Yinuo Xu

Songhao Li, Jonathan Xu, Tiancheng Bao et al.

Agentic AI is rapidly advancing in healthcare and biomedical research. However, in medical image analysis, their performance and adoption remain limited due to the lack of a robust ecosystem, insufficient toolsets, and the absence of real-time interactive expert feedback. Here we present "TissueLab", a co-evolving agentic AI system that allows researchers to ask direct questions, automatically plan and generate explainable workflows, and conduct real-time analyses where experts can visualize intermediate results and refine them. TissueLab integrates tool factories across pathology, radiology, and spatial omics domains. By standardizing inputs, outputs, and capabilities of diverse tools, the system determines when and how to invoke them to address research and clinical questions. Across diverse tasks with clinically meaningful quantifications that inform staging, prognosis, and treatment planning, TissueLab achieves state-of-the-art performance compared with end-to-end vision-language models (VLMs) and other agentic AI systems such as GPT-5. Moreover, TissueLab continuously learns from clinicians, evolving toward improved classifiers and more effective decision strategies. With active learning, it delivers accurate results in unseen disease contexts within minutes, without requiring massive datasets or prolonged retraining. Released as a sustainable open-source ecosystem, TissueLab aims to accelerate computational research and translational adoption in medical imaging while establishing a foundation for the next generation of medical AI.

Yinuo Xu, Shuo Lu, Jianjie Cheng et al.

Deep Research agents tackle knowledge-intensive tasks through multi-round retrieval and decision-oriented generation. While reinforcement learning (RL) has been shown to improve performance in this paradigm, its contributions remain underexplored. To fully understand the role of RL, we conduct a systematic study along three decoupled dimensions: prompt template, reward function, and policy optimization. Our study reveals that: 1) the Fast Thinking template yields greater stability and better performance than the Slow Thinking template used in prior work; 2) the F1-based reward underperforms the EM due to training collapse driven by answer avoidance; this can be mitigated by incorporating action-level penalties, ultimately surpassing EM; 3) REINFORCE outperforms PPO while requiring fewer search actions, whereas GRPO shows the poorest stability among policy optimization methods. Building on these insights, we then introduce Search-R1++, a strong baseline that improves the performance of Search-R1 from 0.403 to 0.442 (Qwen2.5-7B) and 0.289 to 0.331 (Qwen2.5-3B). We hope that our findings can pave the way for more principled and reliable RL training strategies in Deep Research systems.

Shuo Lu, Yinuo Xu, Jianjie Cheng et al.

Deep Research agents predominantly optimize search policies to maximize retrieval probability. However, we identify a critical bottleneck: the retrieval-utilization gap, where models fail to use gold evidence even after it is retrieved, due to context blindness in noisy environments. To bridge this gap, we propose DeepResearch-Slice, a simple yet effective neuro-symbolic framework. Unlike implicit attention, our approach predicts precise span indices to perform a deterministic hard filter before reasoning. Extensive evaluations across six benchmarks show substantial robustness gains. Applying our method to frozen backbones yields a 73 percent relative improvement, from 19.1 percent to 33.0 percent, effectively mitigating noise without requiring parameter updates to the reasoning model. These results highlight the need for explicit grounding mechanisms in open-ended research.

Yinuo Xu, Yan Cui, Mingyao Li et al.

Identifying cell types and subtypes in routine histopathology is fundamental for understanding disease. Existing tile-based models capture nuclear detail but miss the broader tissue context that influences cell identity. Current human annotations are coarse-grained and uneven across studies, making fine-grained, subtype-level classification difficult. In this study, we build a marker-guided dataset from Xenium spatial transcriptomics with single-cell resolution labels for more than two million cells across eight organs and 16 classes to address the lack of high-quality annotations. Leveraging this data resource, we introduce NuClass, a pathologist workflow inspired framework for cell-wise multi-scale integration of nuclear morphology and microenvironmental context. It combines Path local, which focuses on nuclear morphology from 224x224 pixel crops, and Path global, which models the surrounding 1024x1024 pixel neighborhood, through a learnable gating module that balances local and global information. An uncertainty-guided objective directs the global path to prioritize regions where the local path is uncertain, and we provide calibrated confidence estimates and Grad-CAM maps for interpretability. Evaluated on three fully held-out cohorts, NuClass achieves up to 96 percent F1 for its best-performing class, outperforming strong baselines. Our results demonstrate that multi-scale, uncertainty-aware fusion can bridge the gap between slide-level pathological foundation models and reliable, cell-level phenotype prediction.