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Kun Fu

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6 papers

2 author rows

NeurIPS Conference 2025 Conference Paper

A Closer Look at Graph Transformers: Cross-Aggregation and Beyond

Jiaming Zhuo
Ziyi Ma
Yintong Lu
Yuwei Liu
Kun Fu
Di Jin
Chuan Wang
Wu Wenning

Graph Transformers (GTs), which effectively capture long-range dependencies and structural biases simultaneously, have recently emerged as promising alternatives to traditional Graph Neural Networks (GNNs). Advanced approaches for GTs to leverage topology information involve integrating GNN modules or modulating node attributes using positional encodings. Unfortunately, the underlying mechanism driving their effectiveness remains insufficiently understood. In this paper, we revisit these strategies and uncover a shared underlying mechanism—Cross Aggregation—that effectively captures the interaction between graph topology and node attributes. Building on this insight, we propose the Universal Graph Cross-attention Transformer (UGCFormer), a universal GT framework with linear computational complexity. The idea is to interactively learn the representations of graph topology and node attributes through a linearized Dual Cross-attention (DCA) module. In theory, this module can adaptively capture interactions between these two types of graph information, thereby achieving effective aggregation. To alleviate overfitting arising from the dual-channel design, we introduce a consistency constraint that enforces representational alignment. Extensive evaluations on multiple benchmark datasets demonstrate the effectiveness and efficiency of UGCFormer.

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ICLR Conference 2025 Conference Paper

DUALFormer: Dual Graph Transformer

Jiaming Zhuo
Yuwei Liu
Yintong Lu
Ziyi Ma
Kun Fu
Chuan Wang 0002
Yuanfang Guo
Zhen Wang 0004

Graph Transformers (GTs), adept at capturing the locality and globality of graphs, have shown promising potential in node classification tasks. Most state-of-the-art GTs succeed through integrating local Graph Neural Networks (GNNs) with their global Self-Attention (SA) modules to enhance structural awareness. Nonetheless, this architecture faces limitations arising from scalability challenges and the trade-off between capturing local and global information. On the one hand, the quadratic complexity associated with the SA modules poses a significant challenge for many GTs, particularly when scaling them to large-scale graphs. Numerous GTs necessitated a compromise, relinquishing certain aspects of their expressivity to garner computational efficiency. On the other hand, GTs face challenges in maintaining detailed local structural information while capturing long-range dependencies. As a result, they typically require significant computational costs to balance the local and global expressivity. To address these limitations, this paper introduces a novel GT architecture, dubbed DUALFormer, featuring a dual-dimensional design of its GNN and SA modules. Leveraging approximation theory from Linearized Transformers and treating the query as the surrogate representation of node features, DUALFormer \emph{efficiently} performs the computationally intensive global SA module on feature dimensions. Furthermore, by such a separation of local and global modules into dual dimensions, DUALFormer achieves a natural balance between local and global expressivity. In theory, DUALFormer can reduce intra-class variance, thereby enhancing the discriminability of node representations. Extensive experiments on eleven real-world datasets demonstrate its effectiveness and efficiency over existing state-of-the-art GTs.

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AAAI Conference 2025 Conference Paper

ProtCLIP: Function-Informed Protein Multi-Modal Learning

Hanjing Zhou
Mingze Yin
Wei Wu
Mingyang Li
Kun Fu
Jintai Chen
Jian Wu
Zheng Wang

Multi-modality pre-training paradigm that aligns protein sequences and biological descriptions has learned general protein representations and achieved promising performance in various downstream applications. However, these works were still unable to replicate the extraordinary success of language-supervised visual foundation models due to the ineffective usage of aligned protein-text paired data and the lack of an effective function-informed pre-training paradigm. To address these issues, this paper curates a large-scale protein-text paired dataset called ProtAnno with a property-driven sampling strategy, and introduces a novel function-informed protein pre-training paradigm. Specifically, the sampling strategy determines selecting probability based on the sample confidence and property coverage, balancing the data quality and data quantity in face of large-scale noisy data. Furthermore, motivated by significance of the protein specific functional mechanism, the proposed paradigm explicitly model protein static and dynamic functional segments by two segment-wise pre-training objectives, injecting fine-grained information in a function-informed manner. Leveraging all these innovations, we develop ProtCLIP, a multi-modality foundation model that comprehensively represents function-aware protein embeddings. On 22 different protein benchmarks within 5 types, including protein functionality classification, mutation effect prediction, cross-modal transformation, semantic similarity inference and protein-protein interaction prediction, our ProtCLIP consistently achieves SOTA performance, with remarkable improvements of 75% on average in five cross-modal transformation benchmarks, 59.9% in GO-CC and 39.7% in GO-BP protein function prediction. The experimental results verify the extraordinary potential of ProtCLIP serving as the protein multi-modality foundation model.

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AAAI Conference 2025 Conference Paper

Synergy of GFlowNet and Protein Language Model Makes a Diverse Antibody Designer

Mingze Yin
Hanjing Zhou
Yiheng Zhu
Jialu Wu
Wei Wu
Mingyang Li
Kun Fu
Zheng Wang

Antibodies defend our health by binding to antigens with high specificity and potentiality, primarily relying on the Complementarity-Determining Region (CDR). Yet, current experimental methods of discovering new antibody CDRs are heavily time-consuming. Computational design could alleviate this burden; especially, protein language models have proven quite beneficial in many recent studies. However, most existing models solely focus on antibody potentiality and struggle to encapsulate the diverse range of plausible CDR candidates, limiting their effectiveness in real-world scenarios as binding is only one factor in the multitude of drug-forming criteria. In this paper, we introduce PG-AbD, a framework uniting Generative Flow Networks (GFlowNets) and pretrained Protein Language Models (PLMs) to successfully generate highly potent, diverse and novel antibody candidates. We innovatively construct a Products of Experts (PoE) composed by the global-distribution-modeling PLM and the local-distribution-modeling Potts Model to serve as the reward function of GFlowNet. The joint training paradigm is introduced, where PoE is trained by contrastive divergence with the negative samples generated by GFlowNet, and then guides GFlowNet to sample diverse antibody candidates. We evaluate PG-AbD on extensive antibody design benchmarks. It significantly outperforms existing methods in diversity (13.5% on RabDab, 31.1% on SabDab) while maintaining optimal potential and novelty. Generated antibodies are also found to form stable, regular 3D structures with their corresponding antigens, demonstrating the great potential of PG-AbD to accelerate real-world antibody discovery.

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NeurIPS Conference 2024 Conference Paper

Unified Graph Augmentations for Generalized Contrastive Learning on Graphs

Jiaming Zhuo
Yintong Lu
Hui Ning
Kun Fu
Bingxin Niu
Dongxiao He
Chuan Wang
Yuanfang Guo

In real-world scenarios, networks (graphs) and their tasks possess unique characteristics, requiring the development of a versatile graph augmentation (GA) to meet the varied demands of network analysis. Unfortunately, most Graph Contrastive Learning (GCL) frameworks are hampered by the specificity, complexity, and incompleteness of their GA techniques. Firstly, GAs designed for specific scenarios may compromise the universality of models if mishandled. Secondly, the process of identifying and generating optimal augmentations generally involves substantial computational overhead. Thirdly, the effectiveness of the GCL, even the learnable ones, is constrained by the finite selection of GAs available. To overcome the above limitations, this paper introduces a novel unified GA module dubbed UGA after reinterpreting the mechanism of GAs in GCLs from a message-passing perspective. Theoretically, this module is capable of unifying any explicit GAs, including node, edge, attribute, and subgraph augmentations. Based on the proposed UGA, a novel generalized GCL framework dubbed Graph cOntrastive UnifieD Augmentations (GOUDA) is proposed. It seamlessly integrates widely adopted contrastive losses and an introduced independence loss to fulfill the common requirements of consistency and diversity of augmentation across diverse scenarios. Evaluations across various datasets and tasks demonstrate the generality and efficiency of the proposed GOUDA over existing state-of-the-art GCLs.

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AAAI Conference 2023 Conference Paper

Breaking Immutable: Information-Coupled Prototype Elaboration for Few-Shot Object Detection

Xiaonan Lu
Wenhui Diao
Yongqiang Mao
Junxi Li
Peijin Wang
Xian Sun
Kun Fu

Few-shot object detection, expecting detectors to detect novel classes with a few instances, has made conspicuous progress. However, the prototypes extracted by existing meta-learning based methods still suffer from insufficient representative information and lack awareness of query images, which cannot be adaptively tailored to different query images. Firstly, only the support images are involved for extracting prototypes, resulting in scarce perceptual information of query images. Secondly, all pixels of all support images are treated equally when aggregating features into prototype vectors, thus the salient objects are overwhelmed by the cluttered background. In this paper, we propose an Information-Coupled Prototype Elaboration (ICPE) method to generate specific and representative prototypes for each query image. Concretely, a conditional information coupling module is introduced to couple information from the query branch to the support branch, strengthening the query-perceptual information in support features. Besides, we design a prototype dynamic aggregation module that dynamically adjusts intra-image and inter-image aggregation weights to highlight the salient information useful for detecting query images. Experimental results on both Pascal VOC and MS COCO demonstrate that our method achieves state-of-the-art performance in almost all settings. Code will be available at: https://github.com/lxn96/ICPE.

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