Mengying Jiang

Mengying Jiang, Guizhong Liu, Biao Zhao et al.

Relation-aware graph structure embedding is promising for predicting multi-relational drug-drug interactions (DDIs). Typically, most existing methods begin by constructing a multi-relational DDI graph and then learning relation-aware graph structure embeddings (RaGSEs) of drugs from the DDI graph. Nevertheless, most existing approaches are usually limited in learning RaGSEs of new drugs, leading to serious over-fitting when the test DDIs involve such drugs. To alleviate this issue, we propose a novel DDI prediction method based on relation-aware graph structure embedding with co-contrastive learning, RaGSECo. The proposed RaGSECo constructs two heterogeneous drug graphs: a multi-relational DDI graph and a multi-attribute drug-drug similarity (DDS) graph. The two graphs are used respectively for learning and propagating the RaGSEs of drugs, aiming to ensure all drugs, including new ones, can possess effective RaGSEs. Additionally, we present a novel co-contrastive learning module to learn drug-pairs (DPs) representations. This mechanism learns DP representations from two distinct views (interaction and similarity views) and encourages these views to supervise each other collaboratively to obtain more discriminative DP representations. We evaluate the effectiveness of our RaGSECo on three different tasks using two real datasets. The experimental results demonstrate that RaGSECo outperforms existing state-of-the-art prediction methods.

Mengying Jiang, Guizhong Liu, Yuanchao Su et al.

In representation learning on graph-structured data, many popular graph neural networks (GNNs) fail to capture long-range dependencies, leading to performance degradation. Furthermore, this weakness is magnified when the concerned graph is characterized by heterophily (low homophily). To solve this issue, this paper proposes a novel graph learning framework called the graph convolutional network with self-attention (GCN-SA). The proposed scheme exhibits an exceptional generalization capability in node-level representation learning. The proposed GCN-SA contains two enhancements corresponding to edges and node features. For edges, we utilize a self-attention mechanism to design a stable and effective graph-structure-learning module that can capture the internal correlation between any pair of nodes. This graph-structure-learning module can identify reliable neighbors for each node from the entire graph. Regarding the node features, we modify the transformer block to make it more applicable to enable GCN to fuse valuable information from the entire graph. These two enhancements work in distinct ways to help our GCN-SA capture long-range dependencies, enabling it to perform representation learning on graphs with varying levels of homophily. The experimental results on benchmark datasets demonstrate the effectiveness of the proposed GCN-SA. Compared to other outstanding GNN counterparts, the proposed GCN-SA is competitive.

Mengying Jiang, Guizhong Liu, Yuanchao Su et al.

Most existing methods for predicting drug-drug interactions (DDI) predominantly concentrate on capturing the explicit relationships among drugs, overlooking the valuable implicit correlations present between drug pairs (DPs), which leads to weak predictions. To address this issue, this paper introduces a hierarchical multi-relational graph representation learning (HMGRL) approach. Within the framework of HMGRL, we leverage a wealth of drug-related heterogeneous data sources to construct heterogeneous graphs, where nodes represent drugs and edges denote clear and various associations. The relational graph convolutional network (RGCN) is employed to capture diverse explicit relationships between drugs from these heterogeneous graphs. Additionally, a multi-view differentiable spectral clustering (MVDSC) module is developed to capture multiple valuable implicit correlations between DPs. Within the MVDSC, we utilize multiple DP features to construct graphs, where nodes represent DPs and edges denote different implicit correlations. Subsequently, multiple DP representations are generated through graph cutting, each emphasizing distinct implicit correlations. The graph-cutting strategy enables our HMGRL to identify strongly connected communities of graphs, thereby reducing the fusion of irrelevant features. By combining every representation view of a DP, we create high-level DP representations for predicting DDIs. Two genuine datasets spanning three distinct tasks are adopted to gauge the efficacy of our HMGRL. Experimental outcomes unequivocally indicate that HMGRL surpasses several leading-edge methods in performance.

Mengying Jiang

The analogy to heat diffusion has enhanced our understanding of information flow in graphs and inspired the development of Graph Neural Networks (GNNs). However, most diffusion-based GNNs emulate passive heat diffusion, which still suffers from over-smoothing and limits their ability to capture global graph information. Inspired by the heat death of the universe, which posits that energy distribution becomes uniform over time in a closed system, we recognize that, without external input, node representations in a graph converge to identical feature vectors as diffusion progresses. To address this issue, we propose the Active Diffusion-based Graph Neural Network (ADGNN). ADGNN achieves active diffusion by integrating multiple external information sources that dynamically influence the diffusion process, effectively overcoming the over-smoothing problem. Furthermore, our approach realizes true infinite diffusion by directly calculating the closed-form solution of the active diffusion iterative formula. This allows nodes to preserve their unique characteristics while efficiently gaining comprehensive insights into the graph's global structure. We evaluate ADGNN against several state-of-the-art GNN models across various graph tasks. The results demonstrate that ADGNN significantly improves both accuracy and efficiency, highlighting its effectiveness in capturing global graph information and maintaining node distinctiveness.

Mengying Jiang, Guizhong Liu, Yuanchao Su et al.

In representation learning on the graph-structured data, under heterophily (or low homophily), many popular GNNs may fail to capture long-range dependencies, which leads to their performance degradation. To solve the above-mentioned issue, we propose a graph convolutional networks with structure learning (GCN-SL), and furthermore, the proposed approach can be applied to node classification. The proposed GCN-SL contains two improvements: corresponding to node features and edges, respectively. In the aspect of node features, we propose an efficient-spectral-clustering (ESC) and an ESC with anchors (ESC-ANCH) algorithms to efficiently aggregate feature representations from all similar nodes. In the aspect of edges, we build a re-connected adjacency matrix by using a special data preprocessing technique and similarity learning, and the re-connected adjacency matrix can be optimized directly along with GCN-SL parameters. Considering that the original adjacency matrix may provide misleading information for aggregation in GCN, especially the graphs being with a low level of homophily. The proposed GCN-SL can aggregate feature representations from nearby nodes via re-connected adjacency matrix and is applied to graphs with various levels of homophily. Experimental results on a wide range of benchmark datasets illustrate that the proposed GCN-SL outperforms the stateof-the-art GNN counterparts.

Xinliang Wu, Mengying Jiang, Guizhong Liu

Heterogeneous graph is a kind of data structure widely existing in real life. Nowadays, the research of graph neural network on heterogeneous graph has become more and more popular. The existing heterogeneous graph neural network algorithms mainly have two ideas, one is based on meta-path and the other is not. The idea based on meta-path often requires a lot of manual preprocessing, at the same time it is difficult to extend to large scale graphs. In this paper, we proposed the general heterogeneous message passing paradigm and designed R-GSN that does not need meta-path, which is much improved compared to the baseline R-GCN. Experiments have shown that our R-GSN algorithm achieves the state-of-the-art performance on the ogbn-mag large scale heterogeneous graph dataset.

Faxian Cao, Zhijing Yang, Jinchang Ren et al.

For Hyperspectral image (HSI) datasets, each class have their salient feature and classifiers classify HSI datasets according to the class's saliency features, however, there will be different salient features when use different normalization method. In this letter, we report the effect on classifiers by different normalization methods and recommend the best normalization methods for classifier after analyzing the impact of different normalization methods on classifiers. Pavia University datasets, Indian Pines datasets and Kennedy Space Center datasets will apply to several typical classifiers in order to evaluate and analysis the impact of different normalization methods on typical classifiers.

Faxian Cao, Zhijing Yang, Jinchang Ren et al.

As a new machine learning approach, extreme learning machine (ELM) has received wide attentions due to its good performances. However, when directly applied to the hyperspectral image (HSI) classification, the recognition rate is too low. This is because ELM does not use the spatial information which is very important for HSI classification. In view of this, this paper proposes a new framework for spectral-spatial classification of HSI by combining ELM with loopy belief propagation (LBP). The original ELM is linear, and the nonlinear ELMs (or Kernel ELMs) are the improvement of linear ELM (LELM). However, based on lots of experiments and analysis, we found out that the LELM is a better choice than nonlinear ELM for spectral-spatial classification of HSI. Furthermore, we exploit the marginal probability distribution that uses the whole information in the HSI and learn such distribution using the LBP. The proposed method not only maintain the fast speed of ELM, but also greatly improves the accuracy of classification. The experimental results in the well-known HSI data sets, Indian Pines and Pavia University, demonstrate the good performances of the proposed method.