arXiv subjects

Yuan Qi

Publications and source records attributed to Yuan Qi.

At least 37 records · Page 2Linked to original sources

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

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

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

InterveneBench: Benchmarking LLMs for Intervention Reasoning and Causal Study Design in Real Social Systems

Causal inference in social science relies on end-to-end, intervention-centered research-design reasoning grounded in real-world policy interventions, but current benchmarks fail to evaluate this capability of large language models (LLMs). We present InterveneBench, a benchmark designed to assess such reasoning in realistic social settings. Each instance in InterveneBench is derived from an empirical social science study and requires models to reason about policy interventions and identification assumptions without access to predefined causal graphs or structural equations. InterveneBench comprises 744 peer-reviewed studies across diverse policy domains. Experimental results show that state-of-the-art LLMs struggle under this setting. To address this limitation, we further propose a multi-agent framework, STRIDES. It achieves significant performance improvements over state-of-the-art reasoning models. Our code and data are available at https://github.com/Sii-yuning/STRIDES.

cs.CY↗

arXiv2026

PA-Net: Precipitation-Adaptive Mixture-of-Experts for Long-Tail Rainfall Nowcasting

Precipitation nowcasting is vital for flood warning, agricultural management, and emergency response, yet two bottlenecks persist: the prohibitive cost of modeling million-scale spatiotemporal tokens from multi-variate atmospheric fields, and the extreme long-tailed rainfall distribution where heavy-to-torrential events -- those of greatest societal impact -- constitute fewer than 0.1% of all samples. We propose the Precipitation-Adaptive Network (PA-Net), a Transformer framework whose computational budget is explicitly governed by rainfall intensity. Its core component, Precipitation-Adaptive MoE (PA-MoE), dynamically scales the number of activated experts per token according to local precipitation magnitude, channeling richer representational capacity toward the rare yet critical heavy-rainfall tail. A Dual-Axis Compressed Latent Attention mechanism factorizes spatiotemporal attention with convolutional reduction to manage massive context lengths, while an intensity-aware training protocol progressively amplifies learning signals from extreme-rainfall samples. Experiment on ERA5 demonstrate consistent improvements over state-of-the-art baselines, with particularly significant gains in heavy-rain and rainstorm regimes.

cs.AI↗

arXiv2026

SegAnyPET: Universal Promptable Segmentation from Positron Emission Tomography Images

Positron Emission Tomography (PET) is a powerful molecular imaging tool that plays a crucial role in modern medical diagnostics by visualizing radio-tracer distribution to reveal physiological processes. Accurate organ segmentation from PET images is essential for comprehensive multi-systemic analysis of interactions between different organs and pathologies. Existing segmentation methods are limited by insufficient annotation data and varying levels of annotation, resulting in weak generalization ability and difficulty in clinical application. Recent developments in segmentation foundation models have shown superior versatility across diverse segmentation tasks. Despite the efforts of medical adaptations, these works primarily focus on structural medical images with detailed physiological structural information and exhibit limited generalization performance on molecular PET imaging. In this paper, we collect and construct PETS-5k, the largest PET segmentation dataset to date, comprising 5,731 three-dimensional whole-body PET images and encompassing over 1.3M 2D images. Based on the established dataset, we develop SegAnyPET, a modality-specific 3D foundation model for universal promptable segmentation from PET images. To issue the challenge of discrepant annotation quality, we adopt a cross prompting confident learning (CPCL) strategy with an uncertainty-guided self-rectification process to robustly learn segmentation from high-quality labeled data and low-quality noisy labeled data for promptable segmentation. Experimental results demonstrate that SegAnyPET can segment seen and unseen target organs using only one or a few prompt points, outperforming state-of-the-art foundation models and task-specific fully supervised models with higher accuracy and strong generalization ability for universal segmentation.

cs.CV↗

arXiv2026

Developing Foundation Models for Universal Segmentation from 3D Whole-Body Positron Emission Tomography

Positron emission tomography (PET) is a key nuclear medicine imaging modality that visualizes radiotracer distributions to quantify in vivo physiological and metabolic processes, playing an irreplaceable role in disease management. Despite its clinical importance, the development of deep learning models for quantitative PET image analysis remains severely limited, driven by both the inherent segmentation challenge from PET's paucity of anatomical contrast and the high costs of data acquisition and annotation. To bridge this gap, we develop generalist foundational models for universal segmentation from 3D whole-body PET imaging. We first build the largest and most comprehensive PET dataset to date, comprising 11041 3D whole-body PET scans with 59831 segmentation masks for model development. Based on this dataset, we present SegAnyPET, an innovative foundational model with general-purpose applicability to diverse segmentation tasks. Built on a 3D architecture with a prompt engineering strategy for mask generation, SegAnyPET enables universal and scalable organ and lesion segmentation, supports efficient human correction with minimal effort, and enables a clinical human-in-the-loop workflow. Extensive evaluations on multi-center, multi-tracer, multi-disease datasets demonstrate that SegAnyPET achieves strong zero-shot performance across a wide range of segmentation tasks, highlighting its potential to advance the clinical applications of molecular imaging.

cs.CV↗

arXiv2026

PET-F2I: A Comprehensive Benchmark and Parameter-Efficient Fine-Tuning of LLMs for PET/CT Report Impression Generation

PET/CT imaging is pivotal in oncology and nuclear medicine, yet summarizing complex findings into precise diagnostic impressions is labor-intensive. While LLMs have shown promise in medical text generation, their capability in the highly specialized domain of PET/CT remains underexplored. We introduce PET-F2I-41K (PET Findings-to-Impression Benchmark), a large-scale benchmark for PET/CT impression generation using LLMs, constructed from over 41k real-world reports. Using PET-F2I-41K, we conduct a comprehensive evaluation of 27 models across proprietary frontier LLMs, open-source generalist models, and medical-domain LLMs, and we develop a domain-adapted 7B model (PET-F2I-7B) fine-tuned from Qwen2.5-7B-Instruct via LoRA. Beyond standard NLG metrics (e.g., BLEU-4, ROUGE-L, BERTScore), we propose three clinically grounded metrics - Entity Coverage Rate (ECR), Uncovered Entity Rate (UER), and Factual Consistency Rate (FCR) - to assess diagnostic completeness and factual reliability. Experiments reveal that neither frontier nor medical-domain LLMs perform adequately in zero-shot settings. In contrast, PET-F2I-7B achieves substantial gains (e.g., 0.708 BLEU-4) and a 3.0x improvement in entity coverage over the strongest baseline, while offering advantages in cost, latency, and privacy. Beyond this modeling contribution, PET-F2I-41K establishes a standardized evaluation framework to accelerate the development of reliable and clinically deployable reporting systems for PET/CT.

cs.CV↗

arXiv2026

The Choice of Divergence: A Neglected Key to Mitigating Diversity Collapse in Reinforcement Learning with Verifiable Reward

A central paradox in fine-tuning Large Language Models (LLMs) with Reinforcement Learning with Verifiable Reward (RLVR) is the frequent degradation of multi-attempt performance (Pass@k) despite improvements in single-attempt accuracy (Pass@1). This is often accompanied by catastrophic forgetting, where models lose previously acquired skills. While various methods have been proposed, the choice and function of the divergence term have been surprisingly unexamined as a proactive solution. We argue that standard RLVR objectives -- both those using the mode-seeking reverse KL-divergence and those forgoing a divergence term entirely -- lack a crucial mechanism for knowledge retention. The reverse-KL actively accelerates this decay by narrowing the policy, while its absence provides no safeguard against the model drifting from its diverse knowledge base. We propose a fundamental shift in perspective: using the divergence term itself as the solution. Our framework, Diversity-Preserving Hybrid RL (DPH-RL), leverages mass-covering f-divergences (like forward-KL and JS-divergence) to function as a rehearsal mechanism. By continuously referencing the initial policy, this approach forces the model to maintain broad solution coverage. Extensive experiments on math and SQL generation demonstrate that DPH-RL not only resolves the Pass@k degradation but improves both Pass@1 and Pass@k in- and out-of-domain. Additionally, DPH-RL is more training-efficient because it computes f-divergence using generator functions, requiring only sampling from the initial policy and no online reference model. Our work highlights a crucial, overlooked axis for improving RLVR, demonstrating that the proper selection of a divergence measure is a powerful tool for building more general and diverse reasoning models.

cs.LG↗

arXiv2026

AI-for-Science Low-code Platform with Bayesian Adversarial Multi-Agent Framework

Large Language Models (LLMs) demonstrate potentials for automating scientific code generation but face challenges in reliability, error propagation in multi-agent workflows, and evaluation in domains with ill-defined success metrics. We present a Bayesian adversarial multi-agent framework specifically designed for AI for Science (AI4S) tasks in the form of a Low-code Platform (LCP). Three LLM-based agents are coordinated under the Bayesian framework: a Task Manager that structures user inputs into actionable plans and adaptive test cases, a Code Generator that produces candidate solutions, and an Evaluator providing comprehensive feedback. The framework employs an adversarial loop where the Task Manager iteratively refines test cases to challenge the Code Generator, while prompt distributions are dynamically updated using Bayesian principles by integrating code quality metrics: functional correctness, structural alignment, and static analysis. This co-optimization of tests and code reduces dependence on LLM reliability and addresses evaluation uncertainty inherent to scientific tasks. LCP also streamlines human-AI collaboration by translating non-expert prompts into domain-specific requirements, bypassing the need for manual prompt engineering by practitioners without coding backgrounds. Benchmark evaluations demonstrate LCP's effectiveness in generating robust code while minimizing error propagation. The proposed platform is also tested on an Earth Science cross-disciplinary task and demonstrates strong reliability, outperforming competing models.

cs.AI↗

arXiv2026

A Sensitivity Analysis of the Surrogate Index Approach for Estimating Long-Term Treatment Effects

This paper develops a sensitivity analysis of the surrogacy assumption for the surrogate index approach in Athey et al. [2025b]. We introduce "Weighted Surrogate Indices (WSIs)," the analog of the surrogate index under the surrogacy assumption. We show that under comparability, the ATE on WSI identifies the ATE on the long-term outcome when a copula of the treatment and the long-term outcome conditional on baseline covariates and surrogates is known. When the copula is unknown, we establish the identified set of the ATE on the long-term outcome. Furthermore, we construct debiased estimators of the ATE for any given copula and develop asymptotically valid inference in both point-identified and partially identified cases. Using data from a poverty alleviation program in Pakistan, we demonstrate the importance of sensitivity checks as well as the usefulness of our approach.

econ.EM↗

arXiv2026

Structure-based RNA Design by Step-wise Optimization of Latent Diffusion Model

RNA inverse folding, designing sequences to form specific 3D structures, is critical for therapeutics, gene regulation, and synthetic biology. Current methods, focused on sequence recovery, struggle to address structural objectives like secondary structure consistency (SS), minimum free energy (MFE), and local distance difference test (LDDT), leading to suboptimal structural accuracy. To tackle this, we propose a reinforcement learning (RL) framework integrated with a latent diffusion model (LDM). Drawing inspiration from the success of diffusion models in RNA inverse folding, which adeptly model complex sequence-structure interactions, we develop an LDM incorporating pre-trained RNA-FM embeddings from a large-scale RNA model. These embeddings capture co-evolutionary patterns, markedly improving sequence recovery accuracy. However, existing approaches, including diffusion-based methods, cannot effectively handle non-differentiable structural objectives. By contrast, RL excels in this task by using policy-driven reward optimization to navigate complex, non-gradient-based objectives, offering a significant advantage over traditional methods. In summary, we propose the Step-wise Optimization of Latent Diffusion Model (SOLD), a novel RL framework that optimizes single-step noise without sampling the full diffusion trajectory, achieving efficient refinement of multiple structural objectives. Experimental results demonstrate SOLD surpasses its LDM baseline and state-of-the-art methods across all metrics, establishing a robust framework for RNA inverse folding with profound implications for biotechnological and therapeutic applications.

cs.LG↗

arXiv2026

A Pre-trained Reaction Embedding Descriptor Capturing Bond Transformation Patterns

With the rise of data-driven reaction prediction models, effective reaction descriptors are crucial for bridging the gap between real-world chemistry and digital representations. However, general-purpose, reaction-wise descriptors remain scarce. This study introduces RXNEmb, a novel reaction-level descriptor derived from RXNGraphormer, a model pre-trained to distinguish real reactions from fictitious ones with erroneous bond changes, thereby learning intrinsic bond formation and cleavage patterns. We demonstrate its utility by data-driven re-clustering of the USPTO-50k dataset, yielding a classification that more directly reflects bond-change similarities than rule-based categories. Combined with dimensionality reduction, RXNEmb enables visualization of reaction space diversity. Furthermore, attention weight analysis reveals the model's focus on chemically critical sites, providing mechanistic insight. RXNEmb serves as a powerful, interpretable tool for reaction fingerprinting and analysis, paving the way for more data-centric approaches in reaction analysis and discovery.

cs.LG↗

arXiv2025

CTkvr: KV Cache Retrieval for Long-Context LLMs via Centroid then Token Indexing

Large language models (LLMs) are increasingly applied in long-context scenarios such as multi-turn conversations. However, long contexts pose significant challenges for inference efficiency, including high memory overhead from Key-Value (KV) cache and increased latency due to excessive memory accesses. Recent methods for dynamic KV selection struggle with trade-offs: block-level indexing degrades accuracy by retrieving irrelevant KV entries, while token-level indexing incurs high latency from inefficient retrieval mechanisms. In this paper, we propose CTKVR, a novel centroid-then-token KV retrieval scheme that addresses these limitations. CTKVR leverages a key observation: query vectors adjacent in position exhibit high similarity after Rotary Position Embedding (RoPE) and share most of their top-k KV cache entries. Based on this insight, CTKVR employs a two-stage retrieval strategy: lightweight centroids are precomputed during prefilling for centroid-grained indexing, followed by token-level refinement for precise KV retrieval. This approach balances retrieval efficiency and accuracy. To further enhance performance, we implement an optimized system for indexing construction and search using CPU-GPU co-execution. Experimentally, CTKVR achieves superior performance across multiple benchmarks with less than 1% accuracy degradation. Meanwhile, CTKVR delivers 3 times and 4 times throughput speedups on Llama-3-8B and Yi-9B at 96K context length across diverse GPU hardware.

cs.CL↗

arXiv2025

Harnessing Negative Signals: Reinforcement Distillation from Teacher Data for LLM Reasoning

Recent advances in model distillation show that data from advanced reasoning models can effectively train smaller student models. However, standard practices discard incorrect reasoning traces -- valuable, yet underutilized data. This paper addresses the critical question: How can both positive and negative distilled reasoning traces be effectively leveraged to maximize LLM reasoning performance in an offline setting? We employ a two-stage training recipe: first, Supervised Fine-Tuning (SFT) on positive traces, followed by a refinement stage using both positive and negative traces. We find that a simple REINFORCE-style objective, which we term the Reinforcement Distillation (REDI) objective, outperforms established preference optimization methods like DPO and SimPO in this distillation context. Our empirical evaluations demonstrate the effectiveness of this approach. Notably, our Qwen-REDI-1.5B model, trained on just 131k traces from the open Open-R1 dataset, achieves an 83.1% score on MATH-500. Its performance matches that of DeepSeek-R1-Distill-Qwen-1.5B, a model trained on 800k proprietary data. This result showcases the remarkable data efficiency of utilizing previously discarded negative traces.

cs.LG↗