Existing cross-network node classification methods are mainly proposed for closed-set setting, where the source network and the target network share exactly the same label space. Such a setting is restricted in real-world applications, since the target network might contain additional classes that are not present in the source. In this work, we study a more realistic open-set cross-network node classification (O-CNNC) problem, where the target network contains all the known classes in the source and further contains several target-private classes unseen in the source. Borrowing the concept from open-set domain adaptation, all target-private classes are defined as an additional “unknown” class. To address the challenging O-CNNC problem, we propose an unknown-excluded adversarial graph domain alignment (UAGA) model with a separate-adapt training strategy. Firstly, UAGA roughly separates known classes from unknown class, by training a graph neural network encoder and a neighborhood-aggregation node classifier in an adversarial framework. Then, unknown-excluded adversarial domain alignment is customized to align only target nodes from known classes with the source, while pushing target nodes from unknown class far away from the source, by assigning positive and negative domain adaptation coefficient to known class nodes and unknown class nodes. Extensive experiments on real-world datasets demonstrate significant outperformance of the proposed UAGA over state-of-the-art methods on O-CNNC.

Graph neural networks (GNNs) have shown great ability in modeling graphs; however, their performance would significantly degrade when there are noisy edges connecting nodes from different classes. To alleviate negative effect of noisy edges on neighborhood aggregation, some recent GNNs propose to predict the label agreement between node pairs within a single network. However, predicting the label agreement of edges across different networks has not been investigated yet. Our work makes the pioneering attempt to study a novel problem of cross-network homophilous and heterophilous edge classification (CNHHEC) and proposes a novel domain-adaptive graph attention-supervised network (DGASN) to effectively tackle the CNHHEC problem. First, DGASN adopts multihead graph attention network (GAT) as the GNN encoder, which jointly trains node embeddings and edge embeddings via the node classification and edge classification losses. As a result, label-discriminative embeddings can be obtained to distinguish homophilous edges from heterophilous edges. In addition, DGASN applies direct supervision on graph attention learning based on the observed edge labels from the source network, thus lowering the negative effects of heterophilous edges while enlarging the positive effects of homophilous edges during neighborhood aggregation. To facilitate knowledge transfer across networks, DGASN employs adversarial domain adaptation to mitigate domain divergence. Extensive experiments on real-world benchmark datasets demonstrate that the proposed DGASN achieves the state-of-the-art performance in CNHHEC.

Recent years, graph contrastive learning (GCL), which aims to learn representations from unlabeled graphs, has made great progress. However, the existing GCL methods mostly adopt human-designed graph augmentations, which are sensitive to various graph datasets. In addition, the contrastive losses originally developed in computer vision have been directly applied to graph data, where the neighboring nodes are regarded as negatives and consequently pushed far apart from the anchor. However, this is contradictory with the homophily assumption of net-works that connected nodes often belong to the same class and should be close to each other. In this work, we propose an end-to-end automatic GCL method, named NCLA to apply neighbor contrastive learning on learnable graph augmentation. Several graph augmented views with adaptive topology are automatically learned by the multi-head graph attention mechanism, which can be compatible with various graph datasets without prior domain knowledge. In addition, a neighbor contrastive loss is devised to allow multiple positives per anchor by taking network topology as the supervised signals. Both augmentations and embeddings are learned end-to-end in the proposed NCLA. Extensive experiments on the benchmark datasets demonstrate that NCLA yields the state-of-the-art node classification performance on self-supervised GCL and even exceeds the supervised ones, when the labels are extremely limited. Our code is released at https://github.com/shenxiaocam/NCLA.

MOTIVATION: A molecular interaction network can be viewed as a network in which genes with related functions are connected. Therefore, at a systems level, connections between individual genes in a molecular interaction network can be used to infer the collective functional linkages between biologically meaningful gene sets. RESULTS: We present the human interactome resource and the gene set linkage analysis (GSLA) tool for the functional interpretation of biologically meaningful gene sets observed in experiments. GSLA determines whether an observed gene set has significant functional linkages to established biological processes. When an observed gene set is not enriched by known biological processes, traditional enrichment-based interpretation methods cannot produce functional insights, but GSLA can still evaluate whether those genes work in concert to regulate specific biological processes, thereby suggesting the functional implications of the observed gene set. The quality of human interactome resource and the utility of GSLA are illustrated with multiple assessments. AVAILABILITY: http://www.cls.zju.edu.cn/hir/