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 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 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.

scholarly journals Fast Network Embedding Enhancement via High Order Proximity Approximation

2017 ◽  
Author(s):  
Cheng Yang ◽  
Maosong Sun ◽  
Zhiyuan Liu ◽  
Cunchao Tu
Keyword(s):  
Link Prediction ◽  
Representation Learning ◽  
Higher Order ◽  
Network Embedding ◽  
Approximation Bound ◽  
Proximity Matrix ◽  
Construction Step ◽  
Fast Network ◽  
Vector Representations ◽  
Matrix Construction

Many Network Representation Learning (NRL) methods have been proposed to learn vector representations for vertices in a network recently. In this paper, we summarize most existing NRL methods into a unified two-step framework, including proximity matrix construction and dimension reduction. We focus on the analysis of proximity matrix construction step and conclude that an NRL method can be improved by exploring higher order proximities when building the proximity matrix. We propose Network Embedding Update (NEU) algorithm which implicitly approximates higher order proximities with theoretical approximation bound and can be applied on any NRL methods to enhance their performances. We conduct experiments on multi-label classification and link prediction tasks. Experimental results show that NEU can make a consistent and significant improvement over a number of NRL methods with almost negligible running time on all three publicly available datasets.

scholarly journals ANRL: Attributed Network Representation Learning via Deep Neural Networks

2018 ◽  
Author(s):  
Zhen Zhang ◽  
Hongxia Yang ◽  
Jiajun Bu ◽  
Sheng Zhou ◽  
Pinggang Yu ◽  
...  
Keyword(s):  
Network Structure ◽  
Link Prediction ◽  
Deep Neural Networks ◽  
User Behavior ◽  
Representation Learning ◽  
Network Representation ◽  
Node Attribute ◽  
Attributed Network ◽  
Attribute Information ◽  
Low Dimensional

Network representation learning (RL) aims to transform the nodes in a network into low-dimensional vector spaces while preserving the inherent properties of the network. Though network RL has been intensively studied, most existing works focus on either network structure or node attribute information. In this paper, we propose a novel framework, named ANRL, to incorporate both the network structure and node attribute information in a principled way. Specifically, we propose a neighbor enhancement autoencoder to model the node attribute information, which reconstructs its target neighbors instead of itself. To capture the network structure, attribute-aware skip-gram model is designed based on the attribute encoder to formulate the correlations between each node and its direct or indirect neighbors. We conduct extensive experiments on six real-world networks, including two social networks, two citation networks and two user behavior networks. The results empirically show that ANRL can achieve relatively significant gains in node classification and link prediction tasks.

scholarly journals Exploiting node metadata to predict interactions in large networks using graph embedding and neural networks

2021 ◽  
Author(s):  
Rogini Runghen ◽  
Daniel B Stouffer ◽  
Giulio Valentino Dalla Riva
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Link Prediction ◽  
Graph Embedding ◽  
Feature Space ◽  
Machine Learning Techniques ◽  
Large Networks ◽  
Data Set ◽  
Learning Techniques ◽  
Low Dimensional

Collecting network interaction data is difficult. Non-exhaustive sampling and complex hidden processes often result in an incomplete data set. Thus, identifying potentially present but unobserved interactions is crucial both in understanding the structure of large scale data, and in predicting how previously unseen elements will interact. Recent studies in network analysis have shown that accounting for metadata (such as node attributes) can improve both our understanding of how nodes interact with one another, and the accuracy of link prediction. However, the dimension of the object we need to learn to predict interactions in a network grows quickly with the number of nodes. Therefore, it becomes computationally and conceptually challenging for large networks. Here, we present a new predictive procedure combining a graph embedding method with machine learning techniques to predict interactions on the base of nodes' metadata. Graph embedding methods project the nodes of a network onto a---low dimensional---latent feature space. The position of the nodes in the latent feature space can then be used to predict interactions between nodes. Learning a mapping of the nodes' metadata to their position in a latent feature space corresponds to a classic---and low dimensional---machine learning problem. In our current study we used the Random Dot Product Graph model to estimate the embedding of an observed network, and we tested different neural networks architectures to predict the position of nodes in the latent feature space. Flexible machine learning techniques to map the nodes onto their latent positions allow to account for multivariate and possibly complex nodes' metadata. To illustrate the utility of the proposed procedure, we apply it to a large dataset of tourist visits to destinations across New Zealand. We found that our procedure accurately predicts interactions for both existing nodes and nodes newly added to the network, while being computationally feasible even for very large networks. Overall, our study highlights that by exploiting the properties of a well understood statistical model for complex networks and combining it with standard machine learning techniques, we can simplify the link prediction problem when incorporating multivariate node metadata. Our procedure can be immediately applied to different types of networks, and to a wide variety of data from different systems. As such, both from a network science and data science perspective, our work offers a flexible and generalisable procedure for link prediction.

scholarly journals Negative Sampling in Knowledge Representation Learning: A Mini-Review

2020 ◽  
Author(s):  
Jing Qian ◽  
Gangmin Li ◽  
Katie Atkinson ◽  
Yong Yue
Keyword(s):  
Knowledge Representation ◽  
Link Prediction ◽  
Representation Learning ◽  
Cluster Sampling ◽  
Continuous Space ◽  
Knowledge Representations ◽  
Space Efficiency ◽  
Low Dimensional ◽  
Fixed Distribution

Knowledge representation learning (KRL) aims at encoding components of a knowledge graph (KG) into a low-dimensional continuous space, which has brought considerable successes in applying deep learning to graph embedding. Most famous KGs contain only positive instances for space efficiency. Typical KRL techniques, especially translational distance-based models, are trained through discriminating positive and negative samples. Thus, negative sampling is unquestionably a non-trivial step in KG embedding. The quality of generated negative samples can directly influence the performance of final knowledge representations in downstream tasks, such as link prediction and triple classification. This review summarizes current negative sampling methods in KRL and we categorize them into three sorts, fixed distribution-based, generative adversarial net (GAN)-based and cluster sampling. Based on this categorization we discuss the most prevalent existing approaches and their characteristics.

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.

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 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>

Sign in / Sign up

Export Citation Format

Share Document