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Molecular representation learning contributes to multiple downstream tasks such as molecular property prediction and drug design. To properly represent molecules, graph contrastive learning is a promising paradigm as it utilizes self-supervision signals and has no requirements for human annotations. However, prior works fail to incorporate fundamental domain knowledge into graph semantics and thus ignore the correlations between atoms that have common attributes but are not directly connected by bonds. To address these issues, we construct a Chemical Element Knowledge Graph (KG) to summarize microscopic associations between elements and propose a novel Knowledge-enhanced Contrastive Learning (KCL) framework for molecular representation learning. KCL framework consists of three modules. The first module, knowledge-guided graph augmentation, augments the original molecular graph based on the Chemical Element KG. The second module, knowledge-aware graph representation, extracts molecular representations with a common graph encoder for the original molecular graph and a Knowledge-aware Message Passing Neural Network (KMPNN) to encode complex information in the augmented molecular graph. The final module is a contrastive objective, where we maximize agreement between these two views of molecular graphs. Extensive experiments demonstrated that KCL obtained superior performances against state-of-the-art baselines on eight molecular datasets. Visualization experiments properly interpret what KCL has learned from atoms and attributes in the augmented molecular graphs. Our codes and data are available in supplementary materials.

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.

Heterogeneous graph neural networks (HGNNs) as an emerging technique have shown superior capacity of dealing with heterogeneous information network (HIN). However, most HGNNs follow a semi-supervised learning manner, which notably limits their wide use in reality since labels are usually scarce in real applications. Recently, contrastive learning, a self-supervised method, becomes one of the most exciting learning paradigms and shows great potential when there are no labels. In this paper, we study the problem of self-supervised HGNNs and propose a novel co-contrastive learning mechanism for HGNNs, named HeCo. Different from traditional contrastive learning which only focuses on contrasting positive and negative samples, HeCo employs cross-viewcontrastive mechanism. Specifically, two views of a HIN (network schema and meta-path views) are proposed to learn node embeddings, so as to capture both of local and high-order structures simultaneously. Then the cross-view contrastive learning, as well as a view mask mechanism, is proposed, which is able to extract the positive and negative embeddings from two views. This enables the two views to collaboratively supervise each other and finally learn high-level node embeddings. Moreover, two extensions of HeCo are designed to generate harder negative samples with high quality, which further boosts the performance of HeCo. Extensive experiments conducted on a variety of real-world networks show the superior performance of the proposed methods over the state-of-the-arts.

Representation learning on user-item graph for recommendation has evolved from using single ID or interaction history to exploiting higher-order neighbors. This leads to the success of graph convolution networks (GCNs) for recommendation such as PinSage and LightGCN. Despite effectiveness, we argue that they suffer from two limitations: (1) high-degree nodes exert larger impact on the representation learning, deteriorating the recommendations of low-degree (long-tail) items; and (2) representations are vulnerable to noisy interactions, as the neighborhood aggregation scheme further enlarges the impact of observed edges. In this work, we explore self-supervised learning on user-item graph, so as to improve the accuracy and robustness of GCNs for recommendation. The idea is to supplement the classical supervised task of recommendation with an auxiliary self-supervised task, which reinforces node representation learning via self-discrimination. Specifically, we generate multiple views of a node, maximizing the agreement between different views of the same node compared to that of other nodes. We devise three operators to generate the views -- node dropout, edge dropout, and random walk -- that change the graph structure in different manners. We term this new learning paradigm as \textit{Self-supervised Graph Learning} (SGL), implementing it on the state-of-the-art model LightGCN. Through theoretical analyses, we find that SGL has the ability of automatically mining hard negatives. Empirical studies on three benchmark datasets demonstrate the effectiveness of SGL, which improves the recommendation accuracy, especially on long-tail items, and the robustness against interaction noises. Our implementations are available at \url{//github.com/wujcan/SGL}.

Recently, contrastive learning (CL) has emerged as a successful method for unsupervised graph representation learning. Most graph CL methods first perform stochastic augmentation on the input graph to obtain two graph views and maximize the agreement of representations in the two views. Despite the prosperous development of graph CL methods, the design of graph augmentation schemes -- a crucial component in CL -- remains rarely explored. We argue that the data augmentation schemes should preserve intrinsic structures and attributes of graphs, which will force the model to learn representations that are insensitive to perturbation on unimportant nodes and edges. However, most existing methods adopt uniform data augmentation schemes, like uniformly dropping edges and uniformly shuffling features, leading to suboptimal performance. In this paper, we propose a novel graph contrastive representation learning method with adaptive augmentation that incorporates various priors for topological and semantic aspects of the graph. Specifically, on the topology level, we design augmentation schemes based on node centrality measures to highlight important connective structures. On the node attribute level, we corrupt node features by adding more noise to unimportant node features, to enforce the model to recognize underlying semantic information. We perform extensive experiments of node classification on a variety of real-world datasets. Experimental results demonstrate that our proposed method consistently outperforms existing state-of-the-art baselines and even surpasses some supervised counterparts, which validates the effectiveness of the proposed contrastive framework with adaptive augmentation.

Data augmentation has been widely used to improve generalizability of machine learning models. However, comparatively little work studies data augmentation for graphs. This is largely due to the complex, non-Euclidean structure of graphs, which limits possible manipulation operations. Augmentation operations commonly used in vision and language have no analogs for graphs. Our work studies graph data augmentation for graph neural networks (GNNs) in the context of improving semi-supervised node-classification. We discuss practical and theoretical motivations, considerations and strategies for graph data augmentation. Our work shows that neural edge predictors can effectively encode class-homophilic structure to promote intra-class edges and demote inter-class edges in given graph structure, and our main contribution introduces the GAug graph data augmentation framework, which leverages these insights to improve performance in GNN-based node classification via edge prediction. Extensive experiments on multiple benchmarks show that augmentation via GAug improves performance across GNN architectures and datasets.

Potential Drug-Drug Interaction(DDI) occurring while treating complex or co-existing diseases with drug combinations may cause changes in drugs' pharmacological activity. Therefore, DDI prediction has been an important task in the medical healthy machine learning community. Graph-based learning methods have recently aroused widespread interest and are proved to be a priority for this task. However, these methods are often limited to exploiting the inter-view drug molecular structure and ignoring the drug's intra-view interaction relationship, vital to capturing the complex DDI patterns. 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 GCN to encode DDI relationships and a bond-aware attentive message propagating method to capture drug molecular structure information in the MIRACLE learning stage. 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.

A prominent technique for self-supervised representation learning has been to contrast semantically similar and dissimilar pairs of samples. Without access to labels, dissimilar (negative) points are typically taken to be randomly sampled datapoints, implicitly accepting that these points may, in reality, actually have the same label. Perhaps unsurprisingly, we observe that sampling negative examples from truly different labels improves performance, in a synthetic setting where labels are available. Motivated by this observation, we develop a debiased contrastive objective that corrects for the sampling of same-label datapoints, even without knowledge of the true labels. Empirically, the proposed objective consistently outperforms the state-of-the-art for representation learning in vision, language, and reinforcement learning benchmarks. Theoretically, we establish generalization bounds for the downstream classification task.

Contrastive learning has become a key component of self-supervised learning approaches for computer vision. By learning to embed two augmented versions of the same image close to each other and to push the embeddings of different images apart, one can train highly transferable visual representations. As revealed by recent studies, heavy data augmentation and large sets of negatives are both crucial in learning such representations. At the same time, data mixing strategies either at the image or the feature level improve both supervised and semi-supervised learning by synthesizing novel examples, forcing networks to learn more robust features. In this paper, we argue that an important aspect of contrastive learning, i.e., the effect of hard negatives, has so far been neglected. To get more meaningful negative samples, current top contrastive self-supervised learning approaches either substantially increase the batch sizes, or keep very large memory banks; increasing the memory size, however, leads to diminishing returns in terms of performance. We therefore start by delving deeper into a top-performing framework and show evidence that harder negatives are needed to facilitate better and faster learning. Based on these observations, and motivated by the success of data mixing, we propose hard negative mixing strategies at the feature level, that can be computed on-the-fly with a minimal computational overhead. We exhaustively ablate our approach on linear classification, object detection and instance segmentation and show that employing our hard negative mixing procedure improves the quality of visual representations learned by a state-of-the-art self-supervised learning method.

Mining graph data has become a popular research topic in computer science and has been widely studied in both academia and industry given the increasing amount of network data in the recent years. However, the huge amount of network data has posed great challenges for efficient analysis. This motivates the advent of graph representation which maps the graph into a low-dimension vector space, keeping original graph structure and supporting graph inference. The investigation on efficient representation of a graph has profound theoretical significance and important realistic meaning, we therefore introduce some basic ideas in graph representation/network embedding as well as some representative models in this chapter.