arXiv subjects

Dongzhan Zhou

Publications and source records attributed to Dongzhan Zhou.

At least 73 records · Page 4Linked to original sources

arXiv2025

ChemVLM: Exploring the Power of Multimodal Large Language Models in Chemistry Area

Large Language Models (LLMs) have achieved remarkable success and have been applied across various scientific fields, including chemistry. However, many chemical tasks require the processing of visual information, which cannot be successfully handled by existing chemical LLMs. This brings a growing need for models capable of integrating multimodal information in the chemical domain. In this paper, we introduce \textbf{ChemVLM}, an open-source chemical multimodal large language model specifically designed for chemical applications. ChemVLM is trained on a carefully curated bilingual multimodal dataset that enhances its ability to understand both textual and visual chemical information, including molecular structures, reactions, and chemistry examination questions. We develop three datasets for comprehensive evaluation, tailored to Chemical Optical Character Recognition (OCR), Multimodal Chemical Reasoning (MMCR), and Multimodal Molecule Understanding tasks. We benchmark ChemVLM against a range of open-source and proprietary multimodal large language models on various tasks. Experimental results demonstrate that ChemVLM achieves competitive performance across all evaluated tasks. Our model can be found at https://huggingface.co/AI4Chem/ChemVLM-26B.

cs.LG↗

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↗

arXiv2025

From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery

Artificial intelligence (AI) is reshaping scientific discovery, evolving from specialized computational tools into autonomous research partners. We position Agentic Science as a pivotal stage within the broader AI for Science paradigm, where AI systems progress from partial assistance to full scientific agency. Enabled by large language models (LLMs), multimodal systems, and integrated research platforms, agentic AI shows capabilities in hypothesis generation, experimental design, execution, analysis, and iterative refinement -- behaviors once regarded as uniquely human. This survey provides a domain-oriented review of autonomous scientific discovery across life sciences, chemistry, materials science, and physics. We unify three previously fragmented perspectives -- process-oriented, autonomy-oriented, and mechanism-oriented -- through a comprehensive framework that connects foundational capabilities, core processes, and domain-specific realizations. Building on this framework, we (i) trace the evolution of AI for Science, (ii) identify five core capabilities underpinning scientific agency, (iii) model discovery as a dynamic four-stage workflow, (iv) review applications across the above domains, and (v) synthesize key challenges and future opportunities. This work establishes a domain-oriented synthesis of autonomous scientific discovery and positions Agentic Science as a structured paradigm for advancing AI-driven research.

cs.LG↗

arXiv2025

Can Knowledge-Graph-based Retrieval Augmented Generation Really Retrieve What You Need?

Retrieval-Augmented Generation (RAG) based on knowledge graphs (KGs) enhances large language models (LLMs) by providing structured and interpretable external knowledge. However, existing KG-based RAG methods struggle to retrieve accurate and diverse information from text-rich KGs for complex real-world queries. Process Reward Models (PRMs) offer a way to align the retrieval process of KG-based RAG with query-specific knowledge requirements, but they heavily rely on process-level supervision signals that are expensive and hard to obtain on KGs. To address this challenge, we propose GraphFlow, a framework that efficiently retrieves accurate and diverse knowledge required for real-world queries from text-rich KGs. GraphFlow employs a transition-based flow matching objective to jointly optimize a retrieval policy and a flow estimator. The flow estimator factorizes the reward of the retrieval outcome into the intermediate retrieval states. Such reward factorization guides the retrieval policy to retrieve candidates from KGs in proportion to their reward. This allows GraphFlow to explore high-quality regions of KGs that yield diverse and relevant results. We evaluate GraphFlow on the STaRK benchmark, which includes real-world queries from multiple domains over text-rich KGs. GraphFlow outperforms strong KG-RAG baselines, including GPT-4o, by 10% on average in hit rate and recall. It also shows strong generalization to unseen KGs, demonstrating its effectiveness and robustness.

cs.AI↗

arXiv2025

Scaling Physical Reasoning with the PHYSICS Dataset

Large Language Models (LLMs) have achieved remarkable progress on advanced reasoning tasks such as mathematics and coding competitions. Meanwhile, physics, despite being both reasoning-intensive and essential to real-world understanding, received limited academic and industrial attention. This paper introduces PHYSICS, a dataset containing 16,568 high-quality physics problems spanning subjects and difficulty levels, to facilitate this issue. Specifically, PHYSICS is curated with exercises from over 100 textbooks through a carefully designed pipeline for quality control. It covers five major physics domains: Mechanics, Electromagnetism, Thermodynamics, Optics, and Modern Physics. It also spans a wide range of difficulty levels, from high school to graduate-level physics courses. To utilize the data for improving and evaluating the model's physical reasoning capabilities, we split the dataset into training and test sets, and provide reasoning paths generated by powerful reasoning models for the training data to facilitate model training. In addition, for the evaluation part, we find that existing evaluation frameworks exhibit biases in aspects such as units, simplification, and precision in physics domain. To balance efficiency and accuracy, we introduce a Rule+Model evaluation framework tailored to physics problems. Our evaluations on current state-of-the-art open-source and proprietary models highlight the limitations of current models in handling physics-related tasks. We hope that our dataset and evaluation methodology will jointly advance the development of LLMs in the field of physics. The code and data can be found at: https://github.com/Zhengsh123/PHYSICS.

cs.CL↗

arXiv2025

PhysicsMinions: Winning Gold Medals in the Latest Physics Olympiads with a Coevolutionary Multimodal Multi-Agent System

Physics is central to understanding and shaping the real world, and the ability to solve physics problems is a key indicator of real-world physical intelligence. Physics Olympiads, renowned as the crown of competitive physics, provide a rigorous testbed requiring complex reasoning and deep multimodal understanding, yet they remain largely underexplored in AI research. Existing approaches are predominantly single-model based, and open-source MLLMs rarely reach gold-medal-level performance. To address this gap, we propose PhysicsMinions, a coevolutionary multi-agent system for Physics Olympiad. Its architecture features three synergistic studios: a Visual Studio to interpret diagrams, a Logic Studio to formulate solutions, and a Review Studio to perform dual-stage verification. The system coevolves through an iterative refinement loop where feedback from the Review Studio continuously guides the Logic Studio, enabling the system to self-correct and converge towards the ground truth. Evaluated on the HiPhO benchmark spanning 7 latest physics Olympiads, PhysicsMinions delivers three major breakthroughs: (i) Strong generalization: it consistently improves both open-source and closed-source models of different sizes, delivering clear benefits over their single-model baselines; (ii) Historic breakthroughs: it elevates open-source models from only 1-2 to 6 gold medals across 7 Olympiads, achieving the first-ever open-source gold medal in the latest International Physics Olympiad (IPhO) under the average-score metric; and (iii) Scaling to human expert: it further advances the open-source Pass@32 score to 26.8/30 points on the latest IPhO, ranking 4th of 406 contestants and far surpassing the top single-model score of 22.7 (ranked 22nd). Generally, PhysicsMinions offers a generalizable framework for Olympiad-level problem solving, with the potential to extend across disciplines.

cs.AI↗

arXiv2025

Object-AVEdit: An Object-level Audio-Visual Editing Model

There is a high demand for audio-visual editing in video post-production and the film making field. While numerous models have explored audio and video editing, they struggle with object-level audio-visual operations. Specifically, object-level audio-visual editing requires the ability to perform object addition, replacement, and removal across both audio and visual modalities, while preserving the structural information of the source instances during the editing process. In this paper, we present \textbf{Object-AVEdit}, achieving the object-level audio-visual editing based on the inversion-regeneration paradigm. To achieve the object-level controllability during editing, we develop a word-to-sounding-object well-aligned audio generation model, bridging the gap in object-controllability between audio and current video generation models. Meanwhile, to achieve the better structural information preservation and object-level editing effect, we propose an inversion-regeneration holistically-optimized editing algorithm, ensuring both information retention during the inversion and better regeneration effect. Extensive experiments demonstrate that our editing model achieved advanced results in both audio-video object-level editing tasks with fine audio-visual semantic alignment. In addition, our developed audio generation model also achieved advanced performance. More results on our project page: https://gewu-lab.github.io/Object_AVEdit-website/.

cs.MM↗

arXiv2025

SpectrumWorld: Artificial Intelligence Foundation for Spectroscopy

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.

cs.LG↗

arXiv2025

Biology-Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability of Large Language Models

Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we introduce Biology-Instructions, the first large-scale instruction-tuning dataset for multi-omics biological sequences, including DNA, RNA, proteins, and multi-molecules. This dataset bridges LLMs and complex biological sequence-related tasks, enhancing their versatility and reasoning while maintaining conversational fluency. We also highlight significant limitations of current state-of-the-art LLMs on multi-omics tasks without specialized training. To overcome this, we propose ChatMultiOmics, a strong baseline with a novel three-stage training pipeline, demonstrating superior biological understanding through Biology-Instructions. Both resources are publicly available, paving the way for better integration of LLMs in multi-omics analysis. The Biology-Instructions is publicly available at: https://github.com/hhnqqq/Biology-Instructions.

q-bio.BM↗

arXiv2025

HiPhO: How Far Are (M)LLMs from Humans in the Latest High School Physics Olympiad Benchmark?

Recently, the physical capabilities of (M)LLMs have garnered increasing attention. However, existing benchmarks for physics suffer from two major gaps: they neither provide systematic and up-to-date coverage of real-world physics competitions such as physics Olympiads, nor enable direct performance comparison with humans. To bridge these gaps, we present HiPhO, the first benchmark dedicated to high school physics Olympiads with human-aligned evaluation. Specifically, HiPhO highlights three key innovations. (1) Comprehensive Data: It compiles 13 latest Olympiad exams from 2024-2025, spanning both international and regional competitions, and covering mixed modalities that encompass problems spanning text-only to diagram-based. (2) Professional Evaluation: We adopt official marking schemes to perform fine-grained grading at both the answer and step level, fully aligned with human examiners to ensure high-quality and domain-specific evaluation. (3) Comparison with Human Contestants: We assign gold, silver, and bronze medals to models based on official medal thresholds, thereby enabling direct comparison between (M)LLMs and human contestants. Our large-scale evaluation of 30 state-of-the-art (M)LLMs shows that: across 13 exams, open-source MLLMs mostly remain at or below the bronze level; open-source LLMs show promising progress with multiple golds; closed-source reasoning MLLMs can achieve 6 to 12 gold medals; and most models still have a significant gap from full marks. These results highlight the performance gap between open-source models and top students, the strong reasoning abilities of closed-source models, and the remaining room for improvement. HiPhO, a human-aligned Olympiad benchmark for multimodal physical reasoning, is open-source at https://github.com/SciYu/HiPhO with a public leaderboard at https://phyarena.github.io/.

cs.AI↗

arXiv2025

CMPhysBench: A Benchmark for Evaluating Large Language Models in Condensed Matter Physics

We introduce CMPhysBench, designed to assess the proficiency of Large Language Models (LLMs) in Condensed Matter Physics, as a novel Benchmark. CMPhysBench is composed of more than 520 graduate-level meticulously curated questions covering both representative subfields and foundational theoretical frameworks of condensed matter physics, such as magnetism, superconductivity, strongly correlated systems, etc. To ensure a deep understanding of the problem-solving process,we focus exclusively on calculation problems, requiring LLMs to independently generate comprehensive solutions. Meanwhile, leveraging tree-based representations of expressions, we introduce the Scalable Expression Edit Distance (SEED) score, which provides fine-grained (non-binary) partial credit and yields a more accurate assessment of similarity between prediction and ground-truth. Our results show that even the best models, Grok-4, reach only 36 average SEED score and 28% accuracy on CMPhysBench, underscoring a significant capability gap, especially for this practical and frontier domain relative to traditional physics. The code anddataset are publicly available at https://github.com/CMPhysBench/CMPhysBench.

cs.LG↗

arXiv2025

Chem3DLLM: 3D Multimodal Large Language Models for Chemistry

In the real world, a molecule is a 3D geometric structure. Compared to 1D SMILES sequences and 2D molecular graphs, 3D molecules represent the most informative molecular modality. Despite the rapid progress of autoregressive-based language models, they cannot handle the generation of 3D molecular conformation due to several challenges: 1) 3D molecular structures are incompatible with LLMs' discrete token space, 2) integrating heterogeneous inputs like proteins, ligands, and text remains difficult within a unified model, and 3) LLMs lack essential scientific priors, hindering the enforcement of physical and chemical constraints during generation. To tackle these issues, we present Chem3DLLM, a unified protein-conditioned multimodal large language model. Our approach designs a novel reversible text encoding for 3D molecular structures using run-length compression, achieving 3x size reduction while preserving complete structural information. This enables seamless integration of molecular geometry with protein pocket features in a single LLM architecture. We employ reinforcement learning with stability-based rewards to optimize chemical validity and incorporate a lightweight protein embedding projector for end-to-end training. Experimental results on structure-based drug design demonstrate state-of-the-art performance with a Vina score of -7.21, validating our unified multimodal approach for practical drug discovery applications.

cs.CE↗

arXiv2025

DONOD: Efficient and Generalizable Instruction Fine-Tuning for LLMs via Model-Intrinsic Dataset Pruning

Ad-hoc instruction fine-tuning of large language models (LLMs) is widely adopted for domain-specific adaptation. While domain-specific supervised fine-tuning (SFT) is effective and efficient, it often weakens cross-domain generalization and struggles with noisy training data. To address these challenges, we propose DONOD, a lightweight model-intrinsic data pruning method. Our approach evaluates data using two model-parameter-based metrics: Delta of Norm (DON), which captures the cumulative influence on model weights, and Norm of Delta (NOD), which quantifies weight instability. Moreover, by employing the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) algorithm, we effectively filter noisy, unlearnable, and generalization-harming samples without relying on auxiliary models during the SFT process. Experiments on mathematical tasks demonstrate that data selected by DONOD achieves superior fine-tuning efficiency and improved robustness against noisy data. By filtering out 70% of the whole dataset, we improve target-domain accuracy by 14.90% and cross-domain accuracy by 5.67%. Meanwhile, our selected data present superior cross-architecture generalization. Data pruned by smaller models (e.g., Llama 3.1-8B) generalize effectively on larger models (e.g., Llama 2-13B). Compared to existing related methodologies, DONOD demonstrates comparable or superior performance while remaining dataset-agnostic, enabling broader applicability. Code will be made publicly available.

cs.AI↗

arXiv2025

$Δ$-AttnMask: Attention-Guided Masked Hidden States for Efficient Data Selection and Augmentation

Visual Instruction Finetuning (VIF) is pivotal for post-training Vision-Language Models (VLMs). Unlike unimodal instruction finetuning in plain-text large language models, which mainly requires instruction datasets to enable model instruction-following ability, VIF also requires multimodal data to enable joint visual and textual understanding; therefore, it typically requires more data. Consequently, VIF imposes stricter data selection challenges: the method must scale efficiently to handle larger data demands while ensuring the quality of both visual and textual content, as well as their alignment. Despite its critical impact on performance, data selection for VIF remains an understudied area. In this paper, we propose $Δ$-AttnMask. This data-efficient framework quantifies sample quality through attention-guided masking of the model's hidden states, jointly evaluating image-text pairs without requiring domain labels, auxiliary models, or extra training. By computing loss differences ($Δ$) between the original states and states masked using high-attention regions, $Δ$-AttnMask intrinsically assesses sample quality. Experiments across multiple VLMs and datasets show that $Δ$-AttnMask achieves state-of-the-art performance with just 20% of data, accelerating training by 5x while surpassing full-dataset baselines by +10.1% in overall accuracy. Its model-agnostic and data-agnostic design ensures broad applicability across modalities and architectures.

cs.CV↗

arXiv2025

CMT: A Cascade MAR with Topology Predictor for Multimodal Conditional CAD Generation

While accurate and user-friendly Computer-Aided Design (CAD) is crucial for industrial design and manufacturing, existing methods still struggle to achieve this due to their over-simplified representations or architectures incapable of supporting multimodal design requirements. In this paper, we attempt to tackle this problem from both methods and datasets aspects. First, we propose a cascade MAR with topology predictor (CMT), the first multimodal framework for CAD generation based on Boundary Representation (B-Rep). Specifically, the cascade MAR can effectively capture the ``edge-counters-surface'' priors that are essential in B-Reps, while the topology predictor directly estimates topology in B-Reps from the compact tokens in MAR. Second, to facilitate large-scale training, we develop a large-scale multimodal CAD dataset, mmABC, which includes over 1.3 million B-Rep models with multimodal annotations, including point clouds, text descriptions, and multi-view images. Extensive experiments show the superior of CMT in both conditional and unconditional CAD generation tasks. For example, we improve Coverage and Valid ratio by +10.68% and +10.3%, respectively, compared to state-of-the-art methods on ABC in unconditional generation. CMT also improves +4.01 Chamfer on image conditioned CAD generation on mmABC.

cs.CV↗

arXiv2025

Hypergraph Mamba for Efficient Whole Slide Image Understanding

Whole Slide Images (WSIs) in histopathology pose a significant challenge for extensive medical image analysis due to their ultra-high resolution, massive scale, and intricate spatial relationships. Although existing Multiple Instance Learning (MIL) approaches like Graph Neural Networks (GNNs) and Transformers demonstrate strong instance-level modeling capabilities, they encounter constraints regarding scalability and computational expenses. To overcome these limitations, we introduce the WSI-HGMamba, a novel framework that unifies the high-order relational modeling capabilities of the Hypergraph Neural Networks (HGNNs) with the linear-time sequential modeling efficiency of the State Space Models. At the core of our design is the HGMamba block, which integrates message passing, hypergraph scanning & flattening, and bidirectional state space modeling (Bi-SSM), enabling the model to retain both relational and contextual cues while remaining computationally efficient. Compared to Transformer and Graph Transformer counterparts, WSI-HGMamba achieves superior performance with up to 7* reduction in FLOPs. Extensive experiments on multiple public and private WSI benchmarks demonstrate that our method provides a scalable, accurate, and efficient solution for slide-level understanding, making it a promising backbone for next-generation pathology AI systems.

cs.CV↗

arXiv2025

Iterative Pretraining Framework for Interatomic Potentials

Machine learning interatomic potentials (MLIPs) enable efficient molecular dynamics (MD) simulations with ab initio accuracy and have been applied across various domains in physical science. However, their performance often relies on large-scale labeled training data. While existing pretraining strategies can improve model performance, they often suffer from a mismatch between the objectives of pretraining and downstream tasks or rely on extensive labeled datasets and increasingly complex architectures to achieve broad generalization. To address these challenges, we propose Iterative Pretraining for Interatomic Potentials (IPIP), a framework designed to iteratively improve the predictive performance of MLIP models. IPIP incorporates a forgetting mechanism to prevent iterative training from converging to suboptimal local minima. Unlike general-purpose foundation models, which frequently underperform on specialized tasks due to a trade-off between generality and system-specific accuracy, IPIP achieves higher accuracy and efficiency using lightweight architectures. Compared to general-purpose force fields, this approach achieves over 80% reduction in prediction error and up to 4x speedup in the challenging Mo-S-O system, enabling fast and accurate simulations.

physics.comp-ph↗

arXiv2025

InternAgent: When Agent Becomes the Scientist -- Building Closed-Loop System from Hypothesis to Verification

Artificial Intelligence (AI) is accelerating the transformation of scientific research paradigms, not only enhancing research efficiency but also driving innovation. We introduce InternAgent, a unified closed-loop multi-agent framework to conduct Autonomous Scientific Research (ASR) across various scientific research fields, enabling researchers to tackle complicated problems in these fields with unprecedented speed and precision. InternAgent highlights three key advantages: 1) Scalability: InternAgent has demonstrated its versatility across 12 scientific research tasks, capable of generating innovative ideas to enhance the performance of baseline code. 2) Interactivity: InternAgent provides an interface for human expert feedback and multi-agent interaction in automated end-to-end processes, allowing for the seamless integration of domain expert knowledge. 3) Efficiency: InternAgent has achieved promising performance gains in several scientific fields with significantly less time cost compared to human efforts. For instance, in reaction yield prediction, it increased from 27.6% to 35.4% in just 12 hours; in enhancer activity prediction, accuracy rose from 0.65 to 0.79 with only 4 hours of processing; and in 2D semantic segmentation, precision advanced from 78.8% to 81.0% in a mere 30 hours.

cs.AI↗