Yunhe Gao

Difei Gu, Yunhe Gao, Mu Zhou et al.

Accurate disease interpretation from radiology remains challenging due to imaging heterogeneity. Achieving expert-level diagnostic decisions requires integration of subtle image features with clinical knowledge. Yet major vision-language models (VLMs) treat images as holistic entities and overlook fine-grained image details that are vital for disease diagnosis. Clinicians analyze images by utilizing their prior medical knowledge and identify anatomical structures as important region of interests (ROIs). Inspired from this human-centric workflow, we introduce Anatomy-VLM, a fine-grained, vision-language model that incorporates multi-scale information. First, we design a model encoder to localize key anatomical features from entire medical images. Second, these regions are enriched with structured knowledge for contextually-aware interpretation. Finally, the model encoder aligns multi-scale medical information to generate clinically-interpretable disease prediction. Anatomy-VLM achieves outstanding performance on both in- and out-of-distribution datasets. We also validate the performance of Anatomy-VLM on downstream image segmentation tasks, suggesting that its fine-grained alignment captures anatomical and pathology-related knowledge. Furthermore, the Anatomy-VLM's encoder facilitates zero-shot anatomy-wise interpretation, providing its strong expert-level clinical interpretation capabilities.

Zhuowei Li, Haizhou Shi, Yunhe Gao et al.

Large Vision-Language Models (LVLMs) can reason effectively over both textual and visual inputs, but they tend to hallucinate syntactically coherent yet visually ungrounded contents. In this paper, we investigate the internal dynamics of hallucination by examining the tokens logits ranking throughout the generation process, revealing three key patterns in how LVLMs process information: (1) gradual visual information loss - visually grounded tokens gradually become less favored throughout generation, and (2) early excitation - semantically meaningful tokens achieve peak activation in the layers earlier than the final layer. (3) hidden genuine information - visually grounded tokens though not being eventually decoded still retain relatively high rankings at inference. Based on these insights, we propose VISTA (Visual Information Steering with Token-logit Augmentation), a training-free inference-time intervention framework that reduces hallucination while promoting genuine information. VISTA works by combining two complementary approaches: reinforcing visual information in activation space and leveraging early layer activations to promote semantically meaningful decoding. Compared to existing methods, VISTA requires no external supervision and is applicable to various decoding strategies. Extensive experiments show that VISTA on average reduces hallucination by about 40% on evaluated open-ended generation task, and it consistently outperforms existing methods on four benchmarks across four architectures under three decoding strategies. Code is available at https://github.com/LzVv123456/VISTA.

Yunhe Gao, Difei Gu, Mu Zhou et al.

Although explainability is essential in the clinical diagnosis, most deep learning models still function as black boxes without elucidating their decision-making process. In this study, we investigate the explainable model development that can mimic the decision-making process of human experts by fusing the domain knowledge of explicit diagnostic criteria. We introduce a simple yet effective framework, Explicd, towards Explainable language-informed criteria-based diagnosis. Explicd initiates its process by querying domain knowledge from either large language models (LLMs) or human experts to establish diagnostic criteria across various concept axes (e.g., color, shape, texture, or specific patterns of diseases). By leveraging a pretrained vision-language model, Explicd injects these criteria into the embedding space as knowledge anchors, thereby facilitating the learning of corresponding visual concepts within medical images. The final diagnostic outcome is determined based on the similarity scores between the encoded visual concepts and the textual criteria embeddings. Through extensive evaluation of five medical image classification benchmarks, Explicd has demonstrated its inherent explainability and extends to improve classification performance compared to traditional black-box models. Code is available at \url{https://github.com/yhygao/Explicd}.

Zhiqiang Tang, Yunhe Gao, Yi Zhu et al.

Traditional normalization techniques (e.g., Batch Normalization and Instance Normalization) generally and simplistically assume that training and test data follow the same distribution. As distribution shifts are inevitable in real-world applications, well-trained models with previous normalization methods can perform badly in new environments. Can we develop new normalization methods to improve generalization robustness under distribution shifts? In this paper, we answer the question by proposing CrossNorm and SelfNorm. CrossNorm exchanges channel-wise mean and variance between feature maps to enlarge training distribution, while SelfNorm uses attention to recalibrate the statistics to bridge gaps between training and test distributions. CrossNorm and SelfNorm can complement each other, though exploring different directions in statistics usage. Extensive experiments on different fields (vision and language), tasks (classification and segmentation), settings (supervised and semi-supervised), and distribution shift types (synthetic and natural) show the effectiveness. Code is available at https://github.com/amazon-research/crossnorm-selfnorm

Zhiqiang Tang, Yunhe Gao, Leonid Karlinsky et al.

Data augmentation is one of the most important tools in training modern deep neural networks. Recently, great advances have been made in searching for optimal augmentation policies in the image classification domain. However, two key points related to data augmentation remain uncovered by the current methods. First is that most if not all modern augmentation search methods are offline and learning policies are isolated from their usage. The learned policies are mostly constant throughout the training process and are not adapted to the current training model state. Second, the policies rely on class-preserving image processing functions. Hence applying current offline methods to new tasks may require domain knowledge to specify such kind of operations. In this work, we offer an orthogonal online data augmentation scheme together with three new augmentation networks, co-trained with the target learning task. It is both more efficient, in the sense that it does not require expensive offline training when entering a new domain, and more adaptive as it adapts to the learner state. Our augmentation networks require less domain knowledge and are easily applicable to new tasks. Extensive experiments demonstrate that the proposed scheme alone performs on par with the state-of-the-art offline data augmentation methods, as well as improving upon the state-of-the-art in combination with those methods. Code is available at https://github.com/zhiqiangdon/online-augment .

Bangwei Guo, Yunhe Gao, Meng Ye et al.

Medical image segmentation is fundamental to clinical decision-making, yet existing models remain fragmented. They are usually trained on single knowledge sources and specific to individual tasks, modalities, or organs. This fragmentation contrasts sharply with clinical practice, where experts seamlessly integrate diverse knowledge: anatomical priors from training, exemplar-based reasoning from reference cases, and iterative refinement through real-time interaction. We present $\textbf{K-Prism}$, a unified segmentation framework that mirrors this clinical flexibility by systematically integrating three knowledge paradigms: (i) $\textit{semantic priors}$ learned from annotated datasets, (ii) $\textit{in-context knowledge}$ from few-shot reference examples, and (iii) $\textit{interactive feedback}$ from user inputs like clicks or scribbles. Our key insight is that these heterogeneous knowledge sources can be encoded into a dual-prompt representation: 1-D sparse prompts defining $\textit{what}$ to segment and 2-D dense prompts indicating $\textit{where}$ to attend, which are then dynamically routed through a Mixture-of-Experts (MoE) decoder. This design enables flexible switching between paradigms and joint training across diverse tasks without architectural modifications. Comprehensive experiments on 18 public datasets spanning diverse modalities (CT, MRI, X-ray, pathology, ultrasound, etc.) demonstrate that K-Prism achieves state-of-the-art performance across semantic, in-context, and interactive segmentation settings. Code will be released upon publication.

Di Liu, Long Zhao, Qilong Zhangli et al.

The task of shape abstraction with semantic part consistency is challenging due to the complex geometries of natural objects. Recent methods learn to represent an object shape using a set of simple primitives to fit the target. \textcolor{black}{However, in these methods, the primitives used do not always correspond to real parts or lack geometric flexibility for semantic interpretation.} In this paper, we investigate salient and efficient primitive descriptors for accurate shape abstractions, and propose \textit{Deep Deformable Models (DDMs)}. DDM employs global deformations and diffeomorphic local deformations. These properties enable DDM to abstract complex object shapes with significantly fewer primitives that offer broader geometry coverage and finer details. DDM is also capable of learning part-level semantic correspondences due to the differentiable and invertible properties of our primitive deformation. Moreover, DDM learning formulation is based on dynamic and kinematic modeling, which enables joint regularization of each sub-transformation during primitive fitting. Extensive experiments on \textit{ShapeNet} demonstrate that DDM outperforms the state-of-the-art in terms of reconstruction and part consistency by a notable margin.

Qi Chang, Hui Qu, Zhennan Yan et al.

Multi-modality images have been widely used and provide comprehensive information for medical image analysis. However, acquiring all modalities among all institutes is costly and often impossible in clinical settings. To leverage more comprehensive multi-modality information, we propose a privacy secured decentralized multi-modality adaptive learning architecture named ModalityBank. Our method could learn a set of effective domain-specific modulation parameters plugged into a common domain-agnostic network. We demonstrate by switching different sets of configurations, the generator could output high-quality images for a specific modality. Our method could also complete the missing modalities across all data centers, thus could be used for modality completion purposes. The downstream task trained from the synthesized multi-modality samples could achieve higher performance than learning from one real data center and achieve close-to-real performance compare with all real images.

Yunhe Gao, Mu Zhou, Dimitris Metaxas

Transformer architecture has emerged to be successful in a number of natural language processing tasks. However, its applications to medical vision remain largely unexplored. In this study, we present UTNet, a simple yet powerful hybrid Transformer architecture that integrates self-attention into a convolutional neural network for enhancing medical image segmentation. UTNet applies self-attention modules in both encoder and decoder for capturing long-range dependency at different scales with minimal overhead. To this end, we propose an efficient self-attention mechanism along with relative position encoding that reduces the complexity of self-attention operation significantly from $O(n^2)$ to approximate $O(n)$. A new self-attention decoder is also proposed to recover fine-grained details from the skipped connections in the encoder. Our approach addresses the dilemma that Transformer requires huge amounts of data to learn vision inductive bias. Our hybrid layer design allows the initialization of Transformer into convolutional networks without a need of pre-training. We have evaluated UTNet on the multi-label, multi-vendor cardiac magnetic resonance imaging cohort. UTNet demonstrates superior segmentation performance and robustness against the state-of-the-art approaches, holding the promise to generalize well on other medical image segmentations.

Yunhe Gao, Rui Huang, Yiwei Yang et al.

Radiotherapy is a treatment where radiation is used to eliminate cancer cells. The delineation of organs-at-risk (OARs) is a vital step in radiotherapy treatment planning to avoid damage to healthy organs. For nasopharyngeal cancer, more than 20 OARs are needed to be precisely segmented in advance. The challenge of this task lies in complex anatomical structure, low-contrast organ contours, and the extremely imbalanced size between large and small organs. Common segmentation methods that treat them equally would generally lead to inaccurate small-organ labeling. We propose a novel two-stage deep neural network, FocusNetv2, to solve this challenging problem by automatically locating, ROI-pooling, and segmenting small organs with specifically designed small-organ localization and segmentation sub-networks while maintaining the accuracy of large organ segmentation. In addition to our original FocusNet, we employ a novel adversarial shape constraint on small organs to ensure the consistency between estimated small-organ shapes and organ shape prior knowledge. Our proposed framework is extensively tested on both self-collected dataset of 1,164 CT scans and the MICCAI Head and Neck Auto Segmentation Challenge 2015 dataset, which shows superior performance compared with state-of-the-art head and neck OAR segmentation methods.

Yunhe Gao, Zhiqiang Tang, Mu Zhou et al.

Data augmentation has proved extremely useful by increasing training data variance to alleviate overfitting and improve deep neural networks' generalization performance. In medical image analysis, a well-designed augmentation policy usually requires much expert knowledge and is difficult to generalize to multiple tasks due to the vast discrepancies among pixel intensities, image appearances, and object shapes in different medical tasks. To automate medical data augmentation, we propose a regularized adversarial training framework via two min-max objectives and three differentiable augmentation models covering affine transformation, deformation, and appearance changes. Our method is more automatic and efficient than previous automatic augmentation methods, which still rely on pre-defined operations with human-specified ranges and costly bi-level optimization. Extensive experiments demonstrated that our approach, with less training overhead, achieves superior performance over state-of-the-art auto-augmentation methods on both tasks of 2D skin cancer classification and 3D organs-at-risk segmentation.

Yunhe Gao, Rui Huang, Ming Chen et al.

In this paper, we propose an end-to-end deep neural network for solving the problem of imbalanced large and small organ segmentation in head and neck (HaN) CT images. To conduct radiotherapy planning for nasopharyngeal cancer, more than 10 organs-at-risk (normal organs) need to be precisely segmented in advance. However, the size ratio between large and small organs in the head could reach hundreds. Directly using such imbalanced organ annotations to train deep neural networks generally leads to inaccurate small-organ label maps. We propose a novel end-to-end deep neural network to solve this challenging problem by automatically locating, ROI-pooling, and segmenting small organs with specifically designed small-organ sub-networks while maintaining the accuracy of large organ segmentation. A strong main network with densely connected atrous spatial pyramid pooling and squeeze-and-excitation modules is used for segmenting large organs, where large organs' label maps are directly output. For small organs, their probabilistic locations instead of label maps are estimated by the main network. High-resolution and multi-scale feature volumes for each small organ are ROI-pooled according to their locations and are fed into small-organ networks for accurate segmenting small organs. Our proposed network is extensively tested on both collected real data and the \emph{MICCAI Head and Neck Auto Segmentation Challenge 2015} dataset, and shows superior performance compared with state-of-the-art segmentation methods.