Yonghuang Wu

Minghui Zhang, Yangqian Wu, Hanxiao Zhang et al. · harvard

Open international challenges are becoming the de facto standard for assessing computer vision and image analysis algorithms. In recent years, new methods have extended the reach of pulmonary airway segmentation that is closer to the limit of image resolution. Since EXACT'09 pulmonary airway segmentation, limited effort has been directed to quantitative comparison of newly emerged algorithms driven by the maturity of deep learning based approaches and clinical drive for resolving finer details of distal airways for early intervention of pulmonary diseases. Thus far, public annotated datasets are extremely limited, hindering the development of data-driven methods and detailed performance evaluation of new algorithms. To provide a benchmark for the medical imaging community, we organized the Multi-site, Multi-domain Airway Tree Modeling (ATM'22), which was held as an official challenge event during the MICCAI 2022 conference. ATM'22 provides large-scale CT scans with detailed pulmonary airway annotation, including 500 CT scans (300 for training, 50 for validation, and 150 for testing). The dataset was collected from different sites and it further included a portion of noisy COVID-19 CTs with ground-glass opacity and consolidation. Twenty-three teams participated in the entire phase of the challenge and the algorithms for the top ten teams are reviewed in this paper. Quantitative and qualitative results revealed that deep learning models embedded with the topological continuity enhancement achieved superior performance in general. ATM'22 challenge holds as an open-call design, the training data and the gold standard evaluation are available upon successful registration via its homepage.

Pengfei Song, Fangjin Liu, Wenwen Zeng et al.

Contemporary glioma diagnosis integrates molecular features with histopathology to guide clinical decision-making. However, in clinical settings, divergent imaging protocols result in incomplete MRI sequences, leading to two primary challenges: forcing existing frameworks to discard a large portion of clinical data during training and consequently limiting their clinical applicability. To address these limitations, we propose GMENet, a Generative Mixture of Experts Network for multi-center glioma diagnosis with incomplete imaging sequences. Firstly, we design a Cross-attention-based Gated Generation Module that synthesizes missing sequence features from available sequences via cross-attention and dynamic gating mechanisms, incorporating a cycle-consistency loss to preserve semantic integrity. Secondly, we introduce a Dynamically Weighted Experts Fusion Module that performs mixture-of-experts interaction and confidence-aware fusion over original and synthesized dual-sequence features for multi-task prediction. We evaluate GMENet on a multi-center cohort of 1,241 subjects from four in-house datasets and two public repositories. Experiments show that GMENet expands clinically usable training data by 97\%, relative to complete-sequence-only data. Furthermore, it consistently outperforms state-of-the-art methods trained on complete data, demonstrating improved robustness under cross-center distribution shifts.

Yonghuang Wu, Zhenyang Liang, Wenwen Zeng et al.

Foundation models such as Segment Anything Model 3 (SAM3) enable flexible text-guided medical image segmentation, yet their predictions remain highly sensitive to prompt formulation. Even semantically equivalent descriptions can yield inconsistent masks, limiting reliability in clinical and pathology workflows. We reformulate prompt sensitivity as a group-wise consistency problem. Semantically related prompts are organized into \emph{prompt groups} sharing the same ground-truth mask, and a prompt group-aware training framework is introduced for robust text-guided nuclei segmentation. The approach combines (i) a quality-guided group regularization that leverages segmentation loss as an implicit ranking signal, and (ii) a logit-level consistency constraint with a stop-gradient strategy to align predictions within each group. The method requires no architectural modification and leaves inference unchanged. Extensive experiments on multi-dataset nuclei benchmarks show consistent gains under textual prompting and markedly reduced performance variance across prompt quality levels. On six zero-shot cross-dataset tasks, our method improves Dice by an average of 2.16 points. These results demonstrate improved robustness and generalization for vision-language segmentation in computational pathology.

Dongqing Xie, Yonghuang Wu

Whole-slide image (WSI) analysis is challenging due to the gigapixel scale of slides and their inherent hierarchical multi-resolution structure. Existing multiple instance learning (MIL) approaches often model WSIs as unordered collections of patches, which limits their ability to capture structured dependencies between global tissue organization and local cellular patterns. Although recent State Space Models (SSMs) enable efficient modeling of long sequences, how to structure WSI tokens to fully exploit their spatial hierarchy remains an open problem.We propose MoEMambaMIL, a structure-aware SSM framework for WSI analysis that integrates region-nested selective scanning with mixture-of-experts (MoE) modeling. Leveraging multi-resolution preprocessing, MoEMambaMIL organizes patch tokens into region-aware sequences that preserve spatial containment across resolutions. On top of this structured sequence, we decouple resolution-aware encoding and region-adaptive contextual modeling via a combination of static, resolution-specific experts and dynamic sparse experts with learned routing. This design enables efficient long-sequence modeling while promoting expert specialization across heterogeneous diagnostic patterns. Experiments demonstrate that MoEMambaMIL achieves the best performance across 9 downstream tasks.

Dongqing Xie, Yonghuang Wu, Zisheng Ai et al.

The accurate segmentation of brain tumors from multi-modal MRI is critical for clinical diagnosis and treatment planning. While integrating complementary information from various MRI sequences is a common practice, the frequent absence of one or more modalities in real-world clinical settings poses a significant challenge, severely compromising the performance and generalizability of deep learning-based segmentation models. To address this challenge, we propose a novel Cross-Modal Compositional Self-Distillation (CCSD) framework that can flexibly handle arbitrary combinations of input modalities. CCSD adopts a shared-specific encoder-decoder architecture and incorporates two self-distillation strategies: (i) a hierarchical modality self-distillation mechanism that transfers knowledge across modality hierarchies to reduce semantic discrepancies, and (ii) a progressive modality combination distillation approach that enhances robustness to missing modalities by simulating gradual modality dropout during training. Extensive experiments on public brain tumor segmentation benchmarks demonstrate that CCSD achieves state-of-the-art performance across various missing-modality scenarios, with strong generalization and stability.

Yiyang Li, Yonghuang Wu, Ying Luo et al.

Evaluations of large language models (LLMs) suffer from instability, where small changes of random factors such as few-shot examples can lead to drastic fluctuations of scores and even model rankings. Moreover, different LLMs can have different preferences for a certain setting of random factors. As a result, using a fixed setting of random factors, which is often adopted as the paradigm of current evaluations, can lead to potential unfair comparisons between LLMs. To mitigate the volatility of evaluations, we first theoretically analyze the sources of variance induced by changes in random factors. Targeting these specific sources, we then propose the instance-level randomization (ILR) method to reduce variance and enhance fairness in model comparisons. Instead of using a fixed setting across the whole benchmark in a single experiment, we randomize all factors that affect evaluation scores for every single instance, run multiple experiments and report the averaged score. Theoretical analyses and empirical results demonstrate that ILR can reduce the variance and unfair comparisons caused by random factors, as well as achieve similar robustness level with less than half computational cost compared with previous methods.

Wenwen Zeng, Yonghuang Wu, Yifan Chen et al.

Reconstructing dynamic videos from fMRI is important for understanding visual cognition and enabling vivid brain-computer interfaces. However, current methods are critically limited to single-shot clips, failing to address the multi-shot nature of real-world experiences. Multi-shot reconstruction faces fundamental challenges: fMRI signal mixing across shots, the temporal resolution mismatch between fMRI and video obscuring rapid scene changes, and the lack of dedicated multi-shot fMRI-video datasets. To overcome these limitations, we propose a novel divide-and-decode framework for multi-shot fMRI video reconstruction. Our core innovations are: (1) A shot boundary predictor module explicitly decomposing mixed fMRI signals into shot-specific segments. (2) Generative keyframe captioning using LLMs, which decodes robust textual descriptions from each segment, overcoming temporal blur by leveraging high-level semantics. (3) Novel large-scale data synthesis (20k samples) from existing datasets. Experimental results demonstrate our framework outperforms state-of-the-art methods in multi-shot reconstruction fidelity. Ablation studies confirm the critical role of fMRI decomposition and semantic captioning, with decomposition significantly improving decoded caption CLIP similarity by 71.8%. This work establishes a new paradigm for multi-shot fMRI reconstruction, enabling accurate recovery of complex visual narratives through explicit decomposition and semantic prompting.

Yonghuang Wu, Wenwen Zeng, Xuan Xie et al.

Foundation models like Segment Anything Model (SAM) excel in promptable segmentation but suffer from an intent gap: they segment only explicitly prompted objects, failing to generalize to semantically related instances implicitly desired by users. This limitation is critical in domains with dense homogeneous objects (e.g., biomedical nuclei segmentation), where sparse visual prompts typically yield incomplete results, rendering dense annotations impractical due to prohibitive cost. To bridge this gap, we introduce SAMPO (Segment Anything Model with Preference Optimization), a novel framework that teaches visual foundation models to infer high-level categorical intent from sparse visual interactions. Unlike conventional pixel-level fine-tuning, SAMPO optimizes models to implicitly capture target-class characteristics through preference optimization. This approach, which operates without dependency on language models, enables robust multi-object segmentation even under sparse prompting and demonstrates superior data efficiency during fine-tuning. Validated on three medical segmentation tasks, SAMPO achieves state-of-the-art performance: on challenging tasks like PanNuke-T2, our method, when fine-tuned with only 10% of the training data, significantly outperforms all existing methods trained on the full 100% dataset, achieving an improvement of over 9 percentage points compared to the best baseline. Our work establishes a new paradigm for intent-aware alignment in visual foundation models, removing dependencies on auxiliary prompt generators or language-model-assisted preference learning.

Yonghuang Wu, Xuan Xie, Xinyuan Niu et al.

Pathology computing has dramatically improved pathologists' workflow and diagnostic decision-making processes. Although computer-aided diagnostic systems have shown considerable value in whole slide image (WSI) analysis, the problem of multi-classification under sample imbalance remains an intractable challenge. To address this, we propose learning fine-grained information by generating sub-bags with feature distributions similar to the original WSIs. Additionally, we utilize a pseudo-bag generation algorithm to further leverage the abundant and redundant information in WSIs, allowing efficient training in unbalanced-sample multi-classification tasks. Furthermore, we introduce an affinity-based sample selection and curriculum contrastive learning strategy to enhance the stability of model representation learning. Unlike previous approaches, our framework transitions from learning bag-level representations to understanding and exploiting the feature distribution of multi-instance bags. Our method demonstrates significant performance improvements on three datasets, including tumor classification and lymph node metastasis. On average, it achieves a 4.39-point improvement in F1 score compared to the second-best method across the three tasks, underscoring its superior performance.