Shuijin Lin, Shaozhen Yan, Tuo Liu, Haifeng Wang, Chunfeng Lian, Jie Lu, Jianhua Ma, Lin Xie
The biological definition of Alzheimer's disease (AD) relies on multi-modal neuroimaging, yet the clinical utility of positron emission tomography (PET) is limited by cost and radiation exposure, hindering early screening at preclinical or prodromal stages. While generative models offer a promising alternative by synthesizing PET from magnetic resonance imaging (MRI), achieving subject-specific precision remains a primary challenge. Here, we introduce DIReCT$++$, a Domain-Informed ReCTified flow model for synthesizing multi-tracer PET from MRI combined with fundamental clinical information. Our approach integrates a 3D rectified flow architecture to capture complex cross-modal and cross-tracer relationships with a domain-adapted vision-language model (BiomedCLIP) that provides text-guided, personalized generation using clinical scores and imaging knowledge. Extensive evaluations on multi-center datasets demonstrate that DIReCT$++$ not only produces synthetic PET images ($^{18}$F-AV-45 and $^{18}$F-FDG) of superior fidelity and generalizability but also accurately recapitulates disease-specific patterns. Crucially, combining these synthesized PET images with MRI enables precise personalized stratification of mild cognitive impairment (MCI), advancing a scalable, data-efficient tool for the early diagnosis and prognostic prediction of AD. The source code will be released on https://github.com/ladderlab-xjtu/DIReCT-PLUS.
Chengquan Guo, Yuzhou Nie, Chulin Xie, Zinan Lin, Wenbo Guo, Bo Li
Existing research on CodeGen AI security mainly focuses on red teaming, which aims to uncover vulnerabilities and risks in AI-generated code. However, progress on the blue teaming side remains limited, as effective defenses require a deep security analysis of given tasks and edge cases. To fill in this gap, we propose BlueCodeAgent, an end-to-end blue teaming agent powered by automated red teaming. Our red teaming component generates diverse risky instances, providing effective edge cases and guidance for the subsequent blue teaming process. Our blue teaming agent then conducts multi-level defense, leveraging these red teaming examples to detect previously seen and unseen risk scenarios through constitution summarization and dynamic code analysis. Our evaluation across four representative code-related tasks (bias instruction detection, malicious instruction detection, vulnerable code detection, and prompt injection detection) shows that BlueCodeAgent achieves significant gains over diverse baselines. In particular, for vulnerability detection tasks, BlueCodeAgent integrates dynamic analysis to effectively reduce false positives, a challenging problem as base models tend to be over-conservative. Overall, with GPT-4o as the base model, BlueCodeAgent achieves an average F1 score improvement of 14.7% across four tasks compared to directly prompting the model, attributed to its ability to summarize actionable constitutions and perform dynamic analysis. Our code and data are available at https://github.com/1mocat/BlueCodeAgent.
Chengquan Guo, Chulin Xie, Yu Yang, Zhaorun Chen, Zinan Lin, Xander Davies, Yarin Gal, Dawn Song 等 9 位作者
Code agents have gained widespread adoption due to their strong code generation capabilities and integration with code interpreters, enabling dynamic execution, debugging, and interactive programming capabilities. While these advancements have streamlined complex workflows, they have also introduced critical safety and security risks. Current static safety benchmarks and red-teaming tools are inadequate for identifying emerging real-world risky scenarios, as they fail to cover certain boundary conditions, such as the combined effects of different jailbreak tools. In this work, we propose RedCodeAgent, the first automated red-teaming agent designed to systematically uncover vulnerabilities in diverse code agents. With an adaptive memory module, RedCodeAgent can leverage existing jailbreak knowledge, dynamically select the most effective red-teaming tools and tool combinations in a tailored toolbox for a given input query, thus identifying vulnerabilities that might otherwise be overlooked. For reliable evaluation, we develop simulated sandbox environments to additionally evaluate the execution results of code agents, mitigating potential biases of LLM-based judges that only rely on static code. Through extensive evaluations across multiple state-of-the-art code agents, diverse risky scenarios, and various programming languages, RedCodeAgent consistently outperforms existing red-teaming methods, achieving higher attack success rates and lower rejection rates with high efficiency. We further validate RedCodeAgent on real-world code assistants, e.g., Cursor and Codeium, exposing previously unidentified security risks. By automating and optimizing red-teaming processes, RedCodeAgent enables scalable, adaptive, and effective safety assessments of code agents. Our code and data are available at https://github.com/1mocat/RedCodeAgent.
Weicai Long, Yusen Hou The Hong Kong University of Science and Technology (Guangzhou), Junning Feng, Houcheng su Hong Kong University of Science and Technology, Shuo Yang, Donglin Xie, Yanlin Zhang The Hong Kong University of Science and Technology (Guangzhou)
Large Language Models (LLMs) are increasingly adopted as conversational assistants in genomics, where they are mainly used to reason over biological knowledge, annotations, and analysis outputs through natural language interfaces. However, existing benchmarks either focus on specialized DNA models trained for sequence prediction or evaluate biological knowledge using text-only questions, leaving the behavior of general-purpose LLMs when directly exposed to raw genome sequences underexplored. We introduce GenomeQA, a benchmark designed to provide a controlled evaluation setting for general-purpose LLMs on sequence-based genome inference tasks. GenomeQA comprises 5,200 samples drawn from multiple biological databases, with sequence lengths ranging from 6 to 1,000 base pairs (bp), spanning six task families: Enhancer and Promoter Identification, Splice Site Identification, Taxonomic Classification, Histone Mark Prediction, Transcription Factor Binding Site Prediction, and TF Motif Prediction. Across six frontier LLMs, we find that models often outperform random baselines, particularly on tasks driven by local sequence cues such as GC content and short motifs, while performance degrades on tasks that require more indirect or multi-step inference over sequence patterns. GenomeQA establishes a diagnostic benchmark for studying and improving the use of general-purpose LLMs on raw genomic sequences.
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Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表