Zhuo Yang

Wanhao Liu, Jiaqing Xie, Qian Tan et al.

As multimodal language models play an increasingly important role in scientific research, materials science offers a critical testbed due to its interdisciplinary, multimodal, and application-driven nature. However, existing materials benchmarks mainly focus on property prediction, knowledge QA, or characterization understanding, leaving the broader reasoning process from materials knowledge to application underexplored. To fill this gap, we present OmniMatBench, a human-calibrated multimodal reasoning benchmark for materials science. OmniMatBench contains 3,171 expert-curated QA and calculation problems across 19 materials-science subfields, spanning fundamental materials knowledge, structural and engineering materials, materials processing and manufacturing, and functional and applied materials. We evaluate 13 open-source and closed-source MLLMs and find that the best model achieves only a 0.372 overall score, revealing a substantial gap in current materials-science reasoning. Further analysis shows strong variation across subfields, fixed reasoning heuristics, uneven materials knowledge, and limited high-level knowledge application under formula-, retrieval-, and code-assisted settings. OmniMatBench provides crucial insights into the capabilities and limitations of current MLLMs and establishes a foundation for reliable AI assistants in materials-science research.

Sixue Xing, Haoyu He, Kerui Wu et al.

LLM-guided evolutionary search (Evolve systems) has reached state-of-the-art results on mathematical and combinatorial tasks, yet most existing systems report only the best of many runs and leave the run-to-run distribution undocumented. We ask how a fixed budget of LLM calls should be allocated, and how reliably a single run reaches the reported numbers. Sweeping the depth-breadth grid over five models and three tasks, we identify two empirical regularities: a fitness-compute envelope along which capability ordering largely collapses on effective FLOPs, and a bilinear depth-breadth fit with task-specific interaction; both are gated by model-task capability. Motivated by these regularities, we propose BaSE (Bandit-based Self-Evolving), a multi-armed bandit that allocates LLM calls across parallel trajectories. Without changing the model, prompt, or evaluator, BaSE improves mean fitness by 12.3% over the strongest island-protocol baseline across 8 (model, task) cells, with the largest gains on high-variance settings: a reliability gain from allocation alone.

Yongming Yang, Shuwei Shao, Tao Yang et al.

Monocular depth estimation is critical for endoscopists to perform spatial perception and 3D navigation of surgical sites. However, most of the existing methods ignore the important geometric structural consistency, which inevitably leads to performance degradation and distortion of 3D reconstruction. To address this issue, we introduce a gradient loss to penalize edge fluctuations ambiguous around stepped edge structures and a normal loss to explicitly express the sensitivity to frequently small structures, and propose a geometric consistency loss to spreads the spatial information across the sample grids to constrain the global geometric anatomy structures. In addition, we develop a synthetic RGB-Depth dataset that captures the anatomical structures under reflections and illumination variations. The proposed method is extensively validated across different datasets and clinical images and achieves mean RMSE values of 0.066 (stomach), 0.029 (small intestine), and 0.139 (colon) on the EndoSLAM dataset. The generalizability of the proposed method achieves mean RMSE values of 12.604 (T1-L1), 9.930 (T2-L2), and 13.893 (T3-L3) on the ColonDepth dataset. The experimental results show that our method exceeds previous state-of-the-art competitors and generates more consistent depth maps and reasonable anatomical structures. The quality of intraoperative 3D structure perception from endoscopic videos of the proposed method meets the accuracy requirements of video-CT registration algorithms for endoscopic navigation. The dataset and the source code will be available at https://github.com/YYM-SIA/LINGMI-MR.

Zongzheng Zhang, Jingrui Pang, Zhuo Yang et al.

Vision-Language-Action (VLA) models have recently become a central direction in embodied AI, but current systems are restricted to either dual-gripper control or single-arm dexterous hand manipulation. While low-dimensional gripper control can often be handled with simpler methods, high-dimensional dexterous hand control benefits greatly from full end-to-end VLA learning. In this work, we introduce Dexora, the first open-source VLA system that natively targets dual-arm, dual-hand high-DoF manipulation. We design a hybrid teleoperation pipeline that decouples gross arm kinematics (captured with a custom exoskeleton backpack) from fine finger motion (markerless hand tracking via Apple Vision Pro), and that drives both a physical dual-arm dual-hand platform and an identical MuJoCo digital twin. Using that interface, we assemble a large training corpus: an embodiment-matched synthetic corpus (100K simulated trajectories, 6.5M frames) and a real-world dataset of 10K teleoperated episodes (2.92M frames). To mitigate noisy teleoperation demonstrations, we propose a data-quality-aware training recipe: an offline discriminator provides clip-level weights for diffusion-transformer policy training, down-weighting low-quality demonstrations. Empirically, Dexora outperforms competitive VLA baselines on both basic and dexterous benchmarks (e.g., average dexterous success 66.7% vs. 51.7%), attains 90% success on basic tasks, and shows robust out-of-distribution and cross-embodiment generalization. Ablations confirm the importance of real data and the discriminator for dexterity.

Jiarui Xie, Zhuo Yang, Chun-Chun Hu et al.

Powder bed fusion (PBF) is an emerging metal additive manufacturing (AM) technology that enables rapid fabrication of complex geometries. However, defects such as pores and balling may occur and lead to structural unconformities, thus compromising the mechanical performance of the part. This has become a critical challenge for quality assurance as the nature of some defects is stochastic during the process and invisible from the exterior. To address this issue, digital twin (DT) using machine learning (ML)-based modeling can be deployed for AM process monitoring and control. Melt pool is one of the most commonly observed physical phenomena for process monitoring, usually by high-speed cameras. Once labeled and preprocessed, the melt pool images are used to train ML-based models for DT applications such as process anomaly detection and print quality evaluation. Nonetheless, the reusability of DTs is restricted due to the wide variability of AM settings, including AM machines and monitoring instruments. The performance of the ML models trained using the dataset collected from one setting is usually compromised when applied to other settings. This paper proposes a knowledge transfer pipeline between different AM settings to enhance the reusability of AM DTs. The source and target datasets are collected from the National Institute of Standards and Technology and National Cheng Kung University with different cameras, materials, AM machines, and process parameters. The proposed pipeline consists of four steps: data preprocessing, data augmentation, domain alignment, and decision alignment. Compared with the model trained only using the source dataset, this pipeline increased the melt pool anomaly detection accuracy by 31% without any labeled training data from the target dataset.

Sen Wang, Huaiyi Dong, Jingyi Tian et al.

Prevailing 2D-centric visuomotor policies exhibit a pronounced deficiency in novel view generalization, as their reliance on static observations hinders consistent action mapping across unseen views. In response, we introduce GenSplat, a feed-forward 3D Gaussian Splatting framework that facilitates view-generalized policy learning through novel view rendering. GenSplat employs a permutation-equivariant architecture to reconstruct high-fidelity 3D scenes from sparse, uncalibrated inputs in a single forward pass. To ensure structural integrity, we design a 3D-prior distillation strategy that regularizes the 3DGS optimization, preventing the geometric collapse typical of purely photometric supervision. By rendering diverse synthetic views from these stable 3D representations, we systematically augment the observational manifold during training. This augmentation forces the policy to ground its decisions in underlying 3D structures, thereby ensuring robust execution under severe spatial perturbations where baselines severely degrade.

Shuaike Shen, Jiaqing Xie, Zhuo Yang et al.

Recent advances in molecular foundation models have shown impressive performance in molecular property prediction and de novo molecular design, with promising applications in areas such as drug discovery and reaction prediction. Nevertheless, most existing approaches rely exclusively on SMILES representations and overlook both experimental spectra and 3D structural information-two indispensable sources for capturing molecular behavior in real-world scenarios. This limitation reduces their effectiveness in tasks where stereochemistry, spatial conformation, and experimental validation are critical. To overcome these challenges, we propose MolSpectLLM, a molecular foundation model pretrained on Qwen2.5-7B that unifies experimental spectroscopy with molecular 3D structure. By explicitly modeling molecular spectra, MolSpectLLM achieves state-of-the-art performance on spectrum-related tasks, with an average accuracy of 0.53 across NMR, IR, and MS benchmarks. MolSpectLLM also shows strong performance on the spectra analysis task, obtaining 15.5% sequence accuracy and 41.7% token accuracy on Spectra-to-SMILES, substantially outperforming large general-purpose LLMs. More importantly, MolSpectLLM not only achieves strong performance on molecular elucidation tasks, but also generates accurate 3D molecular structures directly from SMILES or spectral inputs, bridging spectral analysis, molecular elucidation, and molecular design. Code are available at \href{https://github.com/Eurekashen/MolSpectLLM}{https://github.com/Eurekashen/MolSpectLLM}.

Jiaqing Xie, Weida Wang, Ben Gao et al.

Quantitative chemistry is central to modern chemical research, yet the ability of large language models (LLMs) to perform its rigorous, step-by-step calculations remains underexplored. To fill this blank, we propose QCBench, a Quantitative Chemistry oriented benchmark comprising 350 computational chemistry problems across 7 chemistry subfields, which contains analytical chemistry, bio/organic chemistry, general chemistry, inorganic chemistry, physical chemistry, polymer chemistry and quantum chemistry. To systematically evaluate the mathematical reasoning abilities of large language models (LLMs), they are categorized into three tiers: easy, medium, and difficult. Each problem, rooted in realistic chemical scenarios, is structured to prevent heuristic shortcuts and demand explicit numerical reasoning. QCBench enables fine-grained diagnosis of computational weaknesses, reveals model-specific limitations across difficulty levels, and lays the groundwork for future improvements such as domain-adaptive fine-tuning or multi-modal integration. Evaluations on 24 LLMs demonstrate a consistent performance degradation with increasing task complexity, highlighting the current gap between language fluency and scientific computation accuracy. Code for QCBench is available at https://github.com/jiaqingxie/QCBench.

Zhuo Yang, Yeyun Chen, Jiaqing Xie et al.

Molecular editing and optimization are multi-step problems that require iteratively improving properties while keeping molecules chemically valid and structurally similar. We frame both tasks as sequential, tool-guided decisions and introduce MolAct, an agentic reinforcement learning framework that employs a two-stage training paradigm: first building editing capability, then optimizing properties while reusing the learned editing behaviors. To the best of our knowledge, this is the first work to formalize molecular design as an Agentic Reinforcement Learning problem, where an LLM agent learns to interleave reasoning, tool-use, and molecular optimization. The framework enables agents to interact in multiple turns, invoking chemical tools for validity checking, property assessment, and similarity control, and leverages their feedback to refine subsequent edits. We instantiate the MolAct framework to train two model families: MolEditAgent for molecular editing tasks and MolOptAgent for molecular optimization tasks. In molecular editing, MolEditAgent-7B delivers 100, 95, and 98 valid add, delete, and substitute edits, outperforming strong closed "thinking" baselines such as DeepSeek-R1; MolEditAgent-3B approaches the performance of much larger open "thinking" models like Qwen3-32B-think. In molecular optimization, MolOptAgent-7B (trained on MolEditAgent-7B) surpasses the best closed "thinking" baseline (e.g., Claude 3.7) on LogP and remains competitive on solubility, while maintaining balanced performance across other objectives. These results highlight that treating molecular design as a multi-step, tool-augmented process is key to reliable and interpretable improvements.

Junchen Liu, Wenbo Hu, Zhuo Yang et al.

Despite significant advancements in Neural Radiance Fields (NeRFs), the renderings may still suffer from aliasing and blurring artifacts, since it remains a fundamental challenge to effectively and efficiently characterize anisotropic areas induced by the cone-casting procedure. This paper introduces a Ripmap-Encoded Platonic Solid representation to precisely and efficiently featurize 3D anisotropic areas, achieving high-fidelity anti-aliasing renderings. Central to our approach are two key components: Platonic Solid Projection and Ripmap encoding. The Platonic Solid Projection factorizes the 3D space onto the unparalleled faces of a certain Platonic solid, such that the anisotropic 3D areas can be projected onto planes with distinguishable characterization. Meanwhile, each face of the Platonic solid is encoded by the Ripmap encoding, which is constructed by anisotropically pre-filtering a learnable feature grid, to enable featurzing the projected anisotropic areas both precisely and efficiently by the anisotropic area-sampling. Extensive experiments on both well-established synthetic datasets and a newly captured real-world dataset demonstrate that our Rip-NeRF attains state-of-the-art rendering quality, particularly excelling in the fine details of repetitive structures and textures, while maintaining relatively swift training times.

Zhuo Yang, Jiaqing Xie, Shuaike Shen et al.

Deep learning holds immense promise for spectroscopy, yet research and evaluation in this emerging field often lack standardized formulations. To address this issue, we introduce SpectrumLab, a pioneering unified platform designed to systematize and accelerate deep learning research in spectroscopy. SpectrumLab integrates three core components: a comprehensive Python library featuring essential data processing and evaluation tools, along with leaderboards; an innovative SpectrumAnnotator module that generates high-quality benchmarks from limited seed data; and SpectrumBench, a multi-layered benchmark suite covering 14 spectroscopic tasks and over 10 spectrum types, featuring spectra curated from over 1.2 million distinct chemical substances. Thorough empirical studies on SpectrumBench with 18 cutting-edge multimodal LLMs reveal critical limitations of current approaches. We hope SpectrumLab will serve as a crucial foundation for future advancements in deep learning-driven spectroscopy.

Zhuo Yang, Daolang Wang, Lingli Ge et al.

Many real-world scientific and industrial applications require the optimization of expensive black-box functions. Bayesian Optimization (BO) provides an effective framework for such problems. However, traditional BO methods are prone to get trapped in local optima and often lack interpretable insights. To address this issue, this paper designs Reasoning BO, a novel framework that leverages reasoning models to guide the sampling process in BO while incorporating multi-agent systems and knowledge graphs for online knowledge accumulation. By integrating the reasoning and contextual understanding capabilities of Large Language Models (LLMs), we can provide strong guidance to enhance the BO process. As the optimization progresses, Reasoning BO provides real-time sampling recommendations along with critical insights grounded in plausible scientific theories, aiding in the discovery of superior solutions within the search space. We systematically evaluate our approach across 10 diverse tasks encompassing synthetic mathematical functions and complex real-world applications. The framework demonstrates its capability to progressively refine sampling strategies through real-time insights and hypothesis evolution, effectively identifying higher-performing regions of the search space for focused exploration. This process highlights the powerful reasoning and context-learning abilities of LLMs in optimization scenarios. For example, in the Direct Arylation task, our method increased the yield to 60.7%, whereas traditional BO achieved only a 25.2% yield. Furthermore, our investigation reveals that smaller LLMs, when fine-tuned through reinforcement learning, can attain comparable performance to their larger counterparts.

Liujia Yang, Zhuo Yang, Jiaqing Xie et al.

Nuclear Magnetic Resonance (NMR) spectroscopy is fundamental for molecular structure elucidation, yet interpreting spectra at scale remains time-consuming and highly expertise-dependent. While recent spectrum-as-language modeling and retrieval-based methods have shown promise, they rely heavily on large corpora of computed spectra and exhibit notable performance drops when applied to experimental measurements. To address these issues, we build NMRSpec, a large-scale corpus of experimental $^1$H and $^{13}$C spectra mined from chemical literature, and propose NMRTrans, which models spectra as unordered peak sets and aligns the model's inductive bias with the physical nature of NMR. To our best knowledge, NMRTrans is the first NMR Transformer trained solely on large-scale experimental spectra and achieves state-of-the-art performance on experimental benchmarks, improving Top-10 Accuracy over the strongest baseline by +17.82 points (61.15% vs. 43.33%), and underscoring the importance of experimental data and structure-aware architectures for reliable NMR structure elucidation.

Zhuo Yang, Yufei Han, Xiangliang Zhang

Despite of the pervasive existence of multi-label evasion attack, it is an open yet essential problem to characterize the origin of the adversarial vulnerability of a multi-label learning system and assess its attackability. In this study, we focus on non-targeted evasion attack against multi-label classifiers. The goal of the threat is to cause miss-classification with respect to as many labels as possible, with the same input perturbation. Our work gains in-depth understanding about the multi-label adversarial attack by first characterizing the transferability of the attack based on the functional properties of the multi-label classifier. We unveil how the transferability level of the attack determines the attackability of the classifier via establishing an information-theoretic analysis of the adversarial risk. Furthermore, we propose a transferability-centered attackability assessment, named Soft Attackability Estimator (SAE), to evaluate the intrinsic vulnerability level of the targeted multi-label classifier. This estimator is then integrated as a transferability-tuning regularization term into the multi-label learning paradigm to achieve adversarially robust classification. The experimental study on real-world data echos the theoretical analysis and verify the validity of the transferability-regularized multi-label learning method.

Zhuo Yang, Yufei Han, Xiangliang Zhang

Evasion attack in multi-label learning systems is an interesting, widely witnessed, yet rarely explored research topic. Characterizing the crucial factors determining the attackability of the multi-label adversarial threat is the key to interpret the origin of the adversarial vulnerability and to understand how to mitigate it. Our study is inspired by the theory of adversarial risk bound. We associate the attackability of a targeted multi-label classifier with the regularity of the classifier and the training data distribution. Beyond the theoretical attackability analysis, we further propose an efficient empirical attackability estimator via greedy label space exploration. It provides provably computational efficiency and approximation accuracy. Substantial experimental results on real-world datasets validate the unveiled attackability factors and the effectiveness of the proposed empirical attackability indicator

Xiaomei Bai, Mengyang Wang, Ivan Lee et al.

Globally, recommendation services have become important due to the fact that they support e-commerce applications and different research communities. Recommender systems have a large number of applications in many fields including economic, education, and scientific research. Different empirical studies have shown that recommender systems are more effective and reliable than keyword-based search engines for extracting useful knowledge from massive amounts of data. The problem of recommending similar scientific articles in scientific community is called scientific paper recommendation. Scientific paper recommendation aims to recommend new articles or classical articles that match researchers' interests. It has become an attractive area of study since the number of scholarly papers increases exponentially. In this survey, we first introduce the importance and advantages of paper recommender systems. Second, we review the recommendation algorithms and methods, such as Content-Based methods, Collaborative Filtering methods, Graph-Based methods and Hybrid methods. Then, we introduce the evaluation methods of different recommender systems. Finally, we summarize open issues in the paper recommender systems, including cold start, sparsity, scalability, privacy, serendipity and unified scholarly data standards. The purpose of this survey is to provide comprehensive reviews on scholarly paper recommendation.

Zhuo Yang, Yufei Han, Guoxian Yu et al.

We propose to formulate multi-label learning as a estimation of class distribution in a non-linear embedding space, where for each label, its positive data embeddings and negative data embeddings distribute compactly to form a positive component and negative component respectively, while the positive component and negative component are pushed away from each other. Duo to the shared embedding space for all labels, the distribution of embeddings preserves instances' label membership and feature matrix, thus encodes the feature-label relation and nonlinear label dependency. Labels of a given instance are inferred in the embedding space by measuring the probabilities of its belongingness to the positive or negative components of each label. Specially, the probabilities are modeled as the distance from the given instance to representative positive or negative prototypes. Extensive experiments validate that the proposed solution can provide distinctively more accurate multi-label classification than other state-of-the-art algorithms.