arXiv subjects

Zonglin Yang

Publications and source records attributed to Zonglin Yang.

At least 19 recordsLinked to original sources

arXiv2026

UOT-Gap: A Variational Principle for the Modality Gap in Vision-Language Models via Unbalanced Optimal Transport

Vision-language models such as CLIP embed images and text in a shared space, where modality-specific distributions often remain separated. Existing accounts connect this modality gap to initialization, contrastive dynamics, and information imbalance, while its distributional and pairwise contributions to retrieval remain unresolved. We introduce UOT-Gap, a training-free variational diagnostic that models frozen image and text embeddings with unbalanced entropic optimal transport (UOT). The UOT optimum separates transport, coupling complexity, and marginal mass variation; a complementary pair-aware residual compares observed image-caption pairs with the UOT soft matching. On Flickr8K and COCO-1K with frozen CLIP, OpenCLIP, and SigLIP encoders, caption degradation reduces Flickr8K Recall@1 from 0.559 to 0.003. Across six dataset-model conditions, the pair-aware residual tracks retrieval degradation with mean absolute Spearman 0.973, compared with 0.392 for the mean gap. The association remains stable across five random COCO-1K subsets at $0.954\pm0.026$, with a minimum of 0.943. UOT barycentric updates reduce the transport objective while degrading retrieval, distinguishing geometric objective descent from task improvement. These results establish UOT-Gap as a diagnostic for caption quality, modality alignment, and retrieval robustness.

cs.CV↗

arXiv2026

Training Trajectories Determine Circuit Removability in Annealable Soft-Prior Transformers

Soft positional priors can help small Transformers learn retrieval circuits, but it is unclear whether the resulting circuits remain functional once the prior is removed. We test this with an annealable soft-prior Transformer whose attention biases can be learned, faded, or zeroed during training and evaluation. On associative recall, unforced models perform well with the prior active ($0.772 \pm 0.020$) but collapse at zero gate ($0.095 \pm 0.009$). Smooth fade-to-zero training preserves high zero-gate accuracy ($0.734 \pm 0.028$), whereas forced-zero training, hard switching, and post hoc continuation fail to recover the same effect. The pattern also appears on Markov induction. Linear regression ICL provides a boundary case because zero-gate training can learn that task directly. Mechanistic traces show that circuit consolidation occurs after the gate reaches zero, even though the responsible heads vary across seeds. These results suggest that circuit removability in small discrete retrieval tasks depends on the training trajectory, not just the final architecture.

cs.LG↗

arXiv2026

WeedExpert-R1: Incentivizing Botanical Reasoning in MLLMs with Reinforcement Learning for Precision Weed Grounding

Precision weed control requires species-level identification and instance-level localization. However, conventional object detectors use a closed vocabulary, limiting their deployment across regions, and cannot explain their predictions in complex agricultural scenes. Multimodal large language models (MLLMs) offer visual grounding and reasoning capabilities, but insufficient botanical knowledge can cause hallucinations in fine-grained weed identification. This study introduces WeedExpert-R1, a multimodal model that learns visually grounded botanical reasoning through verifiable rewards. A domain-specific Chain-of-Thought synthesis pipeline combines a human-curated botanical trait dictionary with an Auditor-Synthesizer LLM workflow to generate reasoning data for supervised fine-tuning. Group Relative Policy Optimization is then applied with rewards for format, accuracy, instance count, and response length. Across 37 weed species from six datasets, WeedExpert-R1-4B achieved 75.82 percent exact-set precision at an IoU threshold of 0.5, 89.30 percent precision, and 87.81 percent recall. It outperformed proprietary models, including GPT-5.4 and Gemini-3.1-Pro, and larger open-source models, including Qwen3-VL-30B-Instruct and Gemma-4-31B-it. Results on unseen species further demonstrate its open-vocabulary capability and potential for deployment across diverse regions and crops without retraining.

cs.CV↗

arXiv2026

MOOSE-Copilot: A Web-Based Interactive Assistant for Unified Exploratory and Fine-Grained Scientific Hypothesis Discovery

Large language models (LLMs) show remarkable potential in scientific hypothesis discovery. However, existing approaches face two critical limitations: they treat divergent exploratory search and convergent fine-grained refinement as isolated tasks, and they operate autonomously with little to no human guidance. We present MOOSE-Copilot, the first unified framework to bridge this abstraction gap through a formalized human-AI interaction (HAII) protocol. Our system empowers scientists to steer the generative process via three explicit signals: initial blueprints, inter-stage routing, and intra-stage feedback. Using an oracle-simulated evaluation in which an LLM provides idealized expert signals, we show that injecting these structured signals significantly outperforms purely autonomous baselines, characterizing the gains achievable under high-quality guidance. Furthermore, we build a web-based interface that turns the framework into a no-code workflow: researchers pose a question, watch the hypothesis search unfold as an interactive tree, and steer it by selecting hypotheses, routing between stages, and injecting feedback-no command-line agents required. This makes end-to-end hypothesis discovery directly accessible to interdisciplinary researchers.

cs.CL↗

arXiv2026

Efficient and provably convergent end-to-end training of deep neural networks with linear constraints

Training a deep neural network with the outputs of selected layers satisfying linear constraints is required in many contemporary data-driven applications. While this can be achieved by incorporating projection layers into the neural network, its end-to-end training remains challenging due to the lack of rigorous theory and efficient algorithms for backpropagation. A key difficulty in developing the theory and efficient algorithms for backpropagation arose from the nonsmoothness of the solution mapping of the projection layer. To address this bottleneck, we introduce an efficiently computable HS-Jacobian to the projection layer. Importantly, we prove that the HS-Jacobian is a conservative mapping for the projection operator onto the polyhedral set, enabling its seamless integration into the nonsmooth automatic differentiation framework for backpropagation. Therefore, many efficient algorithms, such as Adam, can be applied for end-to-end training of deep neural networks with linear constraints. Particularly, we establish convergence guarantees of the HS-Jacobian based Adam algorithm for training linearly constrained deep neural networks. Extensive experiment results on several important applications, including finance, computer vision, and network architecture design, demonstrate the superior performance of our method compared to other existing popular methods.

math.OC↗

arXiv2026

SciIntegrity-Bench: A Benchmark for Evaluating Academic Integrity in AI Scientist Systems

AI scientist systems are increasingly deployed for autonomous research, yet their academic integrity has never been systematically evaluated. We introduce SCIINTEGRITY-BENCH, the first benchmark designed around a dilemmatic evaluation paradigm: each of its 33 scenarios across 11 trap categories is constructed so that honest acknowledgment of failure is the only correct response, while task completion requires misconduct. Across 231 evaluation runs spanning 7 state-of-the-art LLMs, the overall integrity problem rate reaches 34.2%, and no model achieves zero failures. Most strikingly, across missing-data scenarios, all seven models generate synthetic data rather than acknowledging infeasibility, differing only in whether they disclose the substitution. A further prompt ablation study separates two drivers: removing explicit completion pressure sharply reduces undisclosed fabrication from 20.6% to 3.2%, while the underlying synthesis rate remains unchanged, revealing an intrinsic completion bias that persists independent of prompt-level instructions. These findings point to the absence of honest refusal as a trained disposition as the primary driver of observed failures. We release SCIINTEGRITY-BENCH at https://github.com/liuxingtong/Sci-Integrity-Bench.

cs.AI↗

arXiv2026

Cross-Source Supervision for Bone Infection Segmentation in Dual-Modality PET-CT

Early and accurate diagnosis and lesion localization of bone infections are crucial for clinical treatment. PET-CT integrates anatomical information from CT with metabolic information from PET, making it an important imaging modality for diagnosing bone infections. However, accurate lesion segmentation remains challenging due to indistinct lesion boundaries and inconsistencies in annotations generated by different experts or automated systems. In this work, we investigate multimodal segmentation of bone infections under annotation discrepancy. We develop a bimodal end-to-end segmentation framework that integrates PET metabolic signals and CT bone-window anatomy through an early-fusion multimodal representation.To mitigate performance inflation caused by inter-slice correlation in small datasets, this study discards traditional two-dimensional evaluation methods and implements a rigorous patient-level 3D volumetric evaluation and cross-validation. Furthermore, instead of forcing a singular consensus, we propose a decoupled dual-source learning framework where parallel models are trained on independent expert annotations driven by high-sensitivity and high-specificity clinical intents. Experimental results objectively report performance variations at the patient level (Mean + SD and Mean - SD), demonstrating the effectiveness of multimodal PET-CT fusion. The cross-evaluation matrix quantitatively reveals how models successfully internalize distinct expert diagnostic philosophies, providing a robust, diversity-preserving paradigm for clinical AI deployment in bone infection segmentation.

cs.CV↗

arXiv2026

PolyReal: A Benchmark for Real-World Polymer Science Workflows

Multimodal Large Language Models (MLLMs) excel in general domains but struggle with complex, real-world science. We posit that polymer science, an interdisciplinary field spanning chemistry, physics, biology, and engineering, is an ideal high-stakes testbed due to its diverse multimodal data. Yet, existing benchmarks related to polymer science largely overlook real-world workflows, limiting their practical utility and failing to systematically evaluate MLLMs across the full, practice-grounded lifecycle of experimentation. We introduce PolyReal, a novel multimodal benchmark grounded in real-world scientific practices to evaluate MLLMs on the full lifecycle of polymer experimentation. It covers five critical capabilities: (1) foundational knowledge application; (2) lab safety analysis; (3) experiment mechanism reasoning; (4) raw data extraction; and (5) performance & application exploration. Our evaluation of leading MLLMs on PolyReal reveals a capability imbalance. While models perform well on knowledge-intensive reasoning (e.g., Experiment Mechanism Reasoning), they drop sharply on practice-based tasks (e.g., Lab Safety Analysis and Raw Data Extraction). This exposes a severe gap between abstract scientific knowledge and its practical, context-dependent application, showing that these real-world tasks remain challenging for MLLMs. Thus, PolyReal helps address this evaluation gap and provides a practical benchmark for assessing AI systems in real-world scientific workflows.

cs.CV↗

arXiv2026

From 50% to Mastery in 3 Days: A Low-Resource SOP for Localizing Graduate-Level AI Tutors via Shadow-RAG

Deploying high-fidelity AI tutors in schools is often blocked by the Resource Curse -- the need for expensive cloud GPUs and massive data engineering. In this practitioner report, we present a replicable Standard Operating Procedure that breaks this barrier. Using a Vision-Language Model data cleaning strategy and a novel Shadow-RAG architecture, we localized a graduate-level Applied Mathematics tutor using only 3 person-days of non-expert labor and open-weights 32B models deployable on a single consumer-grade GPU. Our pilot study on a full graduate-level final exam reveals a striking emergence phenomenon: while both zero-shot baselines and standard retrieval stagnate around 50-60% accuracy across model generations, the Shadow Agent, which provides structured reasoning guidance, triggers a massive capability surge in newer 32B models, boosting performance from 74% (Naive RAG) to mastery level (90%). In contrast, older models see only modest gains (~10%). This suggests that such guidance is the key to unlocking the latent power of modern small language models. This work offers a cost-effective, scientifically grounded blueprint for ubiquitous AI education.

cs.AI↗

arXiv2026

MOOSE-Star: Unlocking Tractable Training for Scientific Discovery by Breaking the Complexity Barrier

While large language models (LLMs) show promise in scientific discovery, existing research focuses on inference or feedback-driven training, leaving the direct modeling of the generative reasoning process, $P(\text{hypothesis}|\text{background})$ ($P(h|b)$), unexplored. We demonstrate that directly training $P(h|b)$ is mathematically intractable due to the combinatorial complexity ($O(N^k)$) inherent in retrieving and composing inspirations from a vast knowledge base. To break this barrier, we introduce MOOSE-Star, a unified framework that enables tractable and scalable training of $P(h|b)$, while supporting more scalable inference. In the best case, MOOSE-Star reduces complexity from exponential to logarithmic ($O(\log N)$) by (1) training on decomposed subtasks derived from the probabilistic equation of discovery, (2) employing motivation-guided hierarchical search to enable logarithmic retrieval and prune irrelevant subspaces, and (3) utilizing bounded composition for robustness against retrieval noise. To facilitate this, we release TOMATO-Star, a dataset of 108,717 decomposed papers (38,400 GPU hours) for training. Empirically, MOOSE-Star scales continuously with training data and inference budget, whereas direct brute-force sampling hits a complexity wall.

cs.LG↗

arXiv2026

A unified foundational framework for knowledge injection and evaluation of Large Language Models in Combustion Science

To advance foundation Large Language Models (LLMs) for combustion science, this study presents the first end-to-end framework for developing domain-specialized models for the combustion community. The framework comprises an AI-ready multimodal knowledge base at the 3.5 billion-token scale, extracted from over 200,000 peer-reviewed articles, 8,000 theses and dissertations, and approximately 400,000 lines of combustion CFD code; a rigorous and largely automated evaluation benchmark (CombustionQA, 436 questions across eight subfields); and a three-stage knowledge-injection pathway that progresses from lightweight retrieval-augmented generation (RAG) to knowledge-graph-enhanced retrieval and continued pretraining. We first quantitatively validate Stage 1 (naive RAG) and find a hard ceiling: standard RAG accuracy peaks at 60%, far surpassing zero-shot performance (23%) yet well below the theoretical upper bound (87%). We further demonstrate that this stage's performance is severely constrained by context contamination. Consequently, building a domain foundation model requires structured knowledge graphs and continued pretraining (Stages 2 and 3).

cs.CL↗

arXiv2026

Full-Stack Domain Enhancement for Combustion LLMs: Construction and Optimization

Large language models (LLMs) in the direction of task adaptation and capability enhancement for professional fields demonstrate significant application potential. Nevertheless, for complex physical systems such as combustion science, general-purpose LLMs often generate severe hallucinations due to insufficient domain knowledge and the inability to adhere to physical conservation laws. To address this issue, we propose the first full-stack domain-enhanced LLM workflow tailored for the field of combustion science, which integrates automated domain corpus construction, incremental pre-training, instruction fine-tuning, and verifiable reward-based reinforcement learning. This workflow ensures that the model truly internalizes physical laws rather than merely learning textual statistical patterns. We also release FlameBench, a standardized evaluation benchmark specifically designed for complex reasoning tasks in combustion science. Experimental results demonstrate that the model developed in this work significantly outperforms state-of-the-art general-purpose closed-source models and traditional retrieval-augmented generation methods on combustion science reasoning tasks. This work lays a solid technical and resource foundation for the subsequent development of domain-specific scientific research agents with reliable scientific reasoning capabilities.

cs.CL↗

arXiv2025

MiroMind-M1: An Open-Source Advancement in Mathematical Reasoning via Context-Aware Multi-Stage Policy Optimization

Large language models have recently evolved from fluent text generation to advanced reasoning across diverse domains, giving rise to reasoning language models. Among these domains, mathematical reasoning serves as a representative benchmark as it requires precise multi-step logic and abstract reasoning, which can be generalized to other tasks. While closed-source RLMs such as GPT-o3 demonstrate impressive reasoning capabilities, their proprietary nature limits transparency and reproducibility. Although many open-source projects aim to close this gap, most of them lack sufficient openness by omitting critical resources such as datasets and detailed training configurations, which hinders reproducibility. To contribute toward greater transparency in RLM development, we introduce the MiroMind-M1 series, a set of fully open-source RLMs built on the Qwen-2.5 backbone that match or exceed the performance of existing open-source RLMs. Specifically, our models are trained in two stages: SFT on a carefully curated corpus of 719K math-reasoning problems with verified CoT trajectories, followed by RLVR on 62K challenging and verifiable problems. To enhance the robustness and efficiency of the RLVR process, we introduce Context-Aware Multi-Stage Policy Optimization, an algorithm that integrates length-progressive training with an adaptive repetition penalty to encourage context-aware RL training. Our model achieves state-of-the-art or competitive performance and superior token efficiency among Qwen-2.5-based open-source 7B and 32B models on the AIME24, AIME25, and MATH benchmarks. To facilitate reproducibility, we release the complete stack: models (MiroMind-M1-SFT-7B, MiroMind-M1-RL-7B, MiroMind-M1-RL-32B); datasets (MiroMind-M1-SFT-719K, MiroMind-M1-RL-62K); and all training and evaluation configurations. We hope these resources will support further research and foster community advancement.

cs.CL↗

arXiv2025

Optimization of Low-Latency Spiking Neural Networks Utilizing Historical Dynamics of Refractory Periods

The refractory period controls neuron spike firing rate, crucial for network stability and noise resistance. With advancements in spiking neural network (SNN) training methods, low-latency SNN applications have expanded. In low-latency SNNs, shorter simulation steps render traditional refractory mechanisms, which rely on empirical distributions or spike firing rates, less effective. However, omitting the refractory period amplifies the risk of neuron over-activation and reduces the system's robustness to noise. To address this challenge, we propose a historical dynamic refractory period (HDRP) model that leverages membrane potential derivative with historical refractory periods to estimate an initial refractory period and dynamically adjust its duration. Additionally, we propose a threshold-dependent refractory kernel to mitigate excessive neuron state accumulation. Our approach retains the binary characteristics of SNNs while enhancing both noise resistance and overall performance. Experimental results show that HDRP-SNN significantly reduces redundant spikes compared to traditional SNNs, and achieves state-of-the-art (SOTA) accuracy both on static datasets and neuromorphic datasets. Moreover, HDRP-SNN outperforms artificial neural networks (ANNs) and traditional SNNs in noise resistance, highlighting the crucial role of the HDRP mechanism in enhancing the performance of low-latency SNNs.

cs.NE↗

arXiv2025

Harnessing Large Language Models for Scientific Novelty Detection

In an era of exponential scientific growth, identifying novel research ideas is crucial and challenging in academia. Despite potential, the lack of an appropriate benchmark dataset hinders the research of novelty detection. More importantly, simply adopting existing NLP technologies, e.g., retrieving and then cross-checking, is not a one-size-fits-all solution due to the gap between textual similarity and idea conception. In this paper, we propose to harness large language models (LLMs) for scientific novelty detection (ND), associated with two new datasets in marketing and NLP domains. To construct the considerate datasets for ND, we propose to extract closure sets of papers based on their relationship, and then summarize their main ideas based on LLMs. To capture idea conception, we propose to train a lightweight retriever by distilling the idea-level knowledge from LLMs to align ideas with similar conception, enabling efficient and accurate idea retrieval for LLM novelty detection. Experiments show our method consistently outperforms others on the proposed benchmark datasets for idea retrieval and ND tasks. Codes and data are available at https://anonymous.4open.science/r/NoveltyDetection-10FB/.

cs.CL↗

arXiv2025

Accelerating RLHF Training with Reward Variance Increase

Reinforcement learning from human feedback (RLHF) is an essential technique for ensuring that large language models (LLMs) are aligned with human values and preferences during the post-training phase. As an effective RLHF approach, group relative policy optimization (GRPO) has demonstrated success in many LLM-based applications. However, efficient GRPO-based RLHF training remains a challenge. Recent studies reveal that a higher reward variance of the initial policy model leads to faster RLHF training. Inspired by this finding, we propose a practical reward adjustment model to accelerate RLHF training by provably increasing the reward variance and preserving the relative preferences and reward expectation. Our reward adjustment method inherently poses a nonconvex optimization problem, which is NP-hard to solve in general. To overcome the computational challenges, we design a novel $O(n \log n)$ algorithm to find a global solution of the nonconvex reward adjustment model by explicitly characterizing the extreme points of the feasible set. As an important application, we naturally integrate this reward adjustment model into the GRPO algorithm, leading to a more efficient GRPO with reward variance increase (GRPOVI) algorithm for RLHF training. As an interesting byproduct, we provide an indirect explanation for the empirical effectiveness of GRPO with rule-based reward for RLHF training, as demonstrated in DeepSeek-R1. Experiment results demonstrate that the GRPOVI algorithm can significantly improve the RLHF training efficiency compared to the original GRPO algorithm.

cs.LG↗

arXiv2025

MOOSE-Chem2: Exploring LLM Limits in Fine-Grained Scientific Hypothesis Discovery via Hierarchical Search

Large language models (LLMs) have shown promise in automating scientific hypothesis generation, yet existing approaches primarily yield coarse-grained hypotheses lacking critical methodological and experimental details. We introduce and formally define the new task of fine-grained scientific hypothesis discovery, which entails generating detailed, experimentally actionable hypotheses from coarse initial research directions. We frame this as a combinatorial optimization problem and investigate the upper limits of LLMs' capacity to solve it when maximally leveraged. Specifically, we explore four foundational questions: (1) how to best harness an LLM's internal heuristics to formulate the fine-grained hypothesis it itself would judge as the most promising among all the possible hypotheses it might generate, based on its own internal scoring-thus defining a latent reward landscape over the hypothesis space; (2) whether such LLM-judged better hypotheses exhibit stronger alignment with ground-truth hypotheses; (3) whether shaping the reward landscape using an ensemble of diverse LLMs of similar capacity yields better outcomes than defining it with repeated instances of the strongest LLM among them; and (4) whether an ensemble of identical LLMs provides a more reliable reward landscape than a single LLM. To address these questions, we propose a hierarchical search method that incrementally proposes and integrates details into the hypothesis, progressing from general concepts to specific experimental configurations. We show that this hierarchical process smooths the reward landscape and enables more effective optimization. Empirical evaluations on a new benchmark of expert-annotated fine-grained hypotheses from recent literature show that our method consistently outperforms strong baselines.

cs.CL↗

arXiv2025

MOOSE-Chem3: Toward Experiment-Guided Hypothesis Ranking via Simulated Experimental Feedback

Hypothesis ranking is vital for automated scientific discovery, especially in cost-intensive, throughput-limited natural science domains. Current methods focus on pre-experiment ranking, relying solely on language model reasoning without empirical feedback. We introduce experiment-guided ranking, which prioritizes hypotheses based on feedback from prior tests. Due to the impracticality of real experiments, we propose a simulator grounded in domain-specific concepts that models hypothesis performance as a function of similarity to a hidden ground truth, perturbed by noise. Validated against 124 hypotheses with experimentally reported outcomes, the simulator approximates real results with consistent trend alignment. Although deviations exist, they mimic wet-lab noise, promoting more robust ranking strategies. We frame experiment-guided ranking as a sequential decision-making problem and propose an in-context reinforcement learning (ICRL) framework. Our LLM-based policy decomposes hypotheses into functional elements, clusters them by mechanistic roles, and prioritizes recombinations based on feedback. Experiments show our approach significantly outperforms pre-experiment baselines and strong ablations. Our toolkit, comprising the simulator and ICRL framework, enables systematic research on experiment-guided ranking, with the policy serving as a strong proof of concept.

cs.CL↗