Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks--which, differing from algorithms, are more flexible and can support different algorithms--including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

An Adaptive Framework for Generating Systematic Explanatory Answer in Online Q&A Platforms

Question Answering (QA) systems face challenges in handling complex questions that require multi-domain knowledge synthesis. The naive RAG models, although effective in information retrieval, struggle with complex questions that require comprehensive and in-depth answers. The pioneering task is defined as explanatory answer generation, which entails handling identified challenges such as the requirement for comprehensive information and logical coherence within the generated context. To address these issues, we refer to systematic thinking theory and propose SynthRAG, an innovative framework designed to enhance QA performance. SynthRAG improves on conventional models by employing adaptive outlines for dynamic content structuring, generating systematic information to ensure detailed coverage, and producing customized answers tailored to specific user inquiries. This structured approach guarantees logical coherence and thorough integration of information, yielding responses that are both insightful and methodically organized. Empirical evaluations underscore SynthRAG's effectiveness, demonstrating its superiority in handling complex questions, overcoming the limitations of naive RAG models, and significantly improving answer quality and depth. Furthermore, an online deployment on the Zhihu platform revealed that SynthRAG's answers achieved notable user engagement, with each response averaging 5.73 upvotes and surpassing the performance of 79.8% of human contributors, highlighting the practical relevance and impact of the proposed framework. Our code is available at https://github.com/czy1999/SynthRAG .

Day-Night Adaptation: An Innovative Source-free Adaptation Framework for Medical Image Segmentation

Distribution shifts widely exist in medical images acquired from different medical centers, hindering the deployment of semantic segmentation models trained on data from one center (source domain) to another (target domain). While unsupervised domain adaptation (UDA) has shown significant promise in mitigating these shifts, it poses privacy risks due to sharing data between centers. To facilitate adaptation while preserving data privacy, source-free domain adaptation (SFDA) and test-time adaptation (TTA) have emerged as effective paradigms, relying solely on target domain data. However, the scenarios currently addressed by SFDA and TTA are limited, making them less suitable for clinical applications. In a more realistic clinical scenario, the pre-trained model is deployed in a medical centre to assist with clinical tasks during the day and rest at night. During the daytime process, TTA can be employed to enhance inference performance. During the nighttime process, after collecting the test data from the day, the model can be fine-tuned utilizing SFDA to further adapt to the target domain. With above insights, we propose a novel adaptation framework called Day-Night Adaptation (DyNA). This framework adapts the model to the target domain through day-night loops without requiring access to source data. Specifically, we implement distinct adaptation strategies for daytime and nighttime to better meet the demands of clinical settings. During the daytime, model parameters are frozen, and a specific low-frequency prompt is trained for each test sample. Additionally, we construct a memory bank for prompt initialization and develop a warm-up mechanism to enhance prompt training. During nighttime, we integrate a global student model into the traditional teacher-student self-training paradigm to fine-tune the model while ensuring training stability...

SpecTrack: Learned Multi-Rotation Tracking via Speckle Imaging

Precision pose detection is increasingly demanded in fields such as personal fabrication, Virtual Reality (VR), and robotics due to its critical role in ensuring accurate positioning information. However, conventional vision-based systems used in these systems often struggle with achieving high precision and accuracy, particularly when dealing with complex environments or fast-moving objects. To address these limitations, we investigate Laser Speckle Imaging (LSI), an emerging optical tracking method that offers promising potential for improving pose estimation accuracy. Specifically, our proposed LSI-Based Tracking (SpecTrack) leverages the captures from a lensless camera and a retro-reflector marker with a coded aperture to achieve multi-axis rotational pose estimation with high precision. Our extensive trials using our in-house built testbed have shown that SpecTrack achieves an accuracy of 0.31{\deg} (std=0.43{\deg}), significantly outperforming state-of-the-art approaches and improving accuracy up to 200%.

MedUniSeg: 2D and 3D Medical Image Segmentation via a Prompt-driven Universal Model

Universal segmentation models offer significant potential in addressing a wide range of tasks by effectively leveraging discrete annotations. As the scope of tasks and modalities expands, it becomes increasingly important to generate and strategically position task- and modal-specific priors within the universal model. However, existing universal models often overlook the correlations between different priors, and the optimal placement and frequency of these priors remain underexplored. In this paper, we introduce MedUniSeg, a prompt-driven universal segmentation model designed for 2D and 3D multi-task segmentation across diverse modalities and domains. MedUniSeg employs multiple modal-specific prompts alongside a universal task prompt to accurately characterize the modalities and tasks. To generate the related priors, we propose the modal map (MMap) and the fusion and selection (FUSE) modules, which transform modal and task prompts into corresponding priors. These modal and task priors are systematically introduced at the start and end of the encoding process. We evaluate MedUniSeg on a comprehensive multi-modal upstream dataset consisting of 17 sub-datasets. The results demonstrate that MedUniSeg achieves superior multi-task segmentation performance, attaining a 1.2% improvement in the mean Dice score across the 17 upstream tasks compared to nnUNet baselines, while using less than 1/10 of the parameters. For tasks that underperform during the initial multi-task joint training, we freeze MedUniSeg and introduce new modules to re-learn these tasks. This approach yields an enhanced version, MedUniSeg*, which consistently outperforms MedUniSeg across all tasks. Moreover, MedUniSeg surpasses advanced self-supervised and supervised pre-trained models on six downstream tasks, establishing itself as a high-quality, highly generalizable pre-trained segmentation model.

Using Prompts to Guide Large Language Models in Imitating a Real Person's Language Style

Large language models (LLMs), such as GPT series and Llama series have demonstrated strong capabilities in natural language processing, contextual understanding, and text generation. In recent years, researchers are trying to enhance the abilities of LLMs in performing various tasks, and numerous studies have proved that well-designed prompts can significantly improve the performance of LLMs on these tasks. This study compares the language style imitation ability of three different large language models under the guidance of the same zero-shot prompt. It also involves comparing the imitation ability of the same large language model when guided by three different prompts individually. Additionally, by applying a Tree-of-Thoughts (ToT) Prompting method to Llama 3, a conversational AI with the language style of a real person was created. In this study, three evaluation methods were used to evaluate LLMs and prompts. The results show that Llama 3 performs best at imitating language styles, and that the ToT prompting method is the most effective to guide it in imitating language styles. Using a ToT framework, Llama 3 was guided to interact with users in the language style of a specific individual without altering its core parameters, thereby creating a text-based conversational AI that reflects the language style of the individual.

Pre-training Everywhere: Parameter-Efficient Fine-Tuning for Medical Image Analysis via Target Parameter Pre-training

Parameter-efficient fine-tuning (PEFT) techniques have emerged to address issues of overfitting and high computational costs associated with fully fine-tuning in the paradigm of self-supervised learning. Mainstream methods based on PEFT involve adding a few trainable parameters while keeping the pre-trained parameters of the backbone fixed. These methods achieve comparative, and often superior, performance to fully fine-tuning, demonstrating the powerful representation ability of the pre-trained backbone. Despite its success, these methods typically ignore the initialization of the new parameters, often relying solely on random initialization. We argue that if pre-training is significantly beneficial, it should be applied to all parameters requiring representational capacity. Motivated by this insight, we propose a simple yet effective fine-tuning framework based on Target Parameter Pre-training (TPP). The target parameters refer to the new parameters introduced during fine-tuning. TPP includes an additional stage before PEFT to pre-train these target parameters. During this stage, the pre-trained backbone parameters are frozen, and only the target parameters are trainable. A defined pre-text task is used to encourage the target parameters to learn specific representations of downstream data. When PEFT is subsequently employed, the pre-trained target parameters are loaded to enhance fine-tuning efficiency. The proposed TPP framework is versatile, allowing for the integration of various pretext tasks for pre-training and supporting different PEFT methods as backbones. We evaluated the fine-tining performance of our method using five public datasets, including three modalities and two task types. The results demonstrate that the proposed TPP can be easily integrated into existing PEFT methods, significantly improving performance.

From Few to More: Scribble-based Medical Image Segmentation via Masked Context Modeling and Continuous Pseudo Labels

Scribble-based weakly supervised segmentation techniques offer comparable performance to fully supervised methods while significantly reducing annotation costs, making them an appealing alternative. Existing methods often rely on auxiliary tasks to enforce semantic consistency and use hard pseudo labels for supervision. However, these methods often overlook the unique requirements of models trained with sparse annotations. Since the model must predict pixel-wise segmentation maps with limited annotations, the ability to handle varying levels of annotation richness is critical. In this paper, we adopt the principle of `from few to more' and propose MaCo, a weakly supervised framework designed for medical image segmentation. MaCo employs masked context modeling (MCM) and continuous pseudo labels (CPL). MCM uses an attention-based masking strategy to disrupt the input image, compelling the model's predictions to remain consistent with those of the original image. CPL converts scribble annotations into continuous pixel-wise labels by applying an exponential decay function to distance maps, resulting in continuous maps that represent the confidence of each pixel belonging to a specific category, rather than using hard pseudo labels. We evaluate MaCo against other weakly supervised methods using three public datasets. The results indicate that MaCo outperforms competing methods across all datasets, setting a new record in weakly supervised medical image segmentation.

Gradient Alignment Improves Test-Time Adaptation for Medical Image Segmentation

Although recent years have witnessed significant advancements in medical image segmentation, the pervasive issue of domain shift among medical images from diverse centres hinders the effective deployment of pre-trained models. Many Test-time Adaptation (TTA) methods have been proposed to address this issue by fine-tuning pre-trained models with test data during inference. These methods, however, often suffer from less-satisfactory optimization due to suboptimal optimization direction (dictated by the gradient) and fixed step-size (predicated on the learning rate). In this paper, we propose the Gradient alignment-based Test-time adaptation (GraTa) method to improve both the gradient direction and learning rate in the optimization procedure. Unlike conventional TTA methods, which primarily optimize the pseudo gradient derived from a self-supervised objective, our method incorporates an auxiliary gradient with the pseudo one to facilitate gradient alignment. Such gradient alignment enables the model to excavate the similarities between different gradients and correct the gradient direction to approximate the empirical gradient related to the current segmentation task. Additionally, we design a dynamic learning rate based on the cosine similarity between the pseudo and auxiliary gradients, thereby empowering the adaptive fine-tuning of pre-trained models on diverse test data. Extensive experiments establish the effectiveness of the proposed gradient alignment and dynamic learning rate and substantiate the superiority of our GraTa method over other state-of-the-art TTA methods on a benchmark medical image segmentation task. The code and weights of pre-trained source models will be available.

Machine Unlearning with Minimal Gradient Dependence for High Unlearning Ratios

In the context of machine unlearning, the primary challenge lies in effectively removing traces of private data from trained models while maintaining model performance and security against privacy attacks like membership inference attacks. Traditional gradient-based unlearning methods often rely on extensive historical gradients, which becomes impractical with high unlearning ratios and may reduce the effectiveness of unlearning. Addressing these limitations, we introduce Mini-Unlearning, a novel approach that capitalizes on a critical observation: unlearned parameters correlate with retrained parameters through contraction mapping. Our method, Mini-Unlearning, utilizes a minimal subset of historical gradients and leverages this contraction mapping to facilitate scalable, efficient unlearning. This lightweight, scalable method significantly enhances model accuracy and strengthens resistance to membership inference attacks. Our experiments demonstrate that Mini-Unlearning not only works under higher unlearning ratios but also outperforms existing techniques in both accuracy and security, offering a promising solution for applications requiring robust unlearning capabilities.