Zhiling Yan

Cheng Chen, Juzheng Miao, Dufan Wu et al.

The Segment Anything Model (SAM), a foundation model for general image segmentation, has demonstrated impressive zero-shot performance across numerous natural image segmentation tasks. However, SAM's performance significantly declines when applied to medical images, primarily due to the substantial disparity between natural and medical image domains. To effectively adapt SAM to medical images, it is important to incorporate critical third-dimensional information, i.e., volumetric or temporal knowledge, during fine-tuning. Simultaneously, we aim to harness SAM's pre-trained weights within its original 2D backbone to the fullest extent. In this paper, we introduce a modality-agnostic SAM adaptation framework, named as MA-SAM, that is applicable to various volumetric and video medical data. Our method roots in the parameter-efficient fine-tuning strategy to update only a small portion of weight increments while preserving the majority of SAM's pre-trained weights. By injecting a series of 3D adapters into the transformer blocks of the image encoder, our method enables the pre-trained 2D backbone to extract third-dimensional information from input data. The effectiveness of our method has been comprehensively evaluated on four medical image segmentation tasks, by using 10 public datasets across CT, MRI, and surgical video data. Remarkably, without using any prompt, our method consistently outperforms various state-of-the-art 3D approaches, surpassing nnU-Net by 0.9%, 2.6%, and 9.9% in Dice for CT multi-organ segmentation, MRI prostate segmentation, and surgical scene segmentation respectively. Our model also demonstrates strong generalization, and excels in challenging tumor segmentation when prompts are used. Our code is available at: https://github.com/cchen-cc/MA-SAM.

Haixing Dai, Chong Ma, Zhiling Yan et al.

This paper introduces SAMAug, a novel visual point augmentation method for the Segment Anything Model (SAM) that enhances interactive image segmentation performance. SAMAug generates augmented point prompts to provide more information about the user's intention to SAM. Starting with an initial point prompt, SAM produces an initial mask, which is then fed into our proposed SAMAug to generate augmented point prompts. By incorporating these extra points, SAM can generate augmented segmentation masks based on both the augmented point prompts and the initial prompt, resulting in improved segmentation performance. We conducted evaluations using four different point augmentation strategies: random sampling, sampling based on maximum difference entropy, maximum distance, and saliency. Experiment results on the COCO, Fundus, COVID QUEx, and ISIC2018 datasets show that SAMAug can boost SAM's segmentation results, especially using the maximum distance and saliency. SAMAug demonstrates the potential of visual prompt augmentation for computer vision. Codes of SAMAug are available at github.com/yhydhx/SAMAug

Yihan Cao, Siyu Li, Yixin Liu et al.

Recently, ChatGPT, along with DALL-E-2 and Codex,has been gaining significant attention from society. As a result, many individuals have become interested in related resources and are seeking to uncover the background and secrets behind its impressive performance. In fact, ChatGPT and other Generative AI (GAI) techniques belong to the category of Artificial Intelligence Generated Content (AIGC), which involves the creation of digital content, such as images, music, and natural language, through AI models. The goal of AIGC is to make the content creation process more efficient and accessible, allowing for the production of high-quality content at a faster pace. AIGC is achieved by extracting and understanding intent information from instructions provided by human, and generating the content according to its knowledge and the intent information. In recent years, large-scale models have become increasingly important in AIGC as they provide better intent extraction and thus, improved generation results. With the growth of data and the size of the models, the distribution that the model can learn becomes more comprehensive and closer to reality, leading to more realistic and high-quality content generation. This survey provides a comprehensive review on the history of generative models, and basic components, recent advances in AIGC from unimodal interaction and multimodal interaction. From the perspective of unimodality, we introduce the generation tasks and relative models of text and image. From the perspective of multimodality, we introduce the cross-application between the modalities mentioned above. Finally, we discuss the existing open problems and future challenges in AIGC.

Tianyi Zhang, Zhiling Yan, Chunhui Li et al.

In pathology image analysis, obtaining and maintaining high-quality annotated samples is an extremely labor-intensive task. To overcome this challenge, mixing-based methods have emerged as effective alternatives to traditional preprocessing data augmentation techniques. Nonetheless, these methods fail to fully consider the unique features of pathology images, such as local specificity, global distribution, and inner/outer-sample instance relationships. To better comprehend these characteristics and create valuable pseudo samples, we propose the CellMix framework, which employs a novel distribution-oriented in-place shuffle approach. By dividing images into patches based on the granularity of pathology instances and shuffling them within the same batch, the absolute relationships between instances can be effectively preserved when generating new samples. Moreover, we develop a curriculum learning-inspired, loss-driven strategy to handle perturbations and distribution-related noise during training, enabling the model to adaptively fit the augmented data. Our experiments in pathology image classification tasks demonstrate state-of-the-art (SOTA) performance on 7 distinct datasets. This innovative instance relationship-centered method has the potential to inform general data augmentation approaches for pathology image classification. The associated codes are available at https://github.com/sagizty/CellMix.

Zhiling Yan, Kai Zhang, Rong Zhou et al.

In this paper, we critically evaluate the capabilities of the state-of-the-art multimodal large language model, i.e., GPT-4 with Vision (GPT-4V), on Visual Question Answering (VQA) task. Our experiments thoroughly assess GPT-4V's proficiency in answering questions paired with images using both pathology and radiology datasets from 11 modalities (e.g. Microscopy, Dermoscopy, X-ray, CT, etc.) and fifteen objects of interests (brain, liver, lung, etc.). Our datasets encompass a comprehensive range of medical inquiries, including sixteen distinct question types. Throughout our evaluations, we devised textual prompts for GPT-4V, directing it to synergize visual and textual information. The experiments with accuracy score conclude that the current version of GPT-4V is not recommended for real-world diagnostics due to its unreliable and suboptimal accuracy in responding to diagnostic medical questions. In addition, we delineate seven unique facets of GPT-4V's behavior in medical VQA, highlighting its constraints within this complex arena. The complete details of our evaluation cases are accessible at https://github.com/ZhilingYan/GPT4V-Medical-Report.

Rong Zhou, Zhengqing Yuan, Zhiling Yan et al.

Biomedical image segmentation is crucial for accurately diagnosing and analyzing various diseases. However, Convolutional Neural Networks (CNNs) and Transformers, the most commonly used architectures for this task, struggle to effectively capture long-range dependencies due to the inherent locality of CNNs and the computational complexity of Transformers. To address this limitation, we introduce TTT-Unet, a novel framework that integrates Test-Time Training (TTT) layers into the traditional U-Net architecture for biomedical image segmentation. TTT-Unet dynamically adjusts model parameters during the testing time, enhancing the model's ability to capture both local and long-range features. We evaluate TTT-Unet on multiple medical imaging datasets, including 3D abdominal organ segmentation in CT and MR images, instrument segmentation in endoscopy images, and cell segmentation in microscopy images. The results demonstrate that TTT-Unet consistently outperforms state-of-the-art CNN-based and Transformer-based segmentation models across all tasks. The code is available at https://github.com/rongzhou7/TTT-Unet.

Tianyi Zhang, Youdan Feng, Yunlu Feng et al.

The rapid on-site evaluation (ROSE) technique can signifi-cantly accelerate the diagnosis of pancreatic cancer by im-mediately analyzing the fast-stained cytopathological images. Computer-aided diagnosis (CAD) can potentially address the shortage of pathologists in ROSE. However, the cancerous patterns vary significantly between different samples, making the CAD task extremely challenging. Besides, the ROSE images have complicated perturbations regarding color distribution, brightness, and contrast due to different staining qualities and various acquisition device types. To address these challenges, we proposed a shuffle instances-based Vision Transformer (SI-ViT) approach, which can reduce the perturbations and enhance the modeling among the instances. With the regrouped bags of shuffle instances and their bag-level soft labels, the approach utilizes a regression head to make the model focus on the cells rather than various perturbations. Simultaneously, combined with a classification head, the model can effectively identify the general distributive patterns among different instances. The results demonstrate significant improvements in the classification accuracy with more accurate attention regions, indicating that the diverse patterns of ROSE images are effectively extracted, and the complicated perturbations are significantly reduced. It also suggests that the SI-ViT has excellent potential in analyzing cytopathological images. The code and experimental results are available at https://github.com/sagizty/MIL-SI.

Zhiling Yan, Weixiang Sun, Rong Zhou et al.

Medical image segmentation and video object segmentation are essential for diagnosing and analyzing diseases by identifying and measuring biological structures. Recent advances in natural domain have been driven by foundation models like the Segment Anything Model 2 (SAM-2). To explore the performance of SAM-2 in biomedical applications, we designed three evaluation pipelines for single-frame 2D image segmentation, multi-frame 3D image segmentation and multi-frame video segmentation with varied prompt designs, revealing SAM-2's limitations in medical contexts. Consequently, we developed BioSAM-2, an enhanced foundation model optimized for biomedical data based on SAM-2. Our experiments show that BioSAM-2 not only surpasses the performance of existing state-of-the-art foundation models but also matches or even exceeds specialist models, demonstrating its efficacy and potential in the medical domain.

Dingjie Song, Tianlong Xu, Yi-Fan Zhang et al.

Assessing student handwritten scratchwork is crucial for personalized educational feedback but presents unique challenges due to diverse handwriting, complex layouts, and varied problem-solving approaches. Existing educational NLP primarily focuses on textual responses and neglects the complexity and multimodality inherent in authentic handwritten scratchwork. Current multimodal large language models (MLLMs) excel at visual reasoning but typically adopt an "examinee perspective", prioritizing generating correct answers rather than diagnosing student errors. To bridge these gaps, we introduce ScratchMath, a novel benchmark specifically designed for explaining and classifying errors in authentic handwritten mathematics scratchwork. Our dataset comprises 1,720 mathematics samples from Chinese primary and middle school students, supporting two key tasks: Error Cause Explanation (ECE) and Error Cause Classification (ECC), with seven defined error types. The dataset is meticulously annotated through rigorous human-machine collaborative approaches involving multiple stages of expert labeling, review, and verification. We systematically evaluate 16 leading MLLMs on ScratchMath, revealing significant performance gaps relative to human experts, especially in visual recognition and logical reasoning. Proprietary models notably outperform open-source models, with large reasoning models showing strong potential for error explanation. All evaluation data and frameworks are publicly available to facilitate further research.

Zhiling Yan, Sicheng Chen, Tianyi Zhang et al.

Segmentation is a critical task in computational pathology, as it identifies areas affected by disease or abnormal growth and is essential for diagnosis and treatment. However, acquiring high-quality pixel-level supervised segmentation data requires significant workload demands from experienced pathologists, limiting the application of deep learning. To overcome this challenge, relaxing the label conditions to image-level classification labels allows for more data to be used and more scenarios to be enabled. One approach is to leverage Class Activation Map (CAM) to generate pseudo pixel-level annotations for semantic segmentation with only image-level labels. However, this method fails to thoroughly explore the essential characteristics of pathology images, thus identifying only small areas that are insufficient for pseudo masking. In this paper, we propose a novel shuffle-based feedback learning method inspired by curriculum learning to generate higher-quality pseudo-semantic segmentation masks. Specifically, we perform patch level shuffle of pathology images, with the model adaptively adjusting the shuffle strategy based on feedback from previous learning. Experimental results demonstrate that our proposed approach outperforms state-of-the-arts on three different datasets.

Yixin Liu, Kai Zhang, Yuan Li et al.

Sora is a text-to-video generative AI model, released by OpenAI in February 2024. The model is trained to generate videos of realistic or imaginative scenes from text instructions and show potential in simulating the physical world. Based on public technical reports and reverse engineering, this paper presents a comprehensive review of the model's background, related technologies, applications, remaining challenges, and future directions of text-to-video AI models. We first trace Sora's development and investigate the underlying technologies used to build this "world simulator". Then, we describe in detail the applications and potential impact of Sora in multiple industries ranging from film-making and education to marketing. We discuss the main challenges and limitations that need to be addressed to widely deploy Sora, such as ensuring safe and unbiased video generation. Lastly, we discuss the future development of Sora and video generation models in general, and how advancements in the field could enable new ways of human-AI interaction, boosting productivity and creativity of video generation.

Zhiling Yan, Sifan Song, Dingjie Song et al.

Recent "segment anything" efforts show promise by learning from large-scale data, but adapting such models directly to medical images remains challenging due to the complexity of medical data, noisy annotations, and continual learning requirements across diverse modalities and anatomical structures. In this work, we propose SAMed-2, a new foundation model for medical image segmentation built upon the SAM-2 architecture. Specifically, we introduce a temporal adapter into the image encoder to capture image correlations and a confidence-driven memory mechanism to store high-certainty features for later retrieval. This memory-based strategy counters the pervasive noise in large-scale medical datasets and mitigates catastrophic forgetting when encountering new tasks or modalities. To train and evaluate SAMed-2, we curate MedBank-100k, a comprehensive dataset spanning seven imaging modalities and 21 medical segmentation tasks. Our experiments on both internal benchmarks and 10 external datasets demonstrate superior performance over state-of-the-art baselines in multi-task scenarios. The code is available at: https://github.com/ZhilingYan/Medical-SAM-Bench.

Kai Zhang, Rong Zhou, Eashan Adhikarla et al.

Traditional biomedical artificial intelligence (AI) models, designed for specific tasks or modalities, often exhibit limited flexibility in real-world deployment and struggle to utilize holistic information. Generalist AI holds the potential to address these limitations due to its versatility in interpreting different data types and generating tailored outputs for diverse needs. However, existing biomedical generalist AI solutions are typically heavyweight and closed source to researchers, practitioners, and patients. Here, we propose BiomedGPT, the first open-source and lightweight vision-language foundation model, designed as a generalist capable of performing various biomedical tasks. BiomedGPT achieved state-of-the-art results in 16 out of 25 experiments while maintaining a computing-friendly model scale. We also conducted human evaluations to assess the capabilities of BiomedGPT in radiology visual question answering, report generation, and summarization. BiomedGPT exhibits robust prediction ability with a low error rate of 3.8% in question answering, satisfactory performance with an error rate of 8.3% in writing complex radiology reports, and competitive summarization ability with a nearly equivalent preference score to human experts. Our method demonstrates that effective training with diverse data can lead to more practical biomedical AI for improving diagnosis and workflow efficiency.

Weixiang Sun, Yixin Liu, Zhiling Yan et al.

The rapid expansion of AI in healthcare has led to a surge in medical data generation and storage, boosting medical AI development. However, fears of unauthorized use, like training commercial AI models, hinder researchers from sharing their valuable datasets. To encourage data sharing, one promising solution is to introduce imperceptible noise into the data. This method aims to safeguard the data against unauthorized training by inducing degradation in the generalization ability of the trained model. However, they are not effective and efficient when applied to medical data, mainly due to the ignorance of the sparse nature of medical images. To address this problem, we propose the Sparsity-Aware Local Masking (SALM) method, a novel approach that selectively perturbs significant pixel regions rather than the entire image as previously. This simple yet effective approach, by focusing on local areas, significantly narrows down the search space for disturbances and fully leverages the characteristics of sparsity. Our extensive experiments across various datasets and model architectures demonstrate that SALM effectively prevents unauthorized training of different models and outperforms previous SoTA data protection methods.

Zhiling Yan, Dingjie Song, Zhe Fang et al.

The deployment of Large Language Models (LLMs) in high-stakes clinical settings demands rigorous and reliable evaluation. However, existing medical benchmarks remain static, suffering from two critical limitations: (1) data contamination, where test sets inadvertently leak into training corpora, leading to inflated performance estimates; and (2) temporal misalignment, failing to capture the rapid evolution of medical knowledge. Furthermore, current evaluation metrics for open-ended clinical reasoning often rely on either shallow lexical overlap (e.g., ROUGE) or subjective LLM-as-a-Judge scoring, both inadequate for verifying clinical correctness. To bridge these gaps, we introduce LiveMedBench, a continuously updated, contamination-free, and rubric-based benchmark that weekly harvests real-world clinical cases from online medical communities, ensuring strict temporal separation from model training data. We propose a Multi-Agent Clinical Curation Framework that filters raw data noise and validates clinical integrity against evidence-based medical principles. For evaluation, we develop an Automated Rubric-based Evaluation Framework that decomposes physician responses into granular, case-specific criteria, achieving substantially stronger alignment with expert physicians than LLM-as-a-Judge. To date, LiveMedBench comprises 2,756 real-world cases spanning 38 medical specialties and multiple languages, paired with 16,702 unique evaluation criteria. Extensive evaluation of 38 LLMs reveals that even the best-performing model achieves only 39.2%, and 84% of models exhibit performance degradation on post-cutoff cases, confirming pervasive data contamination risks. Error analysis further identifies contextual application-not factual knowledge-as the dominant bottleneck, with 35-48% of failures stemming from the inability to tailor medical knowledge to patient-specific constraints.

Shaozu Yuan, Aijun Dai, Zhiling Yan et al.

In this paper, we present a novel system (denoted as Polaca) to generate poetic Chinese landscape painting with calligraphy. Unlike previous single image-to-image painting generation, Polaca takes the classic poetry as input and outputs the artistic landscape painting image with the corresponding calligraphy. It is equipped with three different modules to complete the whole piece of landscape painting artwork: the first one is a text-to-image module to generate landscape painting image, the second one is an image-to-image module to generate stylistic calligraphy image, and the third one is an image fusion module to fuse the two images into a whole piece of aesthetic artwork.