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Huimin Cheng

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5 papers

2 author rows

AAAI Conference 2026 Conference Paper

DCMM-Transformer: Degree-Corrected Mixed-Membership Attention for Medical Imaging

Huimin Cheng
Xiaowei Yu
Shushan Wu
Luyang Fang
Chao Cao
Jing Zhang
Tianming Liu
Dajiang Zhu

Medical images exhibit latent anatomical groupings, such as organs, tissues, and pathological regions, that standard Vision Transformers (ViTs) fail to exploit. While recent work like SBM-Transformer attempts to incorporate such structures through stochastic binary masking, they suffer from non-differentiability, training instability, and the inability to model complex community structure. We present DCMM-Transformer, a novel ViT architecture for medical image analysis that incorporates a Degree-Corrected Mixed-Membership (DCMM) model as an additive bias in self-attention. Unlike prior approaches that rely on multiplicative masking and binary sampling, our method introduces community structure and degree heterogeneity in a fully differentiable and interpretable manner. Comprehensive experiments across diverse medical imaging datasets, including brain, chest, breast, and ocular modalities, demonstrate the superior performance and generalizability of the proposed approach. Furthermore, the learned group structure and structured attention modulation substantially enhance interpretability by yielding attention maps that are anatomically meaningful and semantically coherent.

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NeurIPS Conference 2025 Conference Paper

JADE: Joint Alignment and Deep Embedding for Multi-Slice Spatial Transcriptomics

Yuanchuan Guo
Jun Liu
Huimin Cheng
Ying Ma

As spatial transcriptomics (ST) datasets increasingly span multiple adjacent or replicated slices, effective joint analysis across slices is needed to reconstruct tissue structures and identify consistent spatial gene expression patterns. This requires resolving spatial correspondences between slices while capturing shared transcriptomic features, two tasks that are typically addressed in isolation. Multi-slice analysis remains challenging due to physical distortions, technical variability, and batch effects. To address these challenges, we introduce Joint Alignment and Deep Embedding for multi-slice ST (JADE), a unified computational framework that simultaneously learns spot-wise alignments and shared low-dimensional embeddings across tissue slices. Unlike existing methods, JADE adopts a roundtrip framework in which each iteration alternates between alignment and embedding refinement. To infer alignment, we employ attention mechanisms that dynamically assess and weight the importance of different embedding dimensions, allowing the model to focus on the most alignment-relevant features while suppressing noise. To the best of our knowledge, JADE is the first method that jointly optimizes alignment and representation learning in a shared latent space, enabling robust multi-slice integration. We demonstrate that JADE outperforms existing alignment and embedding methods across multiple evaluation metrics in the 10x Visium human dorsolateral prefrontal cortex (DLPFC) and Stereo-seq axolotl brain datasets. By bridging spatial alignment and feature integration, JADE provides a scalable and accurate solution for cross-slice analysis of ST data.

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NeurIPS Conference 2025 Conference Paper

Transfer Learning on Edge Connecting Probability Estimation Under Graphon Model

Yuyao Wang
Yu-Hung Cheng
Debarghya Mukherjee
Huimin Cheng

Graphon models provide a flexible nonparametric framework for estimating latent connectivity probabilities in networks, enabling a range of downstream applications such as link prediction and data augmentation. However, accurate graphon estimation typically requires a large graph, whereas in practice, one often only observes a small-sized network. One approach to addressing this issue is to adopt a transfer learning framework, which aims to improve estimation in a small target graph by leveraging structural information from a larger, related source graph. In this paper, we propose a novel method, namely GTRANS, a transfer learning framework that integrates neighborhood smoothing and Gromov-Wasserstein optimal transport to align and transfer structural patterns between graphs. To prevent negative transfer, GTRANS includes an adaptive debiasing mechanism that identifies and corrects for target-specific deviations via residual smoothing. We provide theoretical guarantees on the stability of the estimated alignment matrix and demonstrate the effectiveness of GTRANS in improving the accuracy of target graph estimation through extensive synthetic and real data experiments. These improvements translate directly to enhanced performance in downstream applications, such as the graph classification task and the link prediction task.

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ICML Conference 2024 Conference Paper

Network Tight Community Detection

Jiayi Deng
Xiaodong Yang
Jun Yu
Jun Liu
Zhaiming Shen
Danyang Huang
Huimin Cheng

Conventional community detection methods often categorize all nodes into clusters. However, the presumed community structure of interest may only be valid for a subset of nodes (named as ‘tight nodes’), while the rest of the network may consist of noninformative “scattered nodes”. For example, a protein-protein network often contains proteins that do not belong to specific biological functional modules but are involved in more general processes, or act as bridges between different functional modules. Forcing each of these proteins into a single cluster introduces unwanted biases and obscures the underlying biological implication. To address this issue, we propose a tight community detection (TCD) method to identify tight communities excluding scattered nodes. The algorithm enjoys a strong theoretical guarantee of tight node identification accuracy and is scalable for large networks. The superiority of the proposed method is demonstrated by various synthetic and real experiments.

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ICLR Conference 2023 Conference Paper

Subsampling in Large Graphs Using Ricci Curvature

Shushan Wu
Huimin Cheng
Jiazhang Cai
Ping Ma 0001
Wenxuan Zhong

In the past decades, many large graphs with millions of nodes have been collected/constructed. The high computational cost and significant visualization difficulty hinder the analysis of large graphs. To overcome the difficulties, researchers have developed many graph subsampling approaches to provide a rough sketch that preserves global properties. By selecting representative nodes, these graph subsampling methods can help researchers estimate the graph statistics, e.g., the number of communities, of the large graph from the subsample. However, the available subsampling methods, e.g., degree node sampler and random walk sampler, tend to leave out minority communities because nodes with high degrees are more likely to be sampled. To overcome the shortcomings of the existing methods, we are motivated to apply the community information hidden in the graph to the subsampling method. Though the community structure is unavailable, community structure information can be obtained by applying geometric methods to a graph. An analog of Ricci curvature in the manifold is defined for the graph, i.e., Ollivier Ricci curvature. Based on the asymptotic results about the within-community edge and between-community edge's OR curvature, we propose a subsampling algorithm based on our theoretical results, the Ollivier-Ricci curvature Gradient-based subsampling (ORG-sub) algorithm. The proposed ORG-sub algorithm has two main contributions: First, ORG-sub provides a rigorous theoretical guarantee that the probability of ORG-sub taking all communities into the final subgraph converges to one. Second, extensive experiments on synthetic and benchmark datasets demonstrate the advantages of our algorithm.

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