scholarly journals GSSNN: Graph Smoothing Splines Neural Networks

2020 ◽  
Vol 34 (04) ◽  
pp. 7007-7014
Author(s):  
Shichao Zhu ◽  
Lewei Zhou ◽  
Shirui Pan ◽  
Chuan Zhou ◽  
Guiying Yan ◽  
...  
Keyword(s):  
Neural Networks ◽  
State Of The Art ◽  
Representation Learning ◽  
Smoothing Splines ◽  
Graph Representation ◽  
Graph Classification ◽  
Topological Information ◽  
Graph Representations ◽  
The Arts ◽  
Graph Neural Networks

Graph Neural Networks (GNNs) have achieved state-of-the-art performance in many graph data analysis tasks. However, they still suffer from two limitations for graph representation learning. First, they exploit non-smoothing node features which may result in suboptimal embedding and degenerated performance for graph classification. Second, they only exploit neighbor information but ignore global topological knowledge. Aiming to overcome these limitations simultaneously, in this paper, we propose a novel, flexible, and end-to-end framework, Graph Smoothing Splines Neural Networks (GSSNN), for graph classification. By exploiting the smoothing splines, which are widely used to learn smoothing fitting function in regression, we develop an effective feature smoothing and enhancement module Scaled Smoothing Splines (S3) to learn graph embedding. To integrate global topological information, we design a novel scoring module, which exploits closeness, degree, as well as self-attention values, to select important node features as knots for smoothing splines. These knots can be potentially used for interpreting classification results. In extensive experiments on biological and social datasets, we demonstrate that our model achieves state-of-the-arts and GSSNN is superior in learning more robust graph representations. Furthermore, we show that S3 module is easily plugged into existing GNNs to improve their performance.

scholarly journals Pairwise Half-graph Discrimination: A Simple Graph-level Self-supervised Strategy for Pre-training Graph Neural Networks

2021 ◽  
Author(s):  
Pengyong Li ◽  
Jun Wang ◽  
Ziliang Li ◽  
Yixuan Qiao ◽  
Xianggen Liu ◽  
...  
Keyword(s):  
Neural Networks ◽  
Supervised Learning ◽  
Learning Strategy ◽  
Binary Classification ◽  
Representation Learning ◽  
Graph Representation ◽  
Superior Performance ◽  
Graph Classification ◽  
Training Strategy ◽  
Graph Neural Networks

Self-supervised learning has gradually emerged as a powerful technique for graph representation learning. However, transferable, generalizable, and robust representation learning on graph data still remains a challenge for pre-training graph neural networks. In this paper, we propose a simple and effective self-supervised pre-training strategy, named Pairwise Half-graph Discrimination (PHD), that explicitly pre-trains a graph neural network at graph-level. PHD is designed as a simple binary classification task to discriminate whether two half-graphs come from the same source. Experiments demonstrate that the PHD is an effective pre-training strategy that offers comparable or superior performance on 13 graph classification tasks compared with state-of-the-art strategies, and achieves notable improvements when combined with node-level strategies. Moreover, the visualization of learned representation revealed that PHD strategy indeed empowers the model to learn graph-level knowledge like the molecular scaffold. These results have established PHD as a powerful and effective self-supervised learning strategy in graph-level representation learning.

scholarly journals UniGNN: a Unified Framework for Graph and Hypergraph Neural Networks

2021 ◽  
Author(s):  
Jing Huang ◽  
Jie Yang
Keyword(s):  
Neural Networks ◽  
Message Passing ◽  
State Of The Art ◽  
Representation Learning ◽  
Graph Representation ◽  
Challenging Problem ◽  
Unified Framework ◽  
Real World Datasets ◽  
Graph Neural Networks ◽  
Research Domains

Hypergraph, an expressive structure with flexibility to model the higher-order correlations among entities, has recently attracted increasing attention from various research domains. Despite the success of Graph Neural Networks (GNNs) for graph representation learning, how to adapt the powerful GNN-variants directly into hypergraphs remains a challenging problem. In this paper, we propose UniGNN, a unified framework for interpreting the message passing process in graph and hypergraph neural networks, which can generalize general GNN models into hypergraphs. In this framework, meticulously-designed architectures aiming to deepen GNNs can also be incorporated into hypergraphs with the least effort. Extensive experiments have been conducted to demonstrate the effectiveness of UniGNN on multiple real-world datasets, which outperform the state-of-the-art approaches with a large margin. Especially for the DBLP dataset, we increase the accuracy from 77.4% to 88.8% in the semi-supervised hypernode classification task. We further prove that the proposed message-passing based UniGNN models are at most as powerful as the 1-dimensional Generalized Weisfeiler-Leman (1-GWL) algorithm in terms of distinguishing non-isomorphic hypergraphs. Our code is available at https://github.com/OneForward/UniGNN.

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 K-plex cover pooling for graph neural networks

2021 ◽  
Author(s):  
Davide Bacciu ◽  
Alessio Conte ◽  
Roberto Grossi ◽  
Francesco Landolfi ◽  
Andrea Marino
Keyword(s):  
Neural Networks ◽  
Graph Theory ◽  
State Of The Art ◽  
Graph Classification ◽  
Topological Information ◽  
Community Discovery ◽  
Connectivity Patterns ◽  
Graph Neural Networks ◽  
Pruning Heuristics ◽  
Non Parametric

AbstractGraph pooling methods provide mechanisms for structure reduction that are intended to ease the diffusion of context between nodes further in the graph, and that typically leverage community discovery mechanisms or node and edge pruning heuristics. In this paper, we introduce a novel pooling technique which borrows from classical results in graph theory that is non-parametric and generalizes well to graphs of different nature and connectivity patterns. Our pooling method, named KPlexPool, builds on the concepts of graph covers and k-plexes, i.e. pseudo-cliques where each node can miss up to k links. The experimental evaluation on benchmarks on molecular and social graph classification shows that KPlexPool achieves state of the art performances against both parametric and non-parametric pooling methods in the literature, despite generating pooled graphs based solely on topological information.

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.

scholarly journals Coloring Graph Neural Networks for Node Disambiguation

2020 ◽  
Author(s):  
George Dasoulas ◽  
Ludovic Dos Santos ◽  
Kevin Scaman ◽  
Aladin Virmaux
Keyword(s):  
Neural Networks ◽  
Message Passing ◽  
State Of The Art ◽  
Structural Characteristics ◽  
Expressive Power ◽  
Continuous Functions ◽  
Graph Classification ◽  
Node Attributes ◽  
Graph Neural Networks ◽  
Coloring Graph

In this paper, we show that a simple coloring scheme can improve, both theoretically and empirically, the expressive power of Message Passing Neural Networks (MPNNs). More specifically, we introduce a graph neural network called Colored Local Iterative Procedure (CLIP) that uses colors to disambiguate identical node attributes, and show that this representation is a universal approximator of continuous functions on graphs with node attributes. Our method relies on separability, a key topological characteristic that allows to extend well-chosen neural networks into universal representations. Finally, we show experimentally that CLIP is capable of capturing structural characteristics that traditional MPNNs fail to distinguish, while being state-of-the-art on benchmark graph classification datasets.

scholarly journals TSI-GNN: Extending Graph Neural Networks to Handle Missing Data in Temporal Settings

2021 ◽  
Vol 4 ◽  
Author(s):  
David Gordon ◽  
Panayiotis Petousis ◽  
Henry Zheng ◽  
Davina Zamanzadeh ◽  
Alex A.T. Bui
Keyword(s):  
Neural Networks ◽  
Missing Data ◽  
Bipartite Graph ◽  
Message Passing ◽  
Representation Learning ◽  
Temporal Information ◽  
Graph Representation ◽  
Sequence Information ◽  
Novel Approach ◽  
Graph Neural Networks

We present a novel approach for imputing missing data that incorporates temporal information into bipartite graphs through an extension of graph representation learning. Missing data is abundant in several domains, particularly when observations are made over time. Most imputation methods make strong assumptions about the distribution of the data. While novel methods may relax some assumptions, they may not consider temporality. Moreover, when such methods are extended to handle time, they may not generalize without retraining. We propose using a joint bipartite graph approach to incorporate temporal sequence information. Specifically, the observation nodes and edges with temporal information are used in message passing to learn node and edge embeddings and to inform the imputation task. Our proposed method, temporal setting imputation using graph neural networks (TSI-GNN), captures sequence information that can then be used within an aggregation function of a graph neural network. To the best of our knowledge, this is the first effort to use a joint bipartite graph approach that captures sequence information to handle missing data. We use several benchmark datasets to test the performance of our method against a variety of conditions, comparing to both classic and contemporary methods. We further provide insight to manage the size of the generated TSI-GNN model. Through our analysis we show that incorporating temporal information into a bipartite graph improves the representation at the 30% and 60% missing rate, specifically when using a nonlinear model for downstream prediction tasks in regularly sampled datasets and is competitive with existing temporal methods under different scenarios.

scholarly journals Graph convolutional and attention models for entity classification in multilayer networks

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Lorenzo Zangari ◽  
Roberto Interdonato ◽  
Antonio Calió ◽  
Andrea Tagarelli
Keyword(s):  
State Of The Art ◽  
Structural Characteristics ◽  
Representation Learning ◽  
Efficient Solutions ◽  
Single Type ◽  
Graph Classification ◽  
Multilayer Networks ◽  
Attention Networks ◽  
Convolutional Networks ◽  
Graph Neural Networks

AbstractGraph Neural Networks (GNNs) are powerful tools that are nowadays reaching state of the art performances in a plethora of different tasks such as node classification, link prediction and graph classification. A challenging aspect in this context is to redefine basic deep learning operations, such as convolution, on graph-like structures, where nodes generally have unordered neighborhoods of varying size. State-of-the-art GNN approaches such as Graph Convolutional Networks (GCNs) and Graph Attention Networks (GATs) work on monoplex networks only, i.e., on networks modeling a single type of relation among an homogeneous set of nodes. The aim of this work is to generalize such approaches by proposing a GNN framework for representation learning and semi-supervised classification in multilayer networks with attributed entities, and arbitrary number of layers and intra-layer and inter-layer connections between nodes. We instantiate our framework with two new formulations of GAT and GCN models, namely and , specifically devised for general, attributed multilayer networks. The proposed approaches are evaluated on an entity classification task on nine widely used real-world network datasets coming from different domains and with different structural characteristics. Results show that both our proposed and methods provide effective and efficient solutions to the problem of entity classification in multilayer attributed networks, being faster to learn and offering better accuracy than the competitors. Furthermore, results show how our methods are able to take advantage of the presence of real attributes for the entities, in addition to arbitrary inter-layer connections between the nodes in the various layers.

scholarly journals ASAP: Adaptive Structure Aware Pooling for Learning Hierarchical Graph Representations

2020 ◽  
Vol 34 (04) ◽  
pp. 5470-5477 ◽  
Author(s):  
Ekagra Ranjan ◽  
Soumya Sanyal ◽  
Partha Talukdar
Keyword(s):  
State Of The Art ◽  
Reproducible Research ◽  
Graph Classification ◽  
Cluster Assignment ◽  
Graph Representations ◽  
Average Improvement ◽  
Adaptive Structure ◽  
Soft Cluster ◽  
Graph Neural Networks ◽  
Multiple Graph

Graph Neural Networks (GNN) have been shown to work effectively for modeling graph structured data to solve tasks such as node classification, link prediction and graph classification. There has been some recent progress in defining the notion of pooling in graphs whereby the model tries to generate a graph level representation by downsampling and summarizing the information present in the nodes. Existing pooling methods either fail to effectively capture the graph substructure or do not easily scale to large graphs. In this work, we propose ASAP (Adaptive Structure Aware Pooling), a sparse and differentiable pooling method that addresses the limitations of previous graph pooling architectures. ASAP utilizes a novel self-attention network along with a modified GNN formulation to capture the importance of each node in a given graph. It also learns a sparse soft cluster assignment for nodes at each layer to effectively pool the subgraphs to form the pooled graph. Through extensive experiments on multiple datasets and theoretical analysis, we motivate our choice of the components used in ASAP. Our experimental results show that combining existing GNN architectures with ASAP leads to state-of-the-art results on multiple graph classification benchmarks. ASAP has an average improvement of 4%, compared to current sparse hierarchical state-of-the-art method. We make the source code of ASAP available to encourage reproducible research 1.

scholarly journals Path integral based convolution and pooling for graph neural networks*

2021 ◽  
Vol 2021 (12) ◽  
pp. 124011
Author(s):  
Zheng Ma ◽  
Junyu Xuan ◽  
Yu Guang Wang ◽  
Ming Li ◽  
Pietro Liò
Keyword(s):  
Neural Networks ◽  
Path Integral ◽  
State Of The Art ◽  
Graph Laplacian ◽  
Maximal Entropy ◽  
Optimized Design ◽  
Graph Classification ◽  
Physical Sciences ◽  
Special Cases ◽  
Graph Neural Networks

Abstract Graph neural networks (GNNs) extend the functionality of traditional neural networks to graph-structured data. Similar to CNNs, an optimized design of graph convolution and pooling is key to success. Borrowing ideas from physics, we propose path integral-based GNNs (PAN) for classification and regression tasks on graphs. Specifically, we consider a convolution operation that involves every path linking the message sender and receiver with learnable weights depending on the path length, which corresponds to the maximal entropy random walk. It generalizes the graph Laplacian to a new transition matrix that we call the maximal entropy transition (MET) matrix derived from a path integral formalism. Importantly, the diagonal entries of the MET matrix are directly related to the subgraph centrality, thus leading to a natural and adaptive pooling mechanism. PAN provides a versatile framework that can be tailored for different graph data with varying sizes and structures. We can view most existing GNN architectures as special cases of PAN. Experimental results show that PAN achieves state-of-the-art performance on various graph classification/regression tasks, including a new benchmark dataset from statistical mechanics that we propose to boost applications of GNN in physical sciences.

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