
Classification Tasks ◽  
Node Classification ◽  
Low Dimensional

Network representation learning aims to learn low-dimensional, compressible, and distributed representational vectors of nodes in networks. Due to the expensive costs of obtaining label information of nodes in networks, many unsupervised network representation learning methods have been proposed, where random walk strategy is one of the wildly utilized approaches. However, the existing random walk based methods have some challenges, including: 1. The insufficiency of explaining what network knowledge in the walking path-samplings; 2. The adverse effects caused by the mixture of different information in networks; 3. The poor generality of the methods with hyper-parameters on different networks. This paper proposes an information-explainable random walk based unsupervised network representation learning framework named Probabilistic Accepted Walk (PAW) to obtain network representation from the perspective of the stationary distribution of networks. In the framework, we design two stationary distributions based on nodes’ self-information and local-information of networks to guide our proposed random walk strategy to learn representational vectors of networks through sampling paths of nodes. Numerous experimental results demonstrated that the PAW could obtain more expressive representation than the other six widely used unsupervised network representation learning baselines on four real-world networks in single-label and multi-label node classification tasks.

scholarly journals Inferring the Disease-Associated miRNAs Based on Network Representation Learning and Convolutional Neural Networks

2019 ◽  
Vol 20 (15) ◽  
pp. 3648 ◽  
Author(s):  
Xuan ◽  
Sun ◽  
Wang ◽  
Zhang ◽  
Pan
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Prediction Models ◽  
Prediction Method ◽  
Feature Space ◽  
Representation Learning ◽  
Superior Performance ◽  
Network Representation ◽  
Disease Associations ◽  
Low Dimensional

Identification of disease-associated miRNAs (disease miRNAs) are critical for understanding etiology and pathogenesis. Most previous methods focus on integrating similarities and associating information contained in heterogeneous miRNA-disease networks. However, these methods establish only shallow prediction models that fail to capture complex relationships among miRNA similarities, disease similarities, and miRNA-disease associations. We propose a prediction method on the basis of network representation learning and convolutional neural networks to predict disease miRNAs, called CNNMDA. CNNMDA deeply integrates the similarity information of miRNAs and diseases, miRNA-disease associations, and representations of miRNAs and diseases in low-dimensional feature space. The new framework based on deep learning was built to learn the original and global representation of a miRNA-disease pair. First, diverse biological premises about miRNAs and diseases were combined to construct the embedding layer in the left part of the framework, from a biological perspective. Second, the various connection edges in the miRNA-disease network, such as similarity and association connections, were dependent on each other. Therefore, it was necessary to learn the low-dimensional representations of the miRNA and disease nodes based on the entire network. The right part of the framework learnt the low-dimensional representation of each miRNA and disease node based on non-negative matrix factorization, and these representations were used to establish the corresponding embedding layer. Finally, the left and right embedding layers went through convolutional modules to deeply learn the complex and non-linear relationships among the similarities and associations between miRNAs and diseases. Experimental results based on cross validation indicated that CNNMDA yields superior performance compared to several state-of-the-art methods. Furthermore, case studies on lung, breast, and pancreatic neoplasms demonstrated the powerful ability of CNNMDA to discover potential disease miRNAs.

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