Hao Guan

Hao Guan, Mingxia Liu

Domain adaptation (DA) is an important technique for modern machine learning-based medical data analysis, which aims at reducing distribution differences between different medical datasets. A proper domain adaptation method can significantly enhance the statistical power by pooling data acquired from multiple sites/centers. To this end, we have developed the Domain Adaptation Toolbox for Medical data analysis (DomainATM) - an open-source software package designed for fast facilitation and easy customization of domain adaptation methods for medical data analysis. The DomainATM is implemented in MATLAB with a user-friendly graphical interface, and it consists of a collection of popular data adaptation algorithms that have been extensively applied to medical image analysis and computer vision. With DomainATM, researchers are able to facilitate fast feature-level and image-level adaptation, visualization and performance evaluation of different adaptation methods for medical data analysis. More importantly, the DomainATM enables the users to develop and test their own adaptation methods through scripting, greatly enhancing its utility and extensibility. An overview characteristic and usage of DomainATM is presented and illustrated with three example experiments, demonstrating its effectiveness, simplicity, and flexibility. The software, source code, and manual are available online.

Yu Zhao, Hao Guan, Yongcheng Jing et al.

Large Language Models (LLMs) have shown strong potential in complex medical reasoning yet face diminishing gains under inference scaling laws. While existing studies augment LLMs with various knowledge types, it remains unclear how effectively the additional costs translate into accuracy. In this paper, we explore how meta-cognition of LLMs, i.e., their self-assessment of their own cognitive states, can regulate the reasoning process. Specifically, we propose MedCoG, a Medical Meta-Cognition Agent with Knowledge Graph, where the meta-cognitive assessments of task complexity, familiarity, and knowledge density dynamically regulate utilization of procedural, episodic, and factual knowledge. The LLM-centric on-demand reasoning aims to mitigate the diminishing returns under scaling law by (1) reducing costs via avoiding indiscriminate scaling, (2) improving accuracy via filtering out distractive knowledge. To validate this, we empirically characterize the scaling curve and introduce inference density to quantify inference efficiency. Experiments demonstrate the effectiveness and efficiency of MedCoG on five hard sets of medical benchmarks, yielding 6.2x inference density. Furthermore, the Oracle study highlights the significant potential of meta-cognitive regulation.

Hao Guan, Pew-Thian Yap, Andrea Bozoki et al.

Machine learning in medical imaging often faces a fundamental dilemma, namely, the small sample size problem. Many recent studies suggest using multi-domain data pooled from different acquisition sites/centers to improve statistical power. However, medical images from different sites cannot be easily shared to build large datasets for model training due to privacy protection reasons. As a promising solution, federated learning, which enables collaborative training of machine learning models based on data from different sites without cross-site data sharing, has attracted considerable attention recently. In this paper, we conduct a comprehensive survey of the recent development of federated learning methods in medical image analysis. In this survey, we first introduce the background knowledge of federated learning for dealing with privacy protection and collaborative learning issues in medical imaging. We then present a comprehensive review of recent advances in federated learning methods for medical image analysis. Specifically, existing methods are categorized based on three critical aspects of a federated learning system, including client end, server end, and communication techniques. In each category, we summarize the existing federated learning methods according to specific research problems in medical image analysis and also provide insights into the motivations of different approaches. In addition, we provide a review of existing benchmark medical imaging datasets and software platforms for current federated learning research. We also conduct an experimental study to empirically evaluate typical federated learning methods for medical image analysis. This survey can help to better understand the current research status, challenges, and potential research opportunities in this promising research field.

Hao Guan, Ling Yue, Pew-Thian Yap et al.

Subjective cognitive decline (SCD) is a preclinical stage of Alzheimer's disease (AD) which occurs even before mild cognitive impairment (MCI). Progressive SCD will convert to MCI with the potential of further evolving to AD. Therefore, early identification of progressive SCD with neuroimaging techniques (e.g., structural MRI) is of great clinical value for early intervention of AD. However, existing MRI-based machine/deep learning methods usually suffer the small-sample-size problem which poses a great challenge to related neuroimaging analysis. The central question we aim to tackle in this paper is how to leverage related domains (e.g., AD/NC) to assist the progression prediction of SCD. Meanwhile, we are concerned about which brain areas are more closely linked to the identification of progressive SCD. To this end, we propose an attention-guided autoencoder model for efficient cross-domain adaptation which facilitates the knowledge transfer from AD to SCD. The proposed model is composed of four key components: 1) a feature encoding module for learning shared subspace representations of different domains, 2) an attention module for automatically locating discriminative brain regions of interest defined in brain atlases, 3) a decoding module for reconstructing the original input, 4) a classification module for identification of brain diseases. Through joint training of these four modules, domain invariant features can be learned. Meanwhile, the brain disease related regions can be highlighted by the attention mechanism. Extensive experiments on the publicly available ADNI dataset and a private CLAS dataset have demonstrated the effectiveness of the proposed method. The proposed model is straightforward to train and test with only 5-10 seconds on CPUs and is suitable for medical tasks with small datasets.

Yibo Wang, Yongcheng Jing, Shunyu Liu et al.

Long-context reasoning has significantly empowered large language models (LLMs) to tackle complex tasks, yet it introduces severe efficiency bottlenecks due to the computational complexity. Existing efficient approaches often rely on complex additional training or external models for compression, which limits scalability and discards critical fine-grained information. In this paper, we propose VTC-R1, a new efficient reasoning paradigm that integrates vision-text compression into the reasoning process. Instead of processing lengthy textual traces, VTC-R1 renders intermediate reasoning segments into compact images, which are iteratively fed back into vision-language models as "optical memory." We construct a training dataset based on OpenR1-Math-220K achieving 3.4x token compression and fine-tune representative VLMs-Glyph and Qwen3-VL. Extensive experiments on benchmarks such as MATH500, AIME25, AMC23 and GPQA-D demonstrate that VTC-R1 consistently outperforms standard long-context reasoning. Furthermore, our approach significantly improves inference efficiency, achieving 2.7x speedup in end-to-end latency, highlighting its potential as a scalable solution for reasoning-intensive applications. Our code is available at https://github.com/w-yibo/VTC-R1.

Lingyue Fu, Hao Guan, Kounianhua Du et al.

Knowledge Tracing (KT) aims to determine whether students will respond correctly to the next question, which is a crucial task in intelligent tutoring systems (ITS). In educational KT scenarios, transductive ID-based methods often face severe data sparsity and cold start problems, where interactions between individual students and questions are sparse, and new questions and concepts consistently arrive in the database. In addition, existing KT models only implicitly consider the correlation between concepts and questions, lacking direct modeling of the more complex relationships in the heterogeneous graph of concepts and questions. In this paper, we propose a Structure-aware Inductive Knowledge Tracing model with large language model (dubbed SINKT), which, for the first time, introduces large language models (LLMs) and realizes inductive knowledge tracing. Firstly, SINKT utilizes LLMs to introduce structural relationships between concepts and constructs a heterogeneous graph for concepts and questions. Secondly, by encoding concepts and questions with LLMs, SINKT incorporates semantic information to aid prediction. Finally, SINKT predicts the student's response to the target question by interacting with the student's knowledge state and the question representation. Experiments on four real-world datasets demonstrate that SINKT achieves state-of-the-art performance among 12 existing transductive KT models. Additionally, we explore the performance of SINKT on the inductive KT task and provide insights into various modules.

Lu Liu, Wuqi Zhang, Lili Wei et al.

Decentralized Finance (DeFi) smart contracts manage billions of dollars, making them a prime target for exploits. Price manipulation vulnerabilities, often via flash loans, are a devastating class of attacks causing significant financial losses. Existing detection methods are limited. Reactive approaches analyze attacks only after they occur, while proactive static analysis tools rely on rigid, predefined heuristics, limiting adaptability. Both depend on known attack patterns, failing to identify novel variants or comprehend complex economic logic. We propose PMDetector, a hybrid framework combining static analysis with Large Language Model (LLM)-based reasoning to proactively detect price manipulation vulnerabilities. Our approach uses a formal attack model and a three-stage pipeline. First, static taint analysis identifies potentially vulnerable code paths. Second, a two-stage LLM process filters paths by analyzing defenses and then simulates attacks to evaluate exploitability. Finally, a static analysis checker validates LLM results, retaining only high-risk paths and generating comprehensive vulnerability reports. To evaluate its effectiveness, we built a dataset of 73 real-world vulnerable and 288 benign DeFi protocols. Results show PMDetector achieves 88% precision and 90% recall with Gemini 2.5-flash, significantly outperforming state-of-the-art static analysis and LLM-based approaches. Auditing a vulnerability with PMDetector costs just $0.03 and takes 4.0 seconds with GPT-4.1, offering an efficient and cost-effective alternative to manual audits.

Lingyue Fu, Hao Guan, Bolun Zhang et al.

As Large Language Models (LLMs) demonstrate increasingly sophisticated code processing capabilities, evaluating their performance on engineering-level code remains challenging. Existing repository-level benchmarks primarily focus on single scenarios, such as code generation or bug fixing, without adequately capturing the diversity and complexity of real-world software or project engineering workflows. Furthermore, these benchmarks suffer from limited controllability in question positioning and reliability issues in their generated test cases. To address these limitations, we present CorePipe, a fully automated pipeline that converts repositories into comprehensive test cases, and introduce CoreCodeBench, a configurable multi-scenario repository-level benchmark. To simulate real engineering scenarios, CorePipe generates three types of atomic questions (Development, BugFix, and Test-Driven Development) specifically targeting core code segments. These atomic questions are further combined into three types of composite questions, with difficulty levels flexibly adjusted through hyperparameter tuning. CoreCodeBench provides a comprehensive and extensive repository-level benchmark to investigate the applicability of LLMs in real-world engineering projects. Experiments with 16 LLMs across diverse scenarios reveal varying capabilities and offer multi-dimensional insights into LLM performance in engineering contexts. The code for CorePipe is available at https://github.com/AGI-Eval-Official/CoreCodeBench, and the data for CoreCodeBench can be accessed at https://huggingface.co/collections/tubehhh/corecodebench-68256d2faabf4b1610a08caa.

Hao Guan, Lingyue Fu, Shao Zhang et al.

As autonomous code agents move toward end-to-end software development, evaluating their practical autonomy becomes critical. Current benchmarks hide friction by testing agents in pre-configured environments, and their static evaluation pipelines frequently fail when parsing fully autonomous trajectories. We address these limitations with SWE-Cycle, a benchmark of 489 rigorously filtered instances. SWE-Cycle evaluates agents across three isolated tasks, including environment reconstruction, code implementation, and verification test generation, as well as an end-to-end FullCycle task that integrates all three. The FullCycle task requires agents to work autonomously in a bare repository without human scaffolding. To reliably assess these complex execution paths, we developed SWE-Judge. By combining static code review with dynamic testing, this execution-capable evaluation agent accurately verifies functional correctness and eliminates the systematic measurement errors of traditional static parsers. We evaluate code agents powered by six state-of-the-art LLMs across these four tasks. The results reveal a sharp drop in solve rates when transitioning from isolated tasks to FullCycle execution, exposing critical bottlenecks in handling cross-phase dependencies and maintaining code quality. Together, SWE-Cycle and SWE-Judge provide a comprehensive framework for accurately measuring the end-to-end capabilities of autonomous software agents.

Hao Guan, Li Zhou

Vision-Language Models have demonstrated strong potential in medical image analysis and disease diagnosis. However, after deployment, their performance may deteriorate when the input data distribution shifts from that observed during development. Detecting such performance degradation is essential for clinical reliability, yet remains challenging for large pre-trained VLMs operating without labeled data. In this study, we investigate performance degradation detection under data shift in a state-of-the-art pathology VLM. We examine both input-level data shift and output-level prediction behavior to understand their respective roles in monitoring model reliability. To facilitate systematic analysis of input data shift, we develop DomainSAT, a lightweight toolbox with a graphical interface that integrates representative shift detection algorithms and enables intuitive exploration of data shift. Our analysis shows that while input data shift detection is effective at identifying distributional changes and providing early diagnostic signals, it does not always correspond to actual performance degradation. Motivated by this observation, we further study output-based monitoring and introduce a label-free, confidence-based degradation indicator that directly captures changes in model prediction confidence. We find that this indicator exhibits a close relationship with performance degradation and serves as an effective complement to input shift detection. Experiments on a large-scale pathology dataset for tumor classification demonstrate that combining input data shift detection and output confidence-based indicators enables more reliable detection and interpretation of performance degradation in VLMs under data shift. These findings provide a practical and complementary framework for monitoring the reliability of foundation models in digital pathology.

Jian Cheng, Ziyang Liu, Hao Guan et al.

Chronological age of healthy people is able to be predicted accurately using deep neural networks from neuroimaging data, and the predicted brain age could serve as a biomarker for detecting aging-related diseases. In this paper, a novel 3D convolutional network, called two-stage-age-network (TSAN), is proposed to estimate brain age from T1-weighted MRI data. Compared with existing methods, TSAN has the following improvements. First, TSAN uses a two-stage cascade network architecture, where the first-stage network estimates a rough brain age, then the second-stage network estimates the brain age more accurately from the discretized brain age by the first-stage network. Second, to our knowledge, TSAN is the first work to apply novel ranking losses in brain age estimation, together with the traditional mean square error (MSE) loss. Third, densely connected paths are used to combine feature maps with different scales. The experiments with $6586$ MRIs showed that TSAN could provide accurate brain age estimation, yielding mean absolute error (MAE) of $2.428$ and Pearson's correlation coefficient (PCC) of $0.985$, between the estimated and chronological ages. Furthermore, using the brain age gap between brain age and chronological age as a biomarker, Alzheimer's disease (AD) and Mild Cognitive Impairment (MCI) can be distinguished from healthy control (HC) subjects by support vector machine (SVM). Classification AUC in AD/HC and MCI/HC was $0.904$ and $0.823$, respectively. It showed that brain age gap is an effective biomarker associated with risk of dementia, and has potential for early-stage dementia risk screening. The codes and trained models have been released on GitHub: https://github.com/Milan-BUAA/TSAN-brain-age-estimation.

Hao Guan, David Bates, Li Zhou

Artificial intelligence (AI) is increasingly integrated into modern healthcare, offering powerful support for clinical decision-making. However, in real-world settings, AI systems may experience performance degradation over time, due to factors such as shifting data distributions, changes in patient characteristics, evolving clinical protocols, and variations in data quality. These factors can compromise model reliability, posing safety concerns and increasing the likelihood of inaccurate predictions or adverse outcomes. This review presents a forward-looking perspective on monitoring and maintaining the "health" of AI systems in healthcare. We highlight the urgent need for continuous performance monitoring, early degradation detection, and effective self-correction mechanisms. The paper begins by reviewing common causes of performance degradation at both data and model levels. We then summarize key techniques for detecting data and model drift, followed by an in-depth look at root cause analysis. Correction strategies are further reviewed, ranging from model retraining to test-time adaptation. Our survey spans both traditional machine learning models and state-of-the-art large language models (LLMs), offering insights into their strengths and limitations. Finally, we discuss ongoing technical challenges and propose future research directions. This work aims to guide the development of reliable, robust medical AI systems capable of sustaining safe, long-term deployment in dynamic clinical settings.

Shuyang Xiang, Hao Guan

Large language models typically represent Chinese characters as discrete index-based tokens, largely ignoring their visual form. For logographic scripts, visual structure carries semantic and phonetic information, which may aid prediction. We investigate whether low-resolution visual inputs can serve as an alternative for character-level modeling. Instead of token IDs, our decoder receives grayscale images of individual characters, with resolutions as low as $8 \times 8$ pixels. Remarkably, these inputs achieve 39.2\% accuracy, comparable to the index-based baseline of 39.1\%. Such low-resource settings also exhibit a pronounced \emph{hot-start} effect: by 0.4\% of total training, accuracy reaches above 12\%, while index-based models lag at below 6\%. Overall, our results demonstrate that minimal visual structure can provide a robust and efficient signal for Chinese language modeling, offering an alternative perspective on character representation that complements traditional index-based approaches.

Lingyue Fu, Bolun Zhang, Hao Guan et al.

Recent advances in code agents have enabled automated software development at the project level, supported by large language models (LLMs) and widely adopted tools. However, existing benchmarks for code agent evaluation face two major limitations: high annotation cost and expertise requirements, and rigid evaluation metrics that rely primarily on unit tests. To address these challenges, we propose an agent-driven benchmark construction pipeline that leverages human supervision to efficiently generate diverse and challenging project-level tasks. Based on this approach, we introduce PRDBench, a novel benchmark comprising 50 real-world Python projects across 20 domains, each with structured Product Requirement Document (PRD) requirements, comprehensive evaluation criteria, and reference implementations. PRDBench features rich data sources, high task complexity, and flexible metrics. We further employ an Agent-as-a-Judge paradigm to score agent outputs, enabling the evaluation of various test types beyond unit tests. Extensive experiments on PRDBench demonstrate its effectiveness in assessing the capabilities of both code agents and evaluation agents, providing a scalable and robust framework for annotation and evaluation.

Mark Huasong Meng, Hao Guan, Liuhuo Wan et al.

We present PAODING, a toolkit to debloat pretrained neural network models through the lens of data-free pruning. To preserve the model fidelity, PAODING adopts an iterative process, which dynamically measures the effect of deleting a neuron to identify candidates that have the least impact to the output layer. Our evaluation shows that PAODING can significantly reduce the model size, generalize on different datasets and models, and meanwhile preserve the model fidelity in terms of test accuracy and adversarial robustness. PAODING is publicly available on PyPI via https://pypi.org/project/paoding-dl.

Hao Guan, Chaoyue Wang, Dacheng Tao

Mild cognitive impairment (MCI) conversion prediction, i.e., identifying MCI patients of high risks converting to Alzheimer's disease (AD), is essential for preventing or slowing the progression of AD. Although previous studies have shown that the fusion of multi-modal data can effectively improve the prediction accuracy, their applications are largely restricted by the limited availability or high cost of multi-modal data. Building an effective prediction model using only magnetic resonance imaging (MRI) remains a challenging research topic. In this work, we propose a multi-modal multi-instance distillation scheme, which aims to distill the knowledge learned from multi-modal data to an MRI-based network for MCI conversion prediction. In contrast to existing distillation algorithms, the proposed multi-instance probabilities demonstrate a superior capability of representing the complicated atrophy distributions, and can guide the MRI-based network to better explore the input MRI. To our best knowledge, this is the first study that attempts to improve an MRI-based prediction model by leveraging extra supervision distilled from multi-modal information. Experiments demonstrate the advantage of our framework, suggesting its potentials in the data-limited clinical settings.

Hao Guan, Mingxia Liu

Machine learning techniques used in computer-aided medical image analysis usually suffer from the domain shift problem caused by different distributions between source/reference data and target data. As a promising solution, domain adaptation has attracted considerable attention in recent years. The aim of this paper is to survey the recent advances of domain adaptation methods in medical image analysis. We first present the motivation of introducing domain adaptation techniques to tackle domain heterogeneity issues for medical image analysis. Then we provide a review of recent domain adaptation models in various medical image analysis tasks. We categorize the existing methods into shallow and deep models, and each of them is further divided into supervised, semi-supervised and unsupervised methods. We also provide a brief summary of the benchmark medical image datasets that support current domain adaptation research. This survey will enable researchers to gain a better understanding of the current status, challenges.

Hao Guan, Liu Liu, Sean Moran et al.

Denoising extreme low light images is a challenging task due to the high noise level. When the illumination is low, digital cameras increase the ISO (electronic gain) to amplify the brightness of captured data. However, this in turn amplifies the noise, arising from read, shot, and defective pixel sources. In the raw domain, read and shot noise are effectively modelled using Gaussian and Poisson distributions respectively, whereas defective pixels can be modeled with impulsive noise. In extreme low light imaging, noise removal becomes a critical challenge to produce a high quality, detailed image with low noise. In this paper, we propose a multi-task deep neural network called Noise Decomposition (NODE) that explicitly and separately estimates defective pixel noise, in conjunction with Gaussian and Poisson noise, to denoise an extreme low light image. Our network is purposely designed to work with raw data, for which the noise is more easily modeled before going through non-linear transformations in the image signal processing (ISP) pipeline. Quantitative and qualitative evaluation show the proposed method to be more effective at denoising real raw images than state-of-the-art techniques.