SIR-GN: A Fast Structural Iterative Representation Learning Approach For Graph Nodes

2021 ◽  
Vol 15 (6) ◽  
pp. 1-39
Author(s):  
Mikel Joaristi ◽  
Edoardo Serra
Keyword(s):  
Structural Information ◽  
Representation Learning ◽  
Graph Representation ◽  
Structural Function ◽  
Learning Approach ◽  
Numerical Representation ◽  
Learning Methods ◽  
Computational Performance ◽  
Latent Space ◽  
Graph Nodes

Graph representation learning methods have attracted an increasing amount of attention in recent years. These methods focus on learning a numerical representation of the nodes in a graph. Learning these representations is a powerful instrument for tasks such as graph mining, visualization, and hashing. They are of particular interest because they facilitate the direct use of standard machine learning models on graphs. Graph representation learning methods can be divided into two main categories: methods preserving the connectivity information of the nodes and methods preserving nodes’ structural information. Connectivity-based methods focus on encoding relationships between nodes, with connected nodes being closer together in the resulting latent space. While methods preserving structure generate a latent space where nodes serving a similar structural function in the network are encoded close to each other, independently of them being connected or even close to each other in the graph. While there are a lot of works that focus on preserving node connectivity, only a few works focus on preserving nodes’ structure. Properly encoding nodes’ structural information is fundamental for many real-world applications as it has been demonstrated that this information can be leveraged to successfully solve many tasks where connectivity-based methods usually fail. A typical example is the task of node classification, i.e., the assignment or prediction of a particular label for a node. Current limitations of structural representation methods are their scalability, representation meaning, and no formal proof that guaranteed the preservation of structural properties. We propose a new graph representation learning method, called Structural Iterative Representation learning approach for Graph Nodes ( SIR-GN ). In this work, we propose two variations ( SIR-GN: GMM and SIR-GN: K-Means ) and show how our best variation SIR-GN: K-Means : (1) theoretically guarantees the preservation of graph structural similarities, (2) provides a clear meaning about its representation and a way to interpret it with a specifically designed attribution procedure, and (3) is scalable and fast to compute. In addition, from our experiment, we show that SIR-GN: K-Means is often better or, in the worst-case comparable than the existing structural graph representation learning methods present in the literature. Also, we empirically show its superior scalability and computational performance when compared to other existing approaches.

Unsupervised Structural Graph Node Representation Learning

2020 ◽  
Author(s):  
Mikel Joaristi
Keyword(s):  
Real World ◽  
State Of The Art ◽  
Structural Information ◽  
Representation Learning ◽  
Graph Representation ◽  
Learning Methods ◽  
Structural Graph ◽  
Connectivity Information ◽  
Latent Space ◽  
Previous State

Unsupervised Graph Representation Learning methods learn a numerical representation of the nodes in a graph. The generated representations encode meaningful information about the nodes' properties, making them a powerful tool for tasks in many areas of study, such as social sciences, biology or communication networks. These methods are particularly interesting because they facilitate the direct use of standard Machine Learning models on graphs. Graph representation learning methods can be divided into two main categories depending on the information they encode, methods preserving the nodes connectivity information, and methods preserving nodes' structural information. Connectivity-based methods focus on encoding relationships between nodes, with neighboring nodes being closer together in the resulting latent space. On the other hand, structure-based methods generate a latent space where nodes serving a similar structural function in the network are encoded close to each other, independently of them being connected or even close to each other in the graph. While there are a lot of works that focus on preserving nodes' connectivity information, only a few works study the problem of encoding nodes' structure, specially in an unsupervised way. In this dissertation, we demonstrate that properly encoding nodes' structural information is fundamental for many real-world applications, as it can be leveraged to successfully solve many tasks where connectivity-based methods fail. One concrete example is presented first. In this example, the task consists of detecting malicious entities in a real-world financial network. We show that to solve this problem, connectivity information is not enough and show how leveraging structural information provides considerable performance improvements. This particular example pinpoints the need for further research on the area of structural graph representation learning, together with the limitations of the previous state-of-the-art. We use the acquired knowledge as a starting point and inspiration for the research and development of three independent unsupervised structural graph representation learning methods: Structural Iterative Representation learning approach for Graph Nodes (SIR-GN), Structural Iterative Lexicographic Autoencoded Node Representation (SILA), and Sparse Structural Node Representation (SparseStruct). We show how each of our methods tackles specific limitations on the previous state-of-the-art on structural graph representation learning such as scalability, representation meaning, and lack of formal proof that guarantees the preservation of structural properties. We provide an extensive experimental section where we compare our three proposed methods to the current state-of-the-art on both connectivity-based and structure-based representation learning methods. Finally, in this dissertation, we look at extensions of the basic structural graph representation learning problem. We study the problem of temporal structural graph representation. We also provide a method for representation explainability.

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.

scholarly journals An Attention-Based Graph Neural Network for Heterogeneous Structural Learning

2020 ◽  
Vol 34 (04) ◽  
pp. 4132-4139
Author(s):  
Huiting Hong ◽  
Hantao Guo ◽  
Yucheng Lin ◽  
Xiaoqing Yang ◽  
Zang Li ◽  
...  
Keyword(s):  
Neural Network ◽  
Structural Information ◽  
Representation Learning ◽  
Graph Representation ◽  
Heterogeneous Information ◽  
Domain Experts ◽  
Proposed Model ◽  
Meta Path ◽  
Low Dimensional ◽  
Public Datasets

In this paper, we focus on graph representation learning of heterogeneous information network (HIN), in which various types of vertices are connected by various types of relations. Most of the existing methods conducted on HIN revise homogeneous graph embedding models via meta-paths to learn low-dimensional vector space of HIN. In this paper, we propose a novel Heterogeneous Graph Structural Attention Neural Network (HetSANN) to directly encode structural information of HIN without meta-path and achieve more informative representations. With this method, domain experts will not be needed to design meta-path schemes and the heterogeneous information can be processed automatically by our proposed model. Specifically, we implicitly represent heterogeneous information using the following two methods: 1) we model the transformation between heterogeneous vertices through a projection in low-dimensional entity spaces; 2) afterwards, we apply the graph neural network to aggregate multi-relational information of projected neighborhood by means of attention mechanism. We also present three extensions of HetSANN, i.e., voices-sharing product attention for the pairwise relationships in HIN, cycle-consistency loss to retain the transformation between heterogeneous entity spaces, and multi-task learning with full use of information. The experiments conducted on three public datasets demonstrate that our proposed models achieve significant and consistent improvements compared to state-of-the-art solutions.

scholarly journals Molecular Graph Contrastive Learning with Parameterized Explainable Augmentations

2021 ◽  
Author(s):  
Yingheng Wang ◽  
Yaosen Min ◽  
Erzhuo Shao ◽  
Ji Wu
Keyword(s):  
Neural Networks ◽  
Deep Neural Networks ◽  
Structural Information ◽  
Molecular Graph ◽  
Representation Learning ◽  
Graph Representation ◽  
Input Graph ◽  
Recent Success ◽  
Real World Datasets ◽  
Comparative Results

ABSTRACTLearning generalizable, transferable, and robust representations for molecule data has always been a challenge. The recent success of contrastive learning (CL) for self-supervised graph representation learning provides a novel perspective to learn molecule representations. The most prevailing graph CL framework is to maximize the agreement of representations in different augmented graph views. However, existing graph CL frameworks usually adopt stochastic augmentations or schemes according to pre-defined rules on the input graph to obtain different graph views in various scales (e.g. node, edge, and subgraph), which may destroy topological semantemes and domain prior in molecule data, leading to suboptimal performance. Therefore, designing parameterized, learnable, and explainable augmentation is quite necessary for molecular graph contrastive learning. A well-designed parameterized augmentation scheme can preserve chemically meaningful structural information and intrinsically essential attributes for molecule graphs, which helps to learn representations that are insensitive to perturbation on unimportant atoms and bonds. In this paper, we propose a novel Molecular Graph Contrastive Learning with Parameterized Explainable Augmentations, MolCLE for brevity, that self-adaptively incorporates chemically significative information from both topological and semantic aspects of molecular graphs. Specifically, we apply deep neural networks to parameterize the augmentation process for both the molecular graph topology and atom attributes, to highlight contributive molecular substructures and recognize underlying chemical semantemes. Comprehensive experiments on a variety of real-world datasets demonstrate that our proposed method consistently outperforms compared baselines, which verifies the effectiveness of the proposed framework. Detailedly, our self-supervised MolCLE model surpasses many supervised counterparts, and meanwhile only uses hundreds of thousands of parameters to achieve comparative results against the state-of-the-art baseline, which has tens of millions of parameters. We also provide detailed case studies to validate the explainability of augmented graph views.CCS CONCEPTS• Mathematics of computing → Graph algorithms; • Applied computing → Bioinformatics; • Computing methodologies → Neural networks; Unsupervised learning.

scholarly journals Recent advances in network-based methods for disease gene prediction

2020 ◽  
Author(s):  
Sezin Kircali Ata ◽  
Min Wu ◽  
Yuan Fang ◽  
Le Ou-Yang ◽  
Chee Keong Kwoh ◽  
...  
Keyword(s):  
Empirical Analysis ◽  
Genome Wide Association Study ◽  
Disease Gene ◽  
Gene Prediction ◽  
Representation Learning ◽  
Graph Representation ◽  
Molecular Networks ◽  
Learning Methods ◽  
Gene Association ◽  
Disease Gene Prediction

Abstract Disease–gene association through genome-wide association study (GWAS) is an arduous task for researchers. Investigating single nucleotide polymorphisms that correlate with specific diseases needs statistical analysis of associations. Considering the huge number of possible mutations, in addition to its high cost, another important drawback of GWAS analysis is the large number of false positives. Thus, researchers search for more evidence to cross-check their results through different sources. To provide the researchers with alternative and complementary low-cost disease–gene association evidence, computational approaches come into play. Since molecular networks are able to capture complex interplay among molecules in diseases, they become one of the most extensively used data for disease–gene association prediction. In this survey, we aim to provide a comprehensive and up-to-date review of network-based methods for disease gene prediction. We also conduct an empirical analysis on 14 state-of-the-art methods. To summarize, we first elucidate the task definition for disease gene prediction. Secondly, we categorize existing network-based efforts into network diffusion methods, traditional machine learning methods with handcrafted graph features and graph representation learning methods. Thirdly, an empirical analysis is conducted to evaluate the performance of the selected methods across seven diseases. We also provide distinguishing findings about the discussed methods based on our empirical analysis. Finally, we highlight potential research directions for future studies on disease gene prediction.

scholarly journals Graph Transformer for Graph-to-Sequence Learning

2020 ◽  
Vol 34 (05) ◽  
pp. 7464-7471
Author(s):  
Deng Cai ◽  
Wai Lam
Keyword(s):  
Neural Networks ◽  
Information Exchange ◽  
State Of The Art ◽  
Structural Information ◽  
Representation Learning ◽  
Graph Representation ◽  
Text Generation ◽  
Proposed Model ◽  
Graph Neural Networks ◽  
Meaning Representation

The dominant graph-to-sequence transduction models employ graph neural networks for graph representation learning, where the structural information is reflected by the receptive field of neurons. Unlike graph neural networks that restrict the information exchange between immediate neighborhood, we propose a new model, known as Graph Transformer, that uses explicit relation encoding and allows direct communication between two distant nodes. It provides a more efficient way for global graph structure modeling. Experiments on the applications of text generation from Abstract Meaning Representation (AMR) and syntax-based neural machine translation show the superiority of our proposed model. Specifically, our model achieves 27.4 BLEU on LDC2015E86 and 29.7 BLEU on LDC2017T10 for AMR-to-text generation, outperforming the state-of-the-art results by up to 2.2 points. On the syntax-based translation tasks, our model establishes new single-model state-of-the-art BLEU scores, 21.3 for English-to-German and 14.1 for English-to-Czech, improving over the existing best results, including ensembles, by over 1 BLEU.

scholarly journals Multi-hop Attention Graph Neural Networks

2021 ◽  
Author(s):  
Guangtao Wang ◽  
Rex Ying ◽  
Jing Huang ◽  
Jure Leskovec
Keyword(s):  
Neural Networks ◽  
Large Scale ◽  
Performance Metrics ◽  
State Of The Art ◽  
Structural Information ◽  
Representation Learning ◽  
Attention Mechanism ◽  
Graph Representation ◽  
Knowledge Graph ◽  
Graph Neural Networks

Self-attention mechanism in graph neural networks (GNNs) led to state-of-the-art performance on many graph representation learning tasks. Currently, at every layer, attention is computed between connected pairs of nodes and depends solely on the representation of the two nodes. However, such attention mechanism does not account for nodes that are not directly connected but provide important network context. Here we propose Multi-hop Attention Graph Neural Network (MAGNA), a principled way to incorporate multi-hop context information into every layer of attention computation. MAGNA diffuses the attention scores across the network, which increases the receptive field for every layer of the GNN. Unlike previous approaches, MAGNA uses a diffusion prior on attention values, to efficiently account for all paths between the pair of disconnected nodes. We demonstrate in theory and experiments that MAGNA captures large-scale structural information in every layer, and has a low-pass effect that eliminates noisy high-frequency information from graph data. Experimental results on node classification as well as the knowledge graph completion benchmarks show that MAGNA achieves state-of-the-art results: MAGNA achieves up to 5.7% relative error reduction over the previous state-of-the-art on Cora, Citeseer, and Pubmed. MAGNA also obtains the best performance on a large-scale Open Graph Benchmark dataset. On knowledge graph completion MAGNA advances state-of-the-art on WN18RR and FB15k-237 across four different performance metrics.

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.

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.

Sign in / Sign up

Export Citation Format

Share Document