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A frequent challenge when using graphical models in applications is that the sample size is limited relative to the number of parameters to be learned. Our motivation stems from applications where one has external data, in the form of networks between variables, that provides valuable information to help improve inference. Specifically, we depict the relation between COVID-19 cases and social and geographical network data, and between stock market returns and economic and policy networks extracted from text data. We propose a graphical LASSO framework where likelihood penalties are guided by the external network data. We also propose a spike-and-slab prior framework that depicts how partial correlations depend on the networks, which helps interpret the fitted graphical model and its relationship to the network. We develop computational schemes and software implementations in R and probabilistic programming languages. Our applications show how incorporating network data can significantly improve interpretation, statistical accuracy, and out-of-sample prediction, in some instances using significantly sparser graphical models than would have otherwise been estimated.

Graph neural networks (GNNs) is widely used to learn a powerful representation of graph-structured data. Recent work demonstrates that transferring knowledge from self-supervised tasks to downstream tasks could further improve graph representation. However, there is an inherent gap between self-supervised tasks and downstream tasks in terms of optimization objective and training data. Conventional pre-training methods may be not effective enough on knowledge transfer since they do not make any adaptation for downstream tasks. To solve such problems, we propose a new transfer learning paradigm on GNNs which could effectively leverage self-supervised tasks as auxiliary tasks to help the target task. Our methods would adaptively select and combine different auxiliary tasks with the target task in the fine-tuning stage. We design an adaptive auxiliary loss weighting model to learn the weights of auxiliary tasks by quantifying the consistency between auxiliary tasks and the target task. In addition, we learn the weighting model through meta-learning. Our methods can be applied to various transfer learning approaches, it performs well not only in multi-task learning but also in pre-training and fine-tuning. Comprehensive experiments on multiple downstream tasks demonstrate that the proposed methods can effectively combine auxiliary tasks with the target task and significantly improve the performance compared to state-of-the-art methods.

Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect subgraphs, rendering subgraph prediction tasks challenging to tackle in many impactful applications. Further, subgraph prediction tasks present several unique challenges, because subgraphs can have non-trivial internal topology, but also carry a notion of position and external connectivity information relative to the underlying graph in which they exist. Here, we introduce SUB-GNN, a subgraph neural network to learn disentangled subgraph representations. In particular, we propose a novel subgraph routing mechanism that propagates neural messages between the subgraph's components and randomly sampled anchor patches from the underlying graph, yielding highly accurate subgraph representations. SUB-GNN specifies three channels, each designed to capture a distinct aspect of subgraph structure, and we provide empirical evidence that the channels encode their intended properties. We design a series of new synthetic and real-world subgraph datasets. Empirical results for subgraph classification on eight datasets show that SUB-GNN achieves considerable performance gains, outperforming strong baseline methods, including node-level and graph-level GNNs, by 12.4% over the strongest baseline. SUB-GNN performs exceptionally well on challenging biomedical datasets when subgraphs have complex topology and even comprise multiple disconnected components.

In Multi-Label Text Classification (MLTC), one sample can belong to more than one class. It is observed that most MLTC tasks, there are dependencies or correlations among labels. Existing methods tend to ignore the relationship among labels. In this paper, a graph attention network-based model is proposed to capture the attentive dependency structure among the labels. The graph attention network uses a feature matrix and a correlation matrix to capture and explore the crucial dependencies between the labels and generate classifiers for the task. The generated classifiers are applied to sentence feature vectors obtained from the text feature extraction network (BiLSTM) to enable end-to-end training. Attention allows the system to assign different weights to neighbor nodes per label, thus allowing it to learn the dependencies among labels implicitly. The results of the proposed model are validated on five real-world MLTC datasets. The proposed model achieves similar or better performance compared to the previous state-of-the-art models.

Few-shot learning aims to learn novel categories from very few samples given some base categories with sufficient training samples. The main challenge of this task is the novel categories are prone to dominated by color, texture, shape of the object or background context (namely specificity), which are distinct for the given few training samples but not common for the corresponding categories (see Figure 1). Fortunately, we find that transferring information of the correlated based categories can help learn the novel concepts and thus avoid the novel concept being dominated by the specificity. Besides, incorporating semantic correlations among different categories can effectively regularize this information transfer. In this work, we represent the semantic correlations in the form of structured knowledge graph and integrate this graph into deep neural networks to promote few-shot learning by a novel Knowledge Graph Transfer Network (KGTN). Specifically, by initializing each node with the classifier weight of the corresponding category, a propagation mechanism is learned to adaptively propagate node message through the graph to explore node interaction and transfer classifier information of the base categories to those of the novel ones. Extensive experiments on the ImageNet dataset show significant performance improvement compared with current leading competitors. Furthermore, we construct an ImageNet-6K dataset that covers larger scale categories, i.e, 6,000 categories, and experiments on this dataset further demonstrate the effectiveness of our proposed model.

Graph Neural Networks (GNNs), which generalize deep neural networks to graph-structured data, have drawn considerable attention and achieved state-of-the-art performance in numerous graph related tasks. However, existing GNN models mainly focus on designing graph convolution operations. The graph pooling (or downsampling) operations, that play an important role in learning hierarchical representations, are usually overlooked. In this paper, we propose a novel graph pooling operator, called Hierarchical Graph Pooling with Structure Learning (HGP-SL), which can be integrated into various graph neural network architectures. HGP-SL incorporates graph pooling and structure learning into a unified module to generate hierarchical representations of graphs. More specifically, the graph pooling operation adaptively selects a subset of nodes to form an induced subgraph for the subsequent layers. To preserve the integrity of graph's topological information, we further introduce a structure learning mechanism to learn a refined graph structure for the pooled graph at each layer. By combining HGP-SL operator with graph neural networks, we perform graph level representation learning with focus on graph classification task. Experimental results on six widely used benchmarks demonstrate the effectiveness of our proposed model.

Attributed graph clustering is challenging as it requires joint modelling of graph structures and node attributes. Recent progress on graph convolutional networks has proved that graph convolution is effective in combining structural and content information, and several recent methods based on it have achieved promising clustering performance on some real attributed networks. However, there is limited understanding of how graph convolution affects clustering performance and how to properly use it to optimize performance for different graphs. Existing methods essentially use graph convolution of a fixed and low order that only takes into account neighbours within a few hops of each node, which underutilizes node relations and ignores the diversity of graphs. In this paper, we propose an adaptive graph convolution method for attributed graph clustering that exploits high-order graph convolution to capture global cluster structure and adaptively selects the appropriate order for different graphs. We establish the validity of our method by theoretical analysis and extensive experiments on benchmark datasets. Empirical results show that our method compares favourably with state-of-the-art methods.

Recently, graph neural networks (GNNs) have revolutionized the field of graph representation learning through effectively learned node embeddings, and achieved state-of-the-art results in tasks such as node classification and link prediction. However, current GNN methods are inherently flat and do not learn hierarchical representations of graphs---a limitation that is especially problematic for the task of graph classification, where the goal is to predict the label associated with an entire graph. Here we propose DiffPool, a differentiable graph pooling module that can generate hierarchical representations of graphs and can be combined with various graph neural network architectures in an end-to-end fashion. DiffPool learns a differentiable soft cluster assignment for nodes at each layer of a deep GNN, mapping nodes to a set of clusters, which then form the coarsened input for the next GNN layer. Our experimental results show that combining existing GNN methods with DiffPool yields an average improvement of 5-10% accuracy on graph classification benchmarks, compared to all existing pooling approaches, achieving a new state-of-the-art on four out of five benchmark data sets.

Traditional methods for link prediction can be categorized into three main types: graph structure feature-based, latent feature-based, and explicit feature-based. Graph structure feature methods leverage some handcrafted node proximity scores, e.g., common neighbors, to estimate the likelihood of links. Latent feature methods rely on factorizing networks' matrix representations to learn an embedding for each node. Explicit feature methods train a machine learning model on two nodes' explicit attributes. Each of the three types of methods has its unique merits. In this paper, we propose SEAL (learning from Subgraphs, Embeddings, and Attributes for Link prediction), a new framework for link prediction which combines the power of all the three types into a single graph neural network (GNN). GNN is a new type of neural network which directly accepts graphs as input and outputs their labels. In SEAL, the input to the GNN is a local subgraph around each target link. We prove theoretically that our local subgraphs also reserve a great deal of high-order graph structure features related to link existence. Another key feature is that our GNN can naturally incorporate latent features and explicit features. It is achieved by concatenating node embeddings (latent features) and node attributes (explicit features) in the node information matrix for each subgraph, thus combining the three types of features to enhance GNN learning. Through extensive experiments, SEAL shows unprecedentedly strong performance against a wide range of baseline methods, including various link prediction heuristics and network embedding methods.

In this paper, we propose the joint learning attention and recurrent neural network (RNN) models for multi-label classification. While approaches based on the use of either model exist (e.g., for the task of image captioning), training such existing network architectures typically require pre-defined label sequences. For multi-label classification, it would be desirable to have a robust inference process, so that the prediction error would not propagate and thus affect the performance. Our proposed model uniquely integrates attention and Long Short Term Memory (LSTM) models, which not only addresses the above problem but also allows one to identify visual objects of interests with varying sizes without the prior knowledge of particular label ordering. More importantly, label co-occurrence information can be jointly exploited by our LSTM model. Finally, by advancing the technique of beam search, prediction of multiple labels can be efficiently achieved by our proposed network model.