arXiv subjects

Yuan Qi

Publications and source records attributed to Yuan Qi.

At least 19 recordsLinked to original sources

arXiv2026

MetaStructAtlas: A Grounded 3D Vision-Language Dataset and Benchmark for Functional and Structural Reasoning in Whole-Body PET/CT

The joint interpretation of metabolic function and anatomical structure is essential for clinical diagnosis in whole-body PET/CT. Although recent advances in 3D medical vision-language models have demonstrated remarkable progress, current efforts are limited to regional CT imaging, leaving a critical void in comprehensive whole-body PET/CT analysis. In this work, we introduce MetaStructAtlas, a large-scale dataset for grounded whole-body PET/CT interpretation that synthesizes multimodal imaging with integrated anatomical, metabolic, and semantic annotations. MetaStructAtlas provides 490 co-registered 3D PET and CT volumes with 50,470 organ-level segmentation masks and grounded radiology reports. To facilitate interactive reasoning, we further developed MetaStructVQA, a standardized 3D grounded visual question-answering benchmark containing 100,565 QA pairs. This framework explicitly links diagnostic queries to visual evidence across modalities, encompassing anatomical, morphological, and metabolic characteristics. Finally, we evaluate state-of-the-art 3D medical VLMs on MetaStructVQA, establishing a robust foundation for multimodal representation learning and integrated whole-body reasoning in nuclear medicine.

cs.CV↗

arXiv2026

Unfolding the Interdisciplinary Complexities of Climate Science: Fuxi-Climate Foundational Model

Climate research and decision-making require integrating evidence across physical processes, socio-economic dynamics and policy responses. Large language models (LLMs) have been explored for accessing and synthesizing climate knowledge, but their ability to support structured interdisciplinary reasoning is still limited. Here we present the Fuxi-Climate Foundation Model (CFM), a climate-specialized LLM designed to support consistent reasoning across domains. CFM maintains more stable analytical behavior as interdisciplinary complexity increases, whereas performance in other models becomes more variable. On expert-designed climate transition tasks, CFM produces more structured analyses that explicitly address trade-offs and uncertainty, achieving 45% trade-off coverage and 47.27% uncertainty-aware reasoning. These results indicate that CFM can support more realistic analysis of climate risks and transition pathways, and provide a basis for agent-based systems to explore complex policy and decision scenarios. The model is openly available at https://huggingface.co/SII-yuning/cfm.

cs.CY↗

arXiv2026

Start Classifying: Categorical Critics for LLM Reinforcement Learning

Proximal Policy Optimization (PPO) for large language models typically trains its critic by mean-squared-error (MSE) regression on scalar value targets. Although scalar MSE is statistically valid for estimating the conditional expected return, sparse binary rewards in reinforcement learning with verifiable rewards (RLVR) make critic optimization and calibration especially consequential: small value errors directly distort the scalar advantages used by PPO. We study whether a classification-based training objective can improve this critic signal. HL-Gauss PPO replaces the scalar MSE head with a categorical predictor over a discretized value support, trained by cross-entropy against smoothed HL-Gauss targets. Its output is decoded to a scalar expectation for standard GAE and PPO; the actor update is therefore unchanged and is not distributional. Across mathematical reasoning, tool-augmented math, and Search-R1, and on both Qwen2.5 and Qwen3 backbones, HL-Gauss PPO consistently improves over strong PPO and DAPO baselines. Controls with one-hot, two-hot, and Bernoulli two-bin critics show that neither a larger output head nor binary classification alone explains the gains. On a common collection of reasoning prefixes, HL-Gauss improves Brier score and calibration error and yields more symmetric, lower-variance advantages. These results position categorical value learning as an effective optimization surrogate for PPO critics in RLVR.

cs.LG↗

arXiv2026

Monkey King Bang: A Unified Scientific Multimodal Foundation Model

Scientific discovery is increasingly shifting from isolated disciplines to multi-domain reasoning, and AI for science faces a similar transition. Existing systems are either specialised for individual domains or unify scientific data mainly through text tokenisation and prompt-based interfaces, limiting their ability to handle diverse scientific inputs, produce modality-native outputs, and support joint understanding, reasoning, and generation across scientific domains. We introduce MKB, a unified scientific multimodal model for both understanding and generation, built around a shared Transformer backbone and modality-tailored encoders, adapters, and decoders. MKB covers six scientific branches, including DNA, RNA, proteins, small molecules, earth science, and medical images, and supports native outputs such as biological sequences, molecular strings, meteorological fields, and segmentation masks. Training follows a two-stage modality-then-language curriculum: Stage 1 aligns modality-specific components with the frozen backbone, and Stage 2 consolidates them with the language backbone using mixed scientific and general corpora. Experiments show that MKB achieves competitive scientific understanding across biological and molecular benchmarks, produces high-fidelity native outputs for weather forecasting, biological generation, and medical-image segmentation, and largely retains the general capabilities of its Qwen3-VL backbone. These results demonstrate the feasibility of the proposed paradigm, suggesting that shared-backbone models with modality-tailored components can provide a promising foundation for future cross-domain scientific multimodal exploration. The model and code are publicly available at https://github.com/Shanghai-Academy-of-AI-For-Science/MKB and https://huggingface.co/sais-org/MKB.

cs.LG↗

arXiv2026

DyneTrion: A Spatio-temporally Coherent Generative Emulator for Protein Dynamics Across Timescales

Proteins function through coordinated motion across multiple spatial and temporal scales, underpinning processes such as ligand binding, allostery, and catalysis. However, accessing long-timescale conformational change through molecular dynamics (MD) simulations remains prohibitively expensive for systematic exploration across diverse systems. Here, we present DyneTrion, a generative protein dynamics emulator that jointly enforces geometric symmetry, structural consistency and temporal coherence within a single framework. DyneTrion uses a tri-attention architecture that integrates invariant point attention (IPA) for SE(3)-robust geometric updates, spatial attention anchored to a reference conformation to preserve structural integrity, and temporal attention to model correlated evolution across time frames. Across 100-ns MD trajectory simulation benchmarks, DyneTrion reproduces MD-derived flexibility, ensemble distributions and interaction observables while maintaining stereochemical validity during extrapolation. To evaluate long time-scale generalization, we introduce dynamicPDB, a dataset of over 10,000 proteins with up to 1-$\mu$s all-atom trajectories at 10-ps resolution and accompanying physical annotations. On microsecond trajectories, DyneTrion preserves free-energy landscapes and metastable-state populations, and it supports large conformational propagation in apo-to-holo transitions and fast folders. Together, DyneTrion provides a scalable path from static structure prediction toward time-resolved, ensemble-faithful protein modeling. The code is publicly available at https://github.com/fudan-generative-vision/DyneTrion

q-bio.QM↗

arXiv2026

Infinity-Parser2 Technical Report

We present Infinity-Parser2, a large multimodal model that couples a controllable data-synthesis pipeline with multi-task reinforcement learning for end-to-end document parsing, addressing the persistent scarcity of faithfully annotated parsing corpora. Our contributions are threefold. First, we build a scalable synthesis engine, pairing a controllable rendering framework with an iterative refinement loop, and use it to construct and open-source Infinity-Doc2-5M: a 5-million-sample bilingual (Chinese/English) corpus spanning diverse document types, annotated with element bounding boxes, canonical content forms (Markdown, HTML, LaTeX, SMILES, structured charts), and full-page reading order. Second, we introduce a verifiable, multi-task reward system that enables Joint Reinforcement Learning across eight co-trained objectives (document parsing, layout analysis, table parsing, math formula parsing, chart parsing, chemical formula parsing, document VQA, and general multimodal understanding), unifying perception, structure, and reasoning in a single optimization signal. Third, we release two variants under a shared architecture: Infinity-Parser2-Flash, optimized for low-latency inference with a 3.68x throughput gain over Infinity-Parser-7B, and Infinity-Parser2-Pro, engineered for precision-critical settings. Infinity-Parser2-Pro reaches state-of-the-art 87.6% on olmOCR-Bench and 74.3% on ParseBench, surpassing DeepSeek-OCR-2, PaddleOCR-VL-1.5, and MinerU2.5, with strong generalization to charts, chemical formulas, and document VQA.

cs.AI↗

arXiv2026

Internalizing the Future: A Unified Agentic Training Paradigm for World Model Planning

Large language model (LLM) agents have demonstrated strong capability in sequential decision-making, yet they remains fundamentally reactive in long-horizon tasks. Unlike humans who employ "what-if" reasoning to evaluate potential plans before commitment, standard agents lack an internal world model to simulate future outcomes. Therefore, we propose to internalize future-aware planning by training a single autoregressive model to verbalize both a prospective state rollout and a plan-conditioned success estimate-a textual analogue of the Q-value. Crucially, we identify a format-capability gap: simply fine-tuning agents on look-ahead traces during post-training leads to superficial mimicry of foresight without genuine predictive grounding. To bridge this gap, we introduce a three-stage training paradigm: (i) World Model Agentic Mid-Training (WM-AMT) to inject latent predictive capabilities into the policy; (ii) Format-Eliciting SFT (FE-SFT) to structure this injected capability; and (iii) Foresight-Conditioned Reinforcement Learning (FC-RL) to refine the calibration and utility of the generated simulations. Evaluated on search and mathematical reasoning tasks, our approach consistently outperforms other training baselines. Our results demonstrate that effective internal world modeling in LLM agents requires a capability-first training pipeline to achieve grounded and calibrated foresight.

cs.AI↗

arXiv2026

Learning Implicit Bias in Generative Spaces for Accelerating Protein Dynamics Emulation

Generative emulators of protein dynamics produce plausible trajectories at a fraction of the cost of molecular dynamics, but they inherit their training distribution and tend to revisit known states rather than reach rare ones under long-horizon extrapolation. Inspired by classical enhanced sampling, we introduce an implicit, history-dependent bias in the generative space of a pretrained emulator. Specifically, a history-aware score estimator augments the frozen emulator with a distance-weighted bias that steers reverse-time sampling away from previously generated structures, regularized by an environment-support term. To preserve structural validity at long horizons, a score-based refinement step re-projects drifted samples onto the data manifold using the frozen emulator. Our experiments demonstrate that the method (i) raises diversity by $35\%$ on DynamicPDB-80; (ii) on $12$ zero-shot Fast-Folding proteins, the learned bias alone reaches the unbiased emulator's coverage up to ${\sim}15\times$ faster, and pairing it with refinement reaches the coverage up to ${\sim}37\times$ faster while covering ${\sim}3\times$ as many low-energy states. Code will be released soon.

cs.LG↗

arXiv2026

Nested Spatio-Temporal Time Series Forecasting

Spatiotemporal forecasting is critical for real-world applications like traffic management, yet capturing reliable interactions remains challenging under noisy and non-stationary conditions. Existing methods primarily rely on historical spatial priors, often failing to account for evolving temporal correlations and suffering from systematic errors. In this work, we propose a nested forecasting framework that couples future macro-level regional trends with micro-level historical observations, enabling top-down guidance from abstract future representations for fine-grained forecasting. Specifically, we employ a spectral clustering-based approach to construct semantically coherent regions, providing both theoretical and empirical evidence that this representation effectively filters systematic noise while preserving essential trends. Building on this, we develop a progressive coarse-to-fine predictor to integrate these representative features into the inference process. This enables the model to leverage trend predictions to anticipate dynamic anomalies, such as periodic offsets, in advance. Furthermore, extensive experiments on multiple high-dimensional datasets demonstrate that our method consistently outperforms state-of-the-art baselines, validating the effectiveness of future macro-guided nested forecasting.

cs.LG↗

arXiv2026

FLAG: Foundation model representation with Latent diffusion Alignment via Graph for spatial gene expression prediction

Predicting spatial gene expression from routine H\&E enables large-scale molecular profiling, yet current models treat this as isolated pointwise tasks, thereby overlooking essential biological structures like gene coordination and spatial distribution. To preserve these relationships, we introduce \textbf{FLAG}, a diffusion-based framework that redefines this task as structured distribution modeling. At the same time, we identify the critical \textbf{Gene Dimension Curse}, where joint modeling gene expression and their spatial interactions fail in high-dimensional spaces, and FLAG solves this challenge by integrating a spatial graph encoder for topological consistency and utilizing Gene Foundation Model (GFM) alignment for gene-gene fidelity in the generation process. To rigorously assess model performance, we propose a set of novel structural evaluation metrics, including Gene Structural Correlation (\textbf{GSC}) and Spatial Structural Correlation (\textbf{SSC}). Our experiments demonstrate that FLAG is highly competitive in traditional accuracy (PCC/MSE) while achieving significantly enhanced structural fidelity in capturing both gene-gene and gene-spatial relationships. The code is available at https://github.com/darkflash03/FLAG.

cs.LG↗

arXiv2026

Suiren-1.0 Technical Report: A Family of Molecular Foundation Models

We introduce Suiren-1.0, a family of molecular foundation models for the accurate modeling of diverse organic systems. Suiren-1.0 comprising three specialized variants (Suiren-Base, Suiren-Dimer, and Suiren-ConfAvg) is integrated within an algorithmic framework that bridges the gap between 3D conformational geometry and 2D statistical ensemble spaces. We first pre-train Suiren-Base (1.8B parameters) on a 70M-sample Density Functional Theory dataset using spatial self-supervision and SE(3)-equivariant architectures, achieving robust performance in quantum property prediction. Suiren-Dimer extends this capability through continued pre-training on 13.5M intermolecular interaction samples. To enable efficient downstream application, we propose Conformation Compression Distillation (CCD), a diffusion-based framework that distills complex 3D structural representations into 2D conformation-averaged representations. This yields the lightweight Suiren-ConfAvg, which generates high-fidelity representations from SMILES or molecular graphs. Our extensive evaluations demonstrate that Suiren-1.0 establishes state-of-the-art results across a range of tasks. All models and benchmarks are open-sourced.

physics.chem-ph↗

arXiv2026

ReTokSync: Self-Synchronizing Tokenization Disambiguation for Generative Linguistic Steganography

Generative linguistic steganography (GLS) enables covert communication by embedding secret messages into the natural language generation process. In practical deployment, however, GLS is vulnerable to tokenization ambiguity: the same surface text may be re-tokenized into a different token sequence at the receiver, breaking the shared decoding state between the communicating parties so that a single local mismatch can propagate into complete extraction failure. Existing solutions either remove ambiguous tokens -- distorting the generation distribution and compromising security -- or preserve the distribution at the cost of substantially reduced embedding capacity or prohibitive runtime overhead. To address this issue, we propose ReTokSync (Re-Tokenization Synchronization), a self-synchronizing disambiguation framework that monitors the receiver-view tokenization during generation and triggers a corrective reset only when ambiguity actually occurs. By confining the effect of tokenization ambiguity to sparse residual bit errors rather than global desynchronization, ReTokSync leaves ambiguity-free positions entirely untouched and remains compatible with the underlying steganographic algorithm. Experiments on both English and Chinese settings show that ReTokSync stays closest to the steganographic baseline in distributional security (zero KL divergence), text quality, embedding capacity, and runtime, while achieving extraction accuracy above 99.7\%. Building on this property, we further develop a two-channel covert communication mechanism in which ReTokSync serves as the primary channel and a reliable auxiliary channel corrects the remaining errors, achieving 100\% end-to-end recovery across all evaluated configurations.

cs.CR↗

arXiv2026

SemiSAM-O1: Pushing the Boundary of Annotation-Efficient Medical Image Segmentation with Generalist Knowledge Fusion

Semi-supervised learning (SSL) has become a promising solution to alleviate the annotation burden of deep learning-based medical image segmentation models. While recent advances in foundation model-driven SSL have pushed the boundary to extremely limited annotation scenarios, they fail to maintain robust competitive performance in complex imaging modalities. In this paper, we propose SemiSAM-O1, an annotation-efficient framework using only one annotated template case for segmentation. SemiSAM-O1 extends the specialist-generalist collaborative learning framework to the extreme one-label setting by fully exploiting the foundation model's feature representation capability beyond its prompting interface. SemiSAM-O1 operates in two stages. In the first stage, the foundation model's encoder extracts dense features from all volumes, and class prototypes derived from the single annotated template are propagated to the unlabeled pool via feature similarity to produce coarse initial pseudo-labels. In the second stage, an iterative training-and-refinement loop progressively improves both the segmentation model and the pseudo-labels over multiple rounds, where each round trains the model from scratch on current pseudo-labels and generates updated predictions with voxel-wise uncertainty estimates. An uncertainty-guided refinement step further leverages the foundation model's global feature space to correct high-uncertainty regions by aggregating labels from their most similar confident neighbors, establishing a virtuous cycle of mutual improvement. Extensive experiments on a wide range of segmentation tasks across different modalities and anatomical targets demonstrate that SemiSAM-O1 significantly narrows the performance gap between one-label semi-supervised learning and full supervision, while significantly reducing the computational overhead of online foundation model inference.

cs.CV↗

arXiv2026

Equivariant Asynchronous Diffusion: An Adaptive Denoising Schedule for Accelerated Molecular Conformation Generation

Recent 3D molecular generation methods primarily use asynchronous auto-regressive or synchronous diffusion models. While auto-regressive models build molecules sequentially, they're limited by a short horizon and a discrepancy between training and inference. Conversely, synchronous diffusion models denoise all atoms at once, offering a molecule-level horizon but failing to capture the causal relationships inherent in hierarchical molecular structures. We introduce Equivariant Asynchronous Diffusion (EAD) to overcome these limitations. EAD is a novel diffusion model that combines the strengths of both approaches: it uses an asynchronous denoising schedule to better capture molecular hierarchy while maintaining a molecule-level horizon. Since these relationships are often complex, we propose a dynamic scheduling mechanism to adaptively determine the denoising timestep. Experimental results show that EAD achieves state-of-the-art performance in 3D molecular generation.

cs.LG↗

arXiv2026

Evaluation of Winning Solutions of 2025 Low Power Computer Vision Challenge

The IEEE Low-Power Computer Vision Challenge (LPCVC) aims to promote the development of efficient vision models for edge devices, balancing accuracy with constraints such as latency, memory capacity, and energy use. The 2025 challenge featured three tracks: (1) Image classification under various lighting conditions and styles, (2) Open-Vocabulary Segmentation with Text Prompt, and (3) Monocular Depth Estimation. This paper presents the design of LPCVC 2025, including its competition structure and evaluation framework, which integrates the Qualcomm AI Hub for consistent and reproducible benchmarking. The paper also introduces the top-performing solutions from each track and outlines key trends and observations. The paper concludes with suggestions for future computer vision competitions.

cs.CV↗

arXiv2026

ChemAmp: Amplified Chemistry Tools via Composable Agents

Although LLM-based agents are proven to master tool orchestration in scientific fields, particularly chemistry, their single-task performance remains limited by underlying tool constraints. To this end, we propose tool amplification, a novel paradigm that enhances the collective capabilities of specialized tools through optimized, dynamic coordination within individual tasks. Instantiating this paradigm, we introduce ChemAmp, a computationally lightweight framework that dynamically treats chemistry tools (e.g., UniMol2, Chemformer) as composable building-block agents. It constructs task-specialized super-agents that transcend atomic tool constraints with limited data ($\leq$10 samples). Our evaluations across four core chemistry tasks molecular design, molecule captioning, reaction prediction, and property prediction demonstrate that ChemAmp outperforms chemistry-specialized models, generalist LLMs, and agent systems with tool orchestration. Critically, this bottom-up construction strategy enables 94\% inference token cost reductions versus vanilla multi-agent systems.

cs.LG↗

arXiv2026

Project and Generate: Divergence-Free Neural Operators for Incompressible Flows

Learning-based models for fluid dynamics often operate in unconstrained function spaces, leading to physically inadmissible, unstable simulations. While penalty-based methods offer soft regularization, they provide no structural guarantees, resulting in spurious divergence and long-term collapse. In this work, we introduce a unified framework that enforces the incompressible continuity equation as a hard, intrinsic constraint for both deterministic and generative modeling. First, to project deterministic models onto the divergence-free subspace, we integrate a differentiable spectral Leray projection grounded in the Helmholtz-Hodge decomposition, which restricts the regression hypothesis space to physically admissible velocity fields. Second, to generate physically consistent distributions, we show that simply projecting model outputs is insufficient when the prior is incompatible. To address this, we construct a divergence-free Gaussian reference measure via a curl-based pushforward, ensuring the entire probability flow remains subspace-consistent by construction. Experiments on 2D Navier-Stokes equations demonstrate exact incompressibility up to discretization error and substantially improved stability and physical consistency.

cs.LG↗

arXiv2026

DyJR: Preserving Diversity in Reinforcement Learning with Verifiable Rewards via Dynamic Jensen-Shannon Replay

While Reinforcement Learning (RL) enhances Large Language Model reasoning, on-policy algorithms like GRPO are sample-inefficient as they discard past rollouts. Existing experience replay methods address this by reusing accurate samples for direct policy updates, but this often incurs high computational costs and causes mode collapse via overfitting. We argue that historical data should prioritize sustaining diversity rather than simply reinforcing accuracy. To this end, we propose Dynamic Jensen-Shannon Replay (DyJR), a simple yet effective regularization framework using a dynamic reference distribution from recent trajectories. DyJR introduces two innovations: (1) A Time-Sensitive Dynamic Buffer that uses FIFO and adaptive sizing to retain only temporally proximal samples, synchronizing with model evolution; and (2) Jensen-Shannon Divergence Regularization, which replaces direct gradient updates with a distributional constraint to prevent diversity collapse. Experiments on mathematical reasoning and Text-to-SQL benchmarks demonstrate that DyJR significantly outperforms GRPO as well as baselines such as RLEP and Ex-GRPO, while maintaining training efficiency comparable to the original GRPO. Furthermore, from the perspective of Rank-$k$ token probability evolution, we show that DyJR enhances diversity and mitigates over-reliance on Rank-1 tokens, elucidating how specific sub-modules of DyJR influence the training dynamics.

cs.LG↗