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Drug-drug interaction(DDI) prediction is an important task in the medical health machine learning community. This study presents a new method, multi-view graph contrastive representation learning for drug-drug interaction prediction, MIRACLE for brevity, to capture inter-view molecule structure and intra-view interactions between molecules simultaneously. MIRACLE treats a DDI network as a multi-view graph where each node in the interaction graph itself is a drug molecular graph instance. We use GCNs and bond-aware attentive message passing networks to encode DDI relationships and drug molecular graphs in the MIRACLE learning stage, respectively. Also, we propose a novel unsupervised contrastive learning component to balance and integrate the multi-view information. Comprehensive experiments on multiple real datasets show that MIRACLE outperforms the state-of-the-art DDI prediction models consistently.

Graph Convolutional Network (GCN) has been widely applied in transportation demand prediction due to its excellent ability to capture non-Euclidean spatial dependence among station-level or regional transportation demands. However, in most of the existing research, the graph convolution was implemented on a heuristically generated adjacency matrix, which could neither reflect the real spatial relationships of stations accurately, nor capture the multi-level spatial dependence of demands adaptively. To cope with the above problems, this paper provides a novel graph convolutional network for transportation demand prediction. Firstly, a novel graph convolution architecture is proposed, which has different adjacency matrices in different layers and all the adjacency matrices are self-learned during the training process. Secondly, a layer-wise coupling mechanism is provided, which associates the upper-level adjacency matrix with the lower-level one. It also reduces the scale of parameters in our model. Lastly, a unitary network is constructed to give the final prediction result by integrating the hidden spatial states with gated recurrent unit, which could capture the multi-level spatial dependence and temporal dynamics simultaneously. Experiments have been conducted on two real-world datasets, NYC Citi Bike and NYC Taxi, and the results demonstrate the superiority of our model over the state-of-the-art ones.

Knowledge graphs (KGs) are of great importance to many real world applications, but they generally suffer from incomplete information in the form of missing relations between entities. Knowledge graph completion (also known as relation prediction) is the task of inferring missing facts given existing ones. Most of the existing work is proposed by maximizing the likelihood of observed instance-level triples. Not much attention, however, is paid to the ontological information, such as type information of entities and relations. In this work, we propose a type-augmented relation prediction (TaRP) method, where we apply both the type information and instance-level information for relation prediction. In particular, type information and instance-level information are encoded as prior probabilities and likelihoods of relations respectively, and are combined by following Bayes' rule. Our proposed TaRP method achieves significantly better performance than state-of-the-art methods on three benchmark datasets: FB15K, YAGO26K-906, and DB111K-174. In addition, we show that TaRP achieves significantly improved data efficiency. More importantly, the type information extracted from a specific dataset can generalize well to other datasets through the proposed TaRP model.

The chronological order of user-item interactions can reveal time-evolving and sequential user behaviors in many recommender systems. The items that users will interact with may depend on the items accessed in the past. However, the substantial increase of users and items makes sequential recommender systems still face non-trivial challenges: (1) the hardness of modeling the short-term user interests; (2) the difficulty of capturing the long-term user interests; (3) the effective modeling of item co-occurrence patterns. To tackle these challenges, we propose a memory augmented graph neural network (MA-GNN) to capture both the long- and short-term user interests. Specifically, we apply a graph neural network to model the item contextual information within a short-term period and utilize a shared memory network to capture the long-range dependencies between items. In addition to the modeling of user interests, we employ a bilinear function to capture the co-occurrence patterns of related items. We extensively evaluate our model on five real-world datasets, comparing with several state-of-the-art methods and using a variety of performance metrics. The experimental results demonstrate the effectiveness of our model for the task of Top-K sequential recommendation.

The recent proliferation of knowledge graphs (KGs) coupled with incomplete or partial information, in the form of missing relations (links) between entities, has fueled a lot of research on knowledge base completion (also known as relation prediction). Several recent works suggest that convolutional neural network (CNN) based models generate richer and more expressive feature embeddings and hence also perform well on relation prediction. However, we observe that these KG embeddings treat triples independently and thus fail to cover the complex and hidden information that is inherently implicit in the local neighborhood surrounding a triple. To this effect, our paper proposes a novel attention based feature embedding that captures both entity and relation features in any given entity's neighborhood. Additionally, we also encapsulate relation clusters and multihop relations in our model. Our empirical study offers insights into the efficacy of our attention based model and we show marked performance gains in comparison to state of the art methods on all datasets.

Predicting interactions between structured entities lies at the core of numerous tasks such as drug regimen and new material design. In recent years, graph neural networks have become attractive. They represent structured entities as graphs and then extract features from each individual graph using graph convolution operations. However, these methods have some limitations: i) their networks only extract features from a fix-sized subgraph structure (i.e., a fix-sized receptive field) of each node, and ignore features in substructures of different sizes, and ii) features are extracted by considering each entity independently, which may not effectively reflect the interaction between two entities. To resolve these problems, we present MR-GNN, an end-to-end graph neural network with the following features: i) it uses a multi-resolution based architecture to extract node features from different neighborhoods of each node, and, ii) it uses dual graph-state long short-term memory networks (L-STMs) to summarize local features of each graph and extracts the interaction features between pairwise graphs. Experiments conducted on real-world datasets show that MR-GNN improves the prediction of state-of-the-art methods.

Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.

Knowledge graph embedding aims to learn distributed representations for entities and relations, and is proven to be effective in many applications. Crossover interactions --- bi-directional effects between entities and relations --- help select related information when predicting a new triple, but haven't been formally discussed before. In this paper, we propose CrossE, a novel knowledge graph embedding which explicitly simulates crossover interactions. It not only learns one general embedding for each entity and relation as most previous methods do, but also generates multiple triple specific embeddings for both of them, named interaction embeddings. We evaluate embeddings on typical link prediction tasks and find that CrossE achieves state-of-the-art results on complex and more challenging datasets. Furthermore, we evaluate embeddings from a new perspective --- giving explanations for predicted triples, which is important for real applications. In this work, an explanation for a triple is regarded as a reliable closed-path between the head and the tail entity. Compared to other baselines, we show experimentally that CrossE, benefiting from interaction embeddings, is more capable of generating reliable explanations to support its predictions.

The polypharmacy side effect prediction problem considers cases in which two drugs taken individually do not result in a particular side effect; however, when the two drugs are taken in combination, the side effect manifests. In this work, we demonstrate that multi-relational knowledge graph completion achieves state-of-the-art results on the polypharmacy side effect prediction problem. Empirical results show that our approach is particularly effective when the protein targets of the drugs are well-characterized. In contrast to prior work, our approach provides more interpretable predictions and hypotheses for wet lab validation.