Yinuo Xu

Shuo Lu, Yinuo Xu, Kecheng Yu et al.

Large language models (LLMs) are increasingly asked not only to write static interfaces, but to construct executable interactive worlds from natural language. Browser-native 3D, commonly built with Three.js, is a natural next frontier: generated programs must integrate assets, obey spatial and physical constraints, and keep user-facing controls synchronized with hidden runtime state. Existing web-generation benchmarks and evaluators, however, largely observe only pixels or DOM nodes, while the mechanics of a Three.js world unfold inside an opaque <canvas>. We introduce WorldCoder-Bench, a benchmark for autonomous, physically grounded 3D world synthesis. WorldCoder-Bench contains 2,026 expert-curated tasks across Simulation, Rendering, and Application scenarios, with optional .glb assets and hidden behavioral contracts. We further propose StateProbe, an execution-based protocol that probes generated programs in a sandboxed browser and verifies hidden, mutation-hardened contracts over runtime states and transitions. Beyond verification coverage, we report Return on Automation and Time Efficiency Multiplier to measure correctness-adjusted cost and time savings. Across nine frontier models, the best system reaches only 27.8% verification coverage on WorldCoder-Core and 19.9% on WorldCoder-Robust, with failures dominated by state-schema drift and broken interaction chains rather than missing scene elements. Utility metrics further show that cheap or fast models can still provide substantial value on easier domains. WorldCoder-Bench is available at https://anonymous.4open.science/r/WorldCoder-Bench/.

Mufan Qiu, Genhui Zheng, Yinuo Xu et al.

Predicting how a cell will change its transcriptional state under a developmental signal or a genetic perturbation is the computational core of in-silico biology and the AI Virtual Cell program. Existing approaches either fit static control-to-treated maps that discard time, or solve multi-step ODE / Schrödinger-bridge problems on each dataset independently. We introduce Chreode, a one-step cell world model that predicts action-conditioned cell-state transitions through a structured residual transition operator. It shifts distributional evolution from inference time to training time, enabling single-pass generation while preserving a Waddington-inspired decomposition into downhill landscape flow, rotational in-tangent dynamics, and stochastic spread. The model is pretrained with a shared scVI encoder and a DiT-based dynamics backbone on a 2.4M-cell mouse embryonic atlas spanning 7 datasets. As a fine-tuning initialization, Chreode improves per-target Sinkhorn distance on Weinreb hematopoiesis and Veres islet differentiation over matched scratch models, PI-SDE, and PRESCIENT. As a transferable gene-state embedding for GEARS, the pretrained dynamics representation reduces shared-vocabulary DE20 mean squared error on Norman Perturb-seq from 0.2121 to 0.1858, a 12.4% relative improvement, without changing the GEARS training procedure. We interpret this transfer to perturbation prediction as evidence that pretrained developmental-trajectory dynamics encode differentiation primitives transferable to CRISPR-induced state shifts, since both involve cell-state transitions in a shared latent geometry. The pretrained backbone additionally produces zero-shot clonal fate scores on Weinreb that are competitive with strong dynamic-OT baselines.

Shuo Lu, Jianjie Cheng, Yinuo Xu et al.

Multimodal large language models (MLLMs) have achieved strong performance on perception-oriented tasks, yet their ability to perform mathematical spatial reasoning, defined as the capacity to parse and manipulate two- and three-dimensional relations, remains unclear. Humans easily solve textbook-style spatial reasoning problems with over 95\% accuracy, but we find that most leading MLLMs fail to reach even 60\% on the same tasks. This striking gap highlights spatial reasoning as a fundamental weakness of current models. To investigate this gap, we present MathSpatial, a unified framework for evaluating and improving spatial reasoning in MLLMs. MathSpatial includes three complementary components: (i) MathSpatial-Bench, a benchmark of 2K problems across three categories and eleven subtypes, designed to isolate reasoning difficulty from perceptual noise; (ii) MathSpatial-Corpus, a training dataset of 8K additional problems with verified solutions; and (iii) MathSpatial-SRT, which models reasoning as structured traces composed of three atomic operations--Correlate, Constrain, and Infer. Experiments show that fine-tuning Qwen2.5-VL-7B on MathSpatial achieves competitive accuracy while reducing tokens by 25\%. MathSpatial provides the first large-scale resource that disentangles perception from reasoning, enabling precise measurement and comprehensive understanding of mathematical spatial reasoning in MLLMs.

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.

Yinuo Xu, David Jurgens

Annotator disagreement is widespread in NLP, particularly for subjective and ambiguous tasks such as toxicity detection and stance analysis. While early approaches treated disagreement as noise to be removed, recent work increasingly models it as a meaningful signal reflecting variation in interpretation and perspective. This survey provides a unified view of disagreement-aware NLP methods. We first present a domain-agnostic taxonomy of the sources of disagreement spanning data, task, and annotator factors. We then synthesize modeling approaches using a common framework defined by prediction targets and pooling structure, highlighting a shift from consensus learning toward explicitly modeling disagreement, and toward capturing structured relationships among annotators. We review evaluation metrics for both predictive performance and annotator behavior, and noting that most fairness evaluations remain descriptive rather than normative. We conclude by identifying open challenges and future directions, including integrating multiple sources of variation, developing disagreement-aware interpretability frameworks, and grappling with the practical tradeoffs of perspectivist modeling.

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.

Yongcan Yu, Lingxiao He, Shuo Lu et al.

Recent advances in vision-language models (VLMs) reasoning have been largely attributed to the rise of reinforcement Learning (RL), which has shifted the community's focus away from the supervised fine-tuning (SFT) paradigm. Many studies suggest that introducing the SFT stage not only fails to improve reasoning ability but may also negatively impact model training. In this study, we revisit this RL-centric belief through a systematic and controlled comparison of SFT and RL on VLM Reasoning. Using identical data sources, we find that the relative effectiveness of SFT and RL is conditional and strongly influenced by model capacity, data scale, and data distribution. Contrary to common assumptions, our findings show that SFT plays a crucial role across several scenarios: (1) Effectiveness for weaker models. SFT more reliably elicits reasoning capabilities in smaller or weaker VLMs. (2) Data efficiency. SFT with only 2K achieves comparable or better reasoning performance to RL with 20K. (3) Cross-modal transferability. SFT demonstrates stronger generalization across modalities. Moreover, we identify a pervasive issue of deceptive rewards, where higher rewards fail to correlate with better reasoning accuracy in RL. These results challenge the prevailing "RL over SFT" narrative. They highlight that the role of SFT may have been underestimated and support a more balanced post-training pipeline in which SFT and RL function as complementary components.

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.

Xingyu Fu, Siyi Liu, Yinuo Xu et al.

Can humans identify AI-generated (fake) videos and provide grounded reasons? While video generation models have advanced rapidly, a critical dimension -- whether humans can detect deepfake traces within a generated video, i.e., spatiotemporal grounded visual artifacts that reveal a video as machine generated -- has been largely overlooked. We introduce DeeptraceReward, the first fine-grained, spatially- and temporally- aware benchmark that annotates human-perceived fake traces for video generation reward. The dataset comprises 4.3K detailed annotations across 3.3K high-quality generated videos. Each annotation provides a natural-language explanation, pinpoints a bounding-box region containing the perceived trace, and marks precise onset and offset timestamps. We consolidate these annotations into 9 major categories of deepfake traces that lead humans to identify a video as AI-generated, and train multimodal language models (LMs) as reward models to mimic human judgments and localizations. On DeeptraceReward, our 7B reward model outperforms GPT-5 by 34.7% on average across fake clue identification, grounding, and explanation. Interestingly, we observe a consistent difficulty gradient: binary fake v.s. real classification is substantially easier than fine-grained deepfake trace detection; within the latter, performance degrades from natural language explanations (easiest), to spatial grounding, to temporal labeling (hardest). By foregrounding human-perceived deepfake traces, DeeptraceReward provides a rigorous testbed and training signal for socially aware and trustworthy video generation.

Yinuo Xu, Veronica Derricks, Allison Earl et al.

We present an approach to modeling annotator disagreement in subjective NLP tasks through both architectural and data-centric innovations. Our model, DEM-MoE (Demographic-Aware Mixture of Experts), routes inputs to expert subnetworks based on annotator demographics, enabling it to better represent structured, group-level variation compared to prior models. DEM-MoE consistently performs competitively across demographic groups, and shows especially strong results on datasets with high annotator disagreement. To address sparse demographic coverage, we test whether LLM-generated synthetic annotations via zero-shot persona prompting can be used for data imputation. We show these synthetic judgments align moderately well with human annotations on our data and offer a scalable way to potentially enrich training data. We then propose and evaluate approaches for blending real and synthetic data using strategies tailored to dataset structure. We find that the optimal strategies depend on dataset structure. Together, these contributions improve the representation of diverse perspectives.