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Zonghan Wu

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4 papers

1 author row

AAAI Conference 2026 Conference Paper

PanFoMa: A Lightweight Foundation Model and Benchmark for Pan-Cancer

Xiaoshui Huang
Tianlin Zhu
Yifan Zuo
Xue Xia
Zonghan Wu
Jiebin Yan
Dingli Hua
Zongyi Xu

Single-cell RNA sequencing (scRNA-seq) is essential for decoding tumor heterogeneity. However, pan-cancer research still faces two key challenges: learning discriminative and efficient single-cell representations, and establishing a comprehensive evaluation benchmark. In this paper, we introduce \algoname, a lightweight hybrid neural network that combines the strengths of Transformers and state-space models to achieve a balance between performance and efficiency. \algoname consists of a front-end local-context encoder with shared self-attention layers to capture complex, order-independent gene interactions; and a back-end global sequential feature decoder that efficiently integrates global context using a linear-time state-space model. This modular design preserves the expressive power of Transformers while leveraging the scalability of Mamba to enable transcriptome modeling, effectively capturing both local and global regulatory signals. To enable robust evaluation, we also construct a large-scale pan-cancer single-cell benchmark, \algoname Bench, containing over 3.5 million high-quality cells across 33 cancer subtypes, curated through a rigorous preprocessing pipeline. Experimental results show that \algoname outperforms state-of-the-art models on our pan-cancer benchmark (+4.0\%) and across multiple public tasks, including cell type annotation (+7.4\%), batch integration (+4.0\%) and multi-omics integration (+3.1\%).

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NeurIPS Conference 2025 Conference Paper

FedFree: Breaking Knowledge-sharing Barriers through Layer-wise Alignment in Heterogeneous Federated Learning

Haizhou Du
Yiran Xiang
Yiwen Cai
Xiufeng Liu
Zonghan Wu
Huan Huo
Guodong Long

Heterogeneous Federated Learning (HtFL) enables collaborative learning across clients with diverse model architectures and non-IID data distributions, which are prevalent in real-world edge computing applications. Existing HtFL approaches typically employ proxy datasets to facilitate knowledge sharing or implement coarse-grained model-level knowledge transfer. However, such approaches not only elevate risks of user privacy leakage but also lead to the loss of fine-grained model-specific knowledge, ultimately creating barriers to effective knowledge sharing. To address these challenges, we propose FedFree, a novel data-free and model-free HtFL framework featuring two key innovations. First, FedFree introduces a reverse layer-wise knowledge transfer mechanism that aggregates heterogeneous client models into a global model solely using Gaussian-based pseudo data, eliminating reliance on proxy datasets. Second, it leverages Knowledge Gain Entropy (KGE) to guide targeted layer-wise knowledge alignment, ensuring that each client receives the most relevant global updates tailored to its specific architecture. We provide rigorous theoretical convergence guarantees for FedFree and conduct extensive experiments on CIFAR-10 and CIFAR-100. Results demonstrate that FedFree achieves substantial performance gains, with relative accuracy improving up to 46. 3% over state-of-the-art baselines. The framework consistently excels under highly heterogeneous model/data distributions and in large scale settings.

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IJCAI Conference 2022 Conference Paper

Personalized Federated Learning With a Graph

Fengwen Chen
Guodong Long
Zonghan Wu
Tianyi Zhou
Jing Jiang

Knowledge sharing and model personalization are two key components in the conceptual framework of personalized federated learning (PFL). Existing PFL methods focus on proposing new model personalization mechanisms while simply implementing knowledge sharing by aggregating models from all clients, regardless of their relation graph. This paper aims to enhance the knowledge-sharing process in PFL by leveraging the graph-based structural information among clients. We propose a novel structured federated learning (SFL) framework to learn both the global and personalized models simultaneously using client-wise relation graphs and clients' private data. We cast SFL with graph into a novel optimization problem that can model the client-wise complex relations and graph-based structural topology by a unified framework. Moreover, in addition to using an existing relation graph, SFL could be expanded to learn the hidden relations among clients. Experiments on traffic and image benchmark datasets can demonstrate the effectiveness of the proposed method.

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IJCAI Conference 2019 Conference Paper

Graph WaveNet for Deep Spatial-Temporal Graph Modeling

Zonghan Wu
Shirui Pan
Guodong Long
Jing Jiang
Chengqi Zhang

Spatial-temporal graph modeling is an important task to analyze the spatial relations and temporal trends of components in a system. Existing approaches mostly capture the spatial dependency on a fixed graph structure, assuming that the underlying relation between entities is pre-determined. However, the explicit graph structure (relation) does not necessarily reflect the true dependency and genuine relation may be missing due to the incomplete connections in the data. Furthermore, existing methods are ineffective to capture the temporal trends as the RNNs or CNNs employed in these methods cannot capture long-range temporal sequences. To overcome these limitations, we propose in this paper a novel graph neural network architecture, {Graph WaveNet}, for spatial-temporal graph modeling. By developing a novel adaptive dependency matrix and learn it through node embedding, our model can precisely capture the hidden spatial dependency in the data. With a stacked dilated 1D convolution component whose receptive field grows exponentially as the number of layers increases, Graph WaveNet is able to handle very long sequences. These two components are integrated seamlessly in a unified framework and the whole framework is learned in an end-to-end manner. Experimental results on two public traffic network datasets, METR-LA and PEMS-BAY, demonstrate the superior performance of our algorithm.

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