Antigen-antibody binding is a critical process in the immune response. Although recent progress has advanced antibody design, current methods lack a generative framework for end-to-end modeling of full-atom antibody structures and struggle to fully exploit antigen-specific geometric information for optimizing local binding interfaces and global structures. To overcome these limitations, we introduce AbFlow, a paratope-restricted one-step flow-matching framework for designing full-atom antibodies end-to-end. AbFlow incorporates an extended velocity field network featuring an equivariant Surface Multi-channel Encoder, which uses surface-level antigen interaction data to refine the antibody structure, particularly the CDR-H3 region. Extensive experiments in paratope-centric antibody design, multi-CDRs and full-atom antibody design, binding affinity optimization, and complex structure prediction show that AbFlow produces superior antigen-antibody complexes, especially at the contact interface, and markedly improves the binding affinity of generated antibodies.

Collaborative filtering (CF) models have demonstrated remarkable performance in recommender systems, which represent users and items as embedding vectors. Recently, due to the powerful modeling capability of graph neural networks for user-item interaction graphs, graph-based CF models have gained increasing attention. They encode each user/item and its subgraph into a single super vector by combining graph embeddings after each graph convolution. However, each hop of the neighbor in the user-item subgraphs carries a specific semantic meaning. Encoding all subgraph information into single vectors and inferring user-item relations with dot products can weaken the semantic information between user and item subgraphs, thus leaving untapped potential. Exploiting this untapped potential provides insight into improving performance for existing recommendation models. To this end, we propose the Graph Cross-correlated Network for Recommendation (GCR), which serves as a general recommendation paradigm that explicitly considers correlations between user/item subgraphs. GCR first introduces the Plain Graph Representation (PGR) to extract information directly from each hop of neighbors into corresponding PGR vectors. Then, GCR develops Cross-Correlated Aggregation (CCA) to construct possible cross-correlated terms between PGR vectors of user/item subgraphs. Finally, GCR comprehensively incorporates the cross-correlated terms for recommendations. Experimental results show that GCR outperforms state-of-the-art models on both interaction prediction and click-through rate prediction tasks.

Predicting Click-Through Rate (CTR) in billion-scale recommender systems poses a long-standing challenge for Graph Neural Networks (GNNs) due to the overwhelming computational complexity involved in aggregating billions of neighbors. To tackle this, GNN-based CTR models usually sample hundreds of neighbors out of the billions to facilitate efficient online recommendations. However, sampling only a small portion of neighbors results in a severe sampling bias and the failure to encompass the full spectrum of user or item behavioral patterns. To address this challenge, we name the conventional user-item recommendation graph as "micro recommendation grap" and introduce a revolutionizing MAcro Recommendation Graph (MAG) for billion-scale recommendations to reduce the neighbor count from billions to hundreds in the graph structure infrastructure. Specifically, We group micro nodes (users and items) with similar behavior patterns to form macro nodes and then MAG directly describes the relation between the user/item and the hundred of macro nodes rather than the billions of micro nodes. Subsequently, we introduce tailored Macro Graph Neural Networks (MacGNN) to aggregate information on a macro level and revise the embeddings of macro nodes. MacGNN has already served Taobao's homepage feed for two months, providing recommendations for over one billion users. Extensive offline experiments on three public benchmark datasets and an industrial dataset present that MacGNN significantly outperforms twelve CTR baselines while remaining computationally efficient. Besides, online A/B tests confirm MacGNN's superiority in billion-scale recommender systems.

Molecular perception aims to construct 3D molecules from 3D atom clouds (i.e., atom types and corresponding 3D coordinates), determining bond connections, bond orders, and other molecular attributes within molecules. It is essential for realizing many applications in cheminformatics and bioinformatics, such as modeling quantum chemistry-derived molecular structures in protein-ligand complexes. Additionally, many molecular generation methods can only generate molecular 3D atom clouds, requiring molecular perception as a necessary post-processing. However, existing molecular perception methods mainly rely on predefined chemical rules and fail to leverage 3D geometric information, whose performance is sub-optimal fully. In this study, we propose MPerformer, an SE(3) Transformer-based molecular perceptron exhibiting SE(3)-invariance, to construct 3D molecules from 3D atom clouds efficiently. Besides, we propose a multi-task pretraining-and-finetuning paradigm to learn this model. In the pretraining phase, we jointly minimize an attribute prediction loss and an atom cloud reconstruction loss, mitigating the data imbalance issue of molecular attributes and enhancing the robustness and generalizability of the model. Experiments show that MPerformer significantly outperforms state-of-the-art molecular perception methods in precision and robustness, benefiting various molecular generation scenarios.

With the success of the graph embedding model in both academic and industry areas, the robustness of graph embedding against adversarial attack inevitably becomes a crucial problem in graph learning. Existing works usually perform the attack in a white-box fashion: they need to access the predictions/labels to construct their adversarial loss. However, the inaccessibility of predictions/labels makes the white-box attack impractical for a real graph learning system. This paper promotes current frameworks in a more general and flexible sense -- we consider the ability of various types of graph embedding models to remain resilient against black-box driven attacks. We investigate the theoretical connection between graph signal processing and graph embedding models, and formulate the graph embedding model as a general graph signal process with a corresponding graph filter. Therefore, we design a generalized adversarial attack framework: GF-Attack. Without accessing any labels and model predictions, GF-Attack can perform the attack directly on the graph filter in a black-box fashion. We further prove that GF-Attack can perform an effective attack without assumption on the number of layers/window-size of graph embedding models. To validate the generalization of GF-Attack, we construct GF-Attack on five popular graph embedding models. Extensive experiments validate the effectiveness of GF-Attack on several benchmark datasets.

Variants of Graph Neural Networks (GNNs) for representation learning have been proposed recently and achieved fruitful results in various fields. Among them, Graph Attention Network (GAT) first employs a self-attention strategy to learn attention weights for each edge in the spatial domain. However, learning the attentions over edges can only focus on the local information of graphs and greatly increases the computational costs. In this paper, we first introduce the attention mechanism in the spectral domain of graphs and present Spectral Graph Attention Network (SpGAT) that learns representations for different frequency components regarding weighted filters and graph wavelets bases. In this way, SpGAT can better capture global patterns of graphs in an efficient manner with much fewer learned parameters than that of GAT. Further, to reduce the computational cost of SpGAT brought by the eigen-decomposition, we propose a fast approximation variant SpGAT-Cheby. We thoroughly evaluate the performance of SpGAT and SpGAT-Cheby in semi-supervised node classification tasks and verify the effectiveness of the learned attentions in the spectral domain.

The technique of recursive neighborhood aggregation has dominated the implementation of existing successful Graph Neural Networks (GNNs). However, the recursive information propagation across layers inevitably brings in extra calculations, potentially large variance, and difficulty of parallel computation. In this paper, we propose Graph Unfolding Networks (GUNets) as an alternative mechanism of recursive neighborhood aggregation for graph representation learning. Comparing to generic GNNs, our proposed GUNets are efficient, robust and practically effective. At their core, GUNets unfold the local structure of every node, i.e. the rooted tree, to a set of trajectories, and then adopt set function to capture the topology of the rooted subtree, which is more convenient for parallel computation than the recursive neighborhood aggregation process. More importantly, through a specific design of the set function, our architecture enables efficient and robust learning on large-scale graphs without resorting to any pruning of the rooted subtree that is usually necessary in generic GNNs. Extensive experiments on five large datasets (the number of nodes ranges from 104 to 106) show that our GUNets achieve comparable or even better results than current successful GNNs while gaining significantly more efficiency and lower accuracy variance. Codes can be found at github.com/GUNets/GUNets.

Recent advances in Graph Convolutional Networks (GCNs) have led to state-of-the-art performance on various graph-related tasks. However, most existing GCN models do not explicitly identify whether all the aggregated neighbors are valuable to the learning tasks, which may harm the learning performance. In this paper, we consider the problem of node classification and propose the Label-Aware Graph Convolutional Network (LAGCN) framework which can directly identify valuable neighbors to enhance the performance of existing GCN models. Our contribution is three-fold. First, we propose a label-aware edge classifier that can filter distracting neighbors and add valuable neighbors for each node to refine the original graph into a label-aware (LA) graph. Existing GCN models can directly learn from the LA graph to improve the performance without changing their model architectures. Second, we introduce the concept of positive ratio to evaluate the density of valuable neighbors in the LA graph. Theoretical analysis reveals that using the edge classifier to increase the positive ratio can improve the learning performance of existing GCN models. Third, we conduct extensive node classification experiments on benchmark datasets. The results verify that LAGCN can improve the performance of existing GCN models considerably, in terms of node classification.

Many real data come in the form of non-grid objects, i.e. graphs, from social networks to molecules. Adaptation of deep learning from grid-alike data (e.g. images) to graphs has recently received unprecedented attention from both machine learning and data mining communities, leading to a new cross-domain field---Deep Graph Learning (DGL). Instead of painstaking feature engineering, DGL aims to learn informative representations of graphs in an end-to-end manner. It has exhibited remarkable success in various tasks, such as node/graph classification, link prediction, etc.

The richness in the content of various information networks such as social networks and communication networks provides the unprecedented potential for learning high-quality expressive representations without external supervision. This paper investigates how to preserve and extract the abundant information from graph-structured data into embedding space in an unsupervised manner. To this end, we propose a novel concept, Graphical Mutual Information (GMI), to measure the correlation between input graphs and high-level hidden representations. GMI generalizes the idea of conventional mutual information computations from vector space to the graph domain where measuring mutual information from two aspects of node features and topological structure is indispensable. GMI exhibits several benefits: First, it is invariant to the isomorphic transformation of input graphs—an inevitable constraint in many existing graph representation learning algorithms; Besides, it can be efficiently estimated and maximized by current mutual information estimation methods such as MINE; Finally, our theoretical analysis confirms its correctness and rationality. With the aid of GMI, we develop an unsupervised learning model trained by maximizing GMI between the input and output of a graph neural encoder. Considerable experiments on transductive as well as inductive node classification and link prediction demonstrate that our method outperforms state-of-the-art unsupervised counterparts, and even sometimes exceeds the performance of supervised ones.

Node classification and graph classification are two graph learning problems that predict the class label of a node and the class label of a graph respectively. A node of a graph usually represents a real-world entity, e.g., a user in a social network, or a protein in a protein-protein interaction network. In this work, we consider a more challenging but practically useful setting, in which a node itself is a graph instance. This leads to a hierarchical graph perspective which arises in many domains such as social network, biological network and document collection. For example, in a social network, a group of people with shared interests forms a user group, whereas a number of user groups are interconnected via interactions or common members. We study the node classification problem in the hierarchical graph where a “node” is a graph instance, e.g., a user group in the above example. As labels are usually limited in real-world data, we design two novel semi-supervised solutions named SEmi-supervised grAph cLassification via Cautious/Active Iteration (or SEAL-C/AI in short). SEAL-C/AI adopt an iterative framework that takes turns to build or update two classifiers, one working at the graph instance level and the other at the hierarchical graph level. To simplify the representation of the hierarchical graph, we propose a novel supervised, self-attentive graph embedding method called SAGE, which embeds graph instances of arbitrary size into fixed-length vectors. Through experiments on synthetic data and Tencent QQ group data, we demonstrate that SEAL-C/AI not only outperform competing methods by a significant margin in terms of accuracy/Macro-F1, but also generate meaningful interpretations of the learned representations.