Zhewei Wei

Link prediction for directed graphs is a crucial task with diverse real-world applications. Recent advances in embedding methods and Graph Neural Networks (GNNs) have shown promising improvements. However, these methods often lack a thorough analysis of their expressiveness and suffer from the lack of effective benchmarks for fair evaluation. In this paper, we propose a unified framework to assess the expressiveness of existing methods, highlighting the impact of dual embeddings and decoder design on directed link prediction performance. To address limitations in current benchmark setups, we introduce DirLinkBench, a robust new benchmark with comprehensive coverage, standardized evaluation, and modular extensibility. The results on DirLinkBench show that current methods struggle to achieve strong performance, while DiGAE outperforms other baselines overall. We further revisit DiGAE theoretically, showing its graph convolution aligns with GCN on an undirected bipartite graph. Inspired by these insights, we propose a novel Spectral Directed Graph Auto-Encoder SDGAE that achieves state-of-the-art average performance on DirLinkBench. Finally, we analyze key factors influencing directed link prediction and highlight open challenges in this field. Our code is available at https://github.com/ivam-he/DirLinkBench-SDGAE.

Adaptive graph learning has become a widely adopted paradigm for multivariate time series forecasting when explicit physical topology is unavailable. In these approaches, node embeddings are typically used to construct dense adjacency matrices based on pairwise similarity, implicitly coupling representation learning with relational modeling. However, we observe that under identical training settings but different random initializations, the learned adjacency matrices can vary substantially while predictive performance remains nearly unchanged, indicating that the relational structure is often underdetermined by the forecasting objective. This observation suggests a mismatch between similarity-based structural learning and the forecasting objective. In this work, we revisit node embeddings from a sequence approximation perspective and propose a Diagonal Adaptive Graph (DiAG) module that restricts adaptive learning to diagonal elements. The diagonal coefficients are derived from channel-independent predictions, while off-diagonal interactions are constructed from the similarity of input sequences. This design decouples representation learning from relational modeling, allowing variables to adaptively switch between channel-independent and channel-dependent regimes. Experiments on multiple datasets show that DiAG improves forecasting performance without modifying the channel-independent backbones. These results indicate that channel-dependent forecasting can be achieved as a prediction-driven refinement over channel-independent backbones, without requiring fully learned dense relational structures.

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 flow-matching framework that leverages optimal transport to design 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 paratoep-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.

Many real-world matrix datasets arrive as high-throughput vector streams, making it impractical to store or process them in their entirety. To enable real-time analytics under limited computational, memory, and communication resources, matrix sketching techniques have been developed over recent decades to provide compact approximations of such streaming data. Some algorithms have achieved optimal space and communication complexity. However, these approaches often require frequent time-consuming matrix factorization operations. In particular, under tight approximation error bounds, each matrix factorization computation incurs cubic time complexity, thereby limiting their update efficiency. In this paper, we introduce AeroSketch, a novel matrix sketching framework that leverages recent advances in randomized numerical linear algebra (RandNLA). AeroSketch achieves optimal communication and space costs while delivering near-optimal update time complexity (within logarithmic factors) across persistent, sliding window, and distributed streaming scenarios. Extensive experiments on both synthetic and real-world datasets demonstrate that AeroSketch consistently outperforms state-of-the-art methods in update throughput. In particular, under tight approximation error constraints, AeroSketch reduces the cubic time complexity to the quadratic level. Meanwhile, it maintains comparable approximation quality while retaining optimal communication and space costs.

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 flow-matching framework that leverages optimal transport to design 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 paratoep-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.