Drug-target interaction prediction (DTI) is essential in various applications including drug discovery and clinical application. There are two perspectives of input data widely used in DTI prediction: Intrinsic data represents how drugs or targets are constructed, and extrinsic data represents how drugs or targets are related to other biological entities. However, any of the two perspectives of input data can be scarce for some drugs or targets, especially for those unpopular or newly discovered. Furthermore, ground-truth labels for specific interaction types can also be scarce. Therefore, we propose the first method to tackle DTI prediction under input data and/or label scarcity. To make our model functional when only one perspective of input data is available, we design two separate experts to process intrinsic and extrinsic data respectively and fuse them adaptively according to different samples. Furthermore, to make the two perspectives complement each other and remedy label scarcity, two experts synergize with each other in a mutually supervised way to exploit the enormous unlabeled data. Extensive experiments on 3 real-world datasets under different extents of input data scarcity and/or label scarcity demonstrate our model outperforms states of the art significantly and steadily, with a maximum improvement of 53.53%. We also test our model without any data scarcity and it still outperforms current methods.

Protein-protein Interaction (PPI) prediction, which aims to identify the interactions between proteins within a biological system, is an important problem in understanding disease mechanisms and drug discovery. Recently, Equivariant Graph Neural Networks (E3-GNNs) are advanced computational models that provide a powerful solution for accurately predicting PPIs by preserving the geometric integrity of protein interactions. However, most E3-GNNs model protein interactions at the residue level, potentially neglecting critical atomic details and side-chain conformations. In this paper, we propose a novel model, MEANT, designed to adaptively extract atom-level geometric information from varying numbers of atoms within different residues for PPI prediction. Specifically, we define a full-atom graph that contains atomic geometry and guides the message passing under the structure of residues. We also design a geometric relation extractor to integrate geometric information from different residues and adaptively handle variations in the number of atoms within each residue. Finally, we adopt the attention mechanism to update the residue representation and the atomic coordinates within a residue. Experimental results show that our proposed model, MEANT, significantly outperforms state-of-the-art methods on three typical PPI prediction tasks. Our code and data are available on GitHub at https://github.com/BUPT-GAMMA/MEANT.

Graph Neural Networks (GNNs) can effectively capture both the topology and attribute information of a graph, and have been extensively studied in many domains. Recently, there is an emerging trend that equips GNNs with knowledge distillation for better efficiency or effectiveness. However, to the best of our knowledge, existing knowledge distillation methods applied on GNNs all employed predefined distillation processes, which are controlled by several hyper-parameters without any supervision from the performance of distilled models. Such isolation between distillation and evaluation would lead to suboptimal results. In this work, we aim to propose a general knowledge distillation framework that can be applied on any pretrained GNN models to further improve their performance. To address the isolation problem, we propose to parameterize and learn distillation processes suitable for distilling GNNs. Specifically, instead of introducing a unified temperature hyper-parameter as most previous work did, we will learn node-specific distillation temperatures towards better performance of distilled models. We first parameterize each node's temperature by a function of its neighborhood's encodings and predictions, and then design a novel iterative learning process for model distilling and temperature learning. We also introduce a scalable variant of our method to accelerate model training. Experimental results on five benchmark datasets show that our proposed framework can be applied on five popular GNN models and consistently improve their prediction accuracies with 3.12% relative enhancement on average. Besides, the scalable variant enables 8 times faster training speed at the cost of 1% prediction accuracy.

Dynamic link prediction, which aims at forecasting future edges of a node in a dynamic network, is an important problem in network science and has a wide range of real-world applications. A key property of dynamic networks is that new nodes and links keep coming over time and these new nodes usually have only a few links at their arrivals. However, how to predict future links for these few-shot nodes in a dynamic network has not been well studied. Existing dynamic network representation learning methods were not specialized for few-shot scenarios and thus would lead to suboptimal performances. In this paper, we propose a novel model based on a meta-learning framework, dubbed as MetaDyGNN, for few-shot link prediction in dynamic networks. Specifically, we propose a meta-learner with hierarchical time interval-wise and node-wise adaptions to extract general knowledge behind this problem. We also design a simple and effective dynamic graph neural network (GNN) module to characterize the local structure of each node in meta-learning tasks. As a result, the learned general knowledge serves as model initializations, and can quickly adapt to new nodes with a fine-tuning process on only a few links. Experimental results show that our proposed MetaDyGNN significantly outperforms state-of-the-art methods on three publicly available datasets.