Contrastive Graph Representation Learning via Maximizing Mutual Information

2021 ◽  
Author(s):  
Yuqi Hu ◽  
Chun-Yang Zhang
Keyword(s):  
Mutual Information ◽  
Representation Learning ◽  
Graph Representation

scholarly journals GraphMS: Drug Target Prediction Using Graph Representation Learning with Substructures

2021 ◽  
Vol 11 (7) ◽  
pp. 3239
Author(s):  
Shicheng Cheng ◽  
Liang Zhang ◽  
Bo Jin ◽  
Qiang Zhang ◽  
Xinjiang Lu ◽  
...  
Keyword(s):  
Mutual Information ◽  
Link Prediction ◽  
Drug Target ◽  
State Of The Art ◽  
Target Prediction ◽  
Representation Learning ◽  
Graph Representation ◽  
Operating Characteristics ◽  
Information Index ◽  
Drug Target Prediction

The prediction of drug–target interactions is always a key task in the field of drug redirection. However, traditional methods of predicting drug–target interactions are either mediocre or rely heavily on data stacking. In this work, we proposed our model named GraphMS. We merged heterogeneous graph information and obtained effective node information and substructure information based on mutual information in graph embeddings. We then learned high quality representations for downstream tasks, and proposed an end–to–end auto–encoder model to complete the task of link prediction. Experimental results show that our method outperforms several state–of–the–art models. The model can achieve the area under the receiver operating characteristics (AUROC) curve of 0.959 and area under the precise recall curve (AUPR) of 0.847. We found that the mutual information between the substructure and graph–level representations contributes most to the mutual information index in a relatively sparse network. And the mutual information between the node–level and graph–level representations contributes most in a relatively dense network.

scholarly journals Drug Target Prediction Using Graph Representation Learning via Substructures Contrast

2021 ◽  
Author(s):  
Shicheng Cheng ◽  
Liang Zhang ◽  
Bo Jin ◽  
Qiang Zhang ◽  
Xinjiang Lu
Keyword(s):  
Mutual Information ◽  
Link Prediction ◽  
Drug Target ◽  
Target Prediction ◽  
Representation Learning ◽  
Graph Representation ◽  
Operating Characteristics ◽  
Information Index ◽  
Drug Target Prediction ◽  
Recall Curve

The prediction of drug--target interactions is always a key task in the field of drug redirection. However, traditional methods of predicting drug--target interactions are either mediocre or rely heavily on data stacking. In this work, we merged heterogeneous graph information and obtained effective node information and substructure information based on mutual information in graph embeddings. We then learned high quality representations for downstream tasks, and proposed an end--to--end auto--encoder model to complete the task of link prediction. Experimental results show that our method outperforms several state--of--art models. The model can achieve the area under the receiver operating characteristics (AUROC) curve of 0.959 and area under the precise recall curve (AUPR) of 0.848. We found that the mutual information between the substructure and graph--level representations contributes most to the mutual information index in a relatively sparse network. And the mutual information between the node--level and graph--level representations contributes most in a relatively dense network.

Graph Community Infomax

2022 ◽  
Vol 16 (3) ◽  
pp. 1-21
Author(s):  
Heli Sun ◽  
Yang Li ◽  
Bing Lv ◽  
Wujie Yan ◽  
Liang He ◽  
...  
Keyword(s):  
Mutual Information ◽  
Representation Learning ◽  
Graph Representation ◽  
Network Embedding ◽  
Adversarial Network ◽  
Low Dimension ◽  
Community Information ◽  
Model Graph ◽  
Embedding Methods ◽  
Attributed Networks

Graph representation learning aims at learning low-dimension representations for nodes in graphs, and has been proven very useful in several downstream tasks. In this article, we propose a new model, Graph Community Infomax (GCI), that can adversarial learn representations for nodes in attributed networks. Different from other adversarial network embedding models, which would assume that the data follow some prior distributions and generate fake examples, GCI utilizes the community information of networks, using nodes as positive(or real) examples and negative(or fake) examples at the same time. An autoencoder is applied to learn the embedding vectors for nodes and reconstruct the adjacency matrix, and a discriminator is used to maximize the mutual information between nodes and communities. Experiments on several real-world and synthetic networks have shown that GCI outperforms various network embedding methods on community detection tasks.

scholarly journals Exploiting Mutual Information for Substructure-aware Graph Representation Learning

2020 ◽  
Author(s):  
Pengyang Wang ◽  
Yanjie Fu ◽  
Yuanchun Zhou ◽  
Kunpeng Liu ◽  
Xiaolin Li ◽  
...  
Keyword(s):  
Mutual Information ◽  
Research Question ◽  
Level Structure ◽  
Representation Learning ◽  
Graph Representation ◽  
Graph Structure ◽  
Real World Data ◽  
Structure Information ◽  
Highly Correlated ◽  
Low Dimensional

In this paper, we design and evaluate a new substructure-aware Graph Representation Learning (GRL) approach. GRL aims to map graph structure information into low-dimensional representations. While extensive efforts have been made for modeling global and/or local structure information, GRL can be improved by substructure information. Some recent studies exploit adversarial learning to incorporate substructure awareness, but hindered by unstable convergence. This study will address the major research question: is there a better way to integrate substructure awareness into GRL? As subsets of the graph structure, interested substructures (i.e., subgraph) are unique and representative for differentiating graphs, leading to the high correlation between the representation of the graph-level structure and substructures. Since mutual information (MI) is to evaluate the mutual dependence between two variables, we develop a MI inducted substructure-aware GRL method. We decompose the GRL pipeline into two stages: (1) node-level, where we introduce to maximize MI between the original and learned representation by the intuition that the original and learned representation should be highly correlated; (2) graph-level, where we preserve substructures by maximizing MI between the graph-level structure and substructure representation. Finally, we present extensive experimental results to demonstrate the improved performances of our method with real-world data.

scholarly journals Hyperspectral Image Classification with Localized Graph Convolutional Filtering

2021 ◽  
Vol 13 (3) ◽  
pp. 526
Author(s):  
Shengliang Pu ◽  
Yuanfeng Wu ◽  
Xu Sun ◽  
Xiaotong Sun
Keyword(s):  
Hyperspectral Image ◽  
Principal Component ◽  
Representation Learning ◽  
Classification Performance ◽  
Hyperspectral Data ◽  
Spectral Graph Theory ◽  
Feature Reduction ◽  
Graph Representation ◽  
Novel Method ◽  
Local Graph

The nascent graph representation learning has shown superiority for resolving graph data. Compared to conventional convolutional neural networks, graph-based deep learning has the advantages of illustrating class boundaries and modeling feature relationships. Faced with hyperspectral image (HSI) classification, the priority problem might be how to convert hyperspectral data into irregular domains from regular grids. In this regard, we present a novel method that performs the localized graph convolutional filtering on HSIs based on spectral graph theory. First, we conducted principal component analysis (PCA) preprocessing to create localized hyperspectral data cubes with unsupervised feature reduction. These feature cubes combined with localized adjacent matrices were fed into the popular graph convolution network in a standard supervised learning paradigm. Finally, we succeeded in analyzing diversified land covers by considering local graph structure with graph convolutional filtering. Experiments on real hyperspectral datasets demonstrated that the presented method offers promising classification performance compared with other popular competitors.

scholarly journals A Novel Method to Predict Drug-Target Interactions Based on Large-Scale Graph Representation Learning

Cancers ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 2111
Author(s):  
Bo-Wei Zhao ◽  
Zhu-Hong You ◽  
Lun Hu ◽  
Zhen-Hao Guo ◽  
Lei Wang ◽  
...  
Keyword(s):  
Drug Target ◽  
Large Scale ◽  
Computational Models ◽  
Structural Information ◽  
Characteristic Curve ◽  
Representation Learning ◽  
Graph Representation ◽  
Convolutional Network ◽  
Novel Method

Identification of drug-target interactions (DTIs) is a significant step in the drug discovery or repositioning process. Compared with the time-consuming and labor-intensive in vivo experimental methods, the computational models can provide high-quality DTI candidates in an instant. In this study, we propose a novel method called LGDTI to predict DTIs based on large-scale graph representation learning. LGDTI can capture the local and global structural information of the graph. Specifically, the first-order neighbor information of nodes can be aggregated by the graph convolutional network (GCN); on the other hand, the high-order neighbor information of nodes can be learned by the graph embedding method called DeepWalk. Finally, the two kinds of feature are fed into the random forest classifier to train and predict potential DTIs. The results show that our method obtained area under the receiver operating characteristic curve (AUROC) of 0.9455 and area under the precision-recall curve (AUPR) of 0.9491 under 5-fold cross-validation. Moreover, we compare the presented method with some existing state-of-the-art methods. These results imply that LGDTI can efficiently and robustly capture undiscovered DTIs. Moreover, the proposed model is expected to bring new inspiration and provide novel perspectives to relevant researchers.

Sign in / Sign up

Export Citation Format

Share Document