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Register a new userGIPA: General Information Propagation Algorithm for Graph Learning
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Yongchao Liu
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Graph neural networks (GNNs) have been popularly used in analyzing graph-structured data, showing promising results in various applications such as node classification, link prediction and network recommendation. In this paper, we present a new graph attention neural network, namely GIPA, for attributed graph data learning. GIPA consists of three key components: attention, feature propagation and aggregation. Specifically, the attention component introduces a new multi-layer perceptron based multi-head to generate better non-linear feature mapping and representation than conventional implementations such as dot-product. The propagation component considers not only node features but also edge features, which differs from existing GNNs that merely consider node features. The aggregation component uses a residual connection to generate the final embedding. We evaluate the performance of GIPA using the Open Graph Benchmark proteins (ogbn-proteins for short) dataset. The experimental results reveal that GIPA can beat the state-of-the-art models in terms of prediction accuracy, e.g., GIPA achieves an average test ROC-AUC of $0.8700pm 0.0010$ and outperforms all the previous methods listed in the ogbn-proteins leaderboard.
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The use of drug combinations often leads to polypharmacy side effects (POSE). A recent method formulates POSE prediction as a link prediction problem on a graph of drugs and proteins, and solves it with Graph Convolutional Networks (GCNs). However, due to the complex relationships in POSE, this method has high computational cost and memory demand. This paper proposes a flexible Tri-graph Information Propagation (TIP) model that operates on three subgraphs to learn representations progressively by propagation from protein-protein graph to drug-drug graph via protein-drug graph. Experiments show that TIP improves accuracy by 7%+, time efficiency by 83$times$, and space efficiency by 3$times$.
Heterogeneous graph representation learning aims to learn low-dimensional vector representations of different types of entities and relations to empower downstream tasks. Existing methods either capture semantic relationships but indirectly leverage node/edge attributes in a complex way, or leverage node/edge attributes directly without taking semantic relationships into account. When involving multiple convolution operations, they also have poor scalability. To overcome these limitations, this paper proposes a flexible and efficient Graph information propagation Network (GripNet) framework. Specifically, we introduce a new supergraph data structure consisting of supervertices and superedges. A supervertex is a semantically-coherent subgraph. A superedge defines an information propagation path between two supervertices. GripNet learns new representations for the supervertex of interest by propagating information along the defined path using multiple layers. We construct multiple large-scale graphs and evaluate GripNet against competing methods to show its superiority in link prediction, node classification, and data integration.
Graph neural networks are emerging as continuation of deep learning success w.r.t. graph data. Tens of different graph neural network variants have been proposed, most following a neighborhood aggregation scheme, where the node features are updated via aggregating features of its neighboring nodes from layer to layer. Though related research surges, the power of GNNs are still not on-par-with their counterpart CNNs in computer vision and RNNs in natural language processing. We rethink this problem from the perspective of information propagation, and propose to enhance information propagation among GNN layers by combining heterogeneous aggregations. We argue that as richer information are propagated from shallow to deep layers, the discriminative capability of features formulated by GNN can benefit from it. As our first attempt in this direction, a new generic GNN layer formulation and upon this a new GNN variant referred as HAG-Net is proposed. We empirically validate the effectiveness of HAG-Net on a number of graph classification benchmarks, and elaborate all the design options and criterions along with.
Graph neural networks (GNNs) have emerged as effective approaches for graph analysis, especially in the scenario of semi-supervised learning. Despite its success, GNN often suffers from over-smoothing and over-fitting problems, which affects its performance on node classification tasks. We analyze that an alternative method, the label propagation algorithm (LPA), avoids the aforementioned problems thus it is a promising choice for graph semi-supervised learning. Nevertheless, the intrinsic limitations of LPA on feature exploitation and relation modeling make propagating labels become less effective. To overcome these limitations, we introduce a novel framework for graph semi-supervised learning termed as Cyclic Label Propagation (CycProp for abbreviation), which integrates GNNs into the process of label propagation in a cyclic and mutually reinforcing manner to exploit the advantages of both GNNs and LPA. In particular, our proposed CycProp updates the node embeddings learned by GNN module with the augmented information by label propagation, while fine-tunes the weighted graph of label propagation with the help of node embedding in turn. After the model converges, reliably predicted labels and informative node embeddings are obtained with the LPA and GNN modules respectively. Extensive experiments on various real-world datasets are conducted, and the experimental results empirically demonstrate that the proposed CycProp model can achieve relatively significant gains over the state-of-the-art methods.
Graph Neural Networks (GNNs) for prediction tasks like node classification or edge prediction have received increasing attention in recent machine learning from graphically structured data. However, a large quantity of labeled graphs is difficult to obtain, which significantly limits the true success of GNNs. Although active learning has been widely studied for addressing label-sparse issues with other data types like text, images, etc., how to make it effective over graphs is an open question for research. In this paper, we present an investigation on active learning with GNNs for node classification tasks. Specifically, we propose a new method, which uses node feature propagation followed by K-Medoids clustering of the nodes for instance selection in active learning. With a theoretical bound analysis we justify the design choice of our approach. In our experiments on four benchmark datasets, the proposed method outperforms other representative baseline methods consistently and significantly.
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