arXiv subjects

Shufei Zhang

Publications and source records attributed to Shufei Zhang.

At least 19 recordsLinked to original sources

arXiv2026

AMRM-Pure: Semantic-Preserving Adversarial Purification

Adversarial purification is a defense technique that employs generative models to remove adversarial perturbations. Current methods often rely on powerful generators, typically diffusion models, and focus on reducing the gap between adversarial and clean samples in the feature space, while overlooking semantic correlation within a single sample. To address this issue, we explore adversarial purification from the perspective of preserving semantic relationships among image patches. We employ an Attentive Mask Reconstruction Model (AMRM), which shows superior performance. Our theoretical and experimental analysis reveals that AMRM is highly sensitive to adversarial noise, as such noise significantly distorts patch relationships. Based on this observation, we propose AMRM-Pure, a purification framework that denoises adversarial inputs by preserving patch-level semantics, and formulate this process as a tractable optimization problem with respect to the input. To further enhance robustness, we finetune AMRM-Pure with classification loss to strengthen semantic consistency. We apply our insight to two AMRM architectures, including Mask Autoencoder (MAE) and MaskDiT. Extensive experiments confirm the effectiveness of our method, establishing new state-of-the-art performance across multiple benchmarks.

cs.CR↗

arXiv2026

Do LLMs Truly Generalize in the Molecular Domain? A Perturbation-Based Analysis

Large Language Models (LLMs) have recently shown promise in molecular discovery, yet a gap remains between their probabilistic nature over discrete sequential tokens and the rigid topological constraints of chemical space. This raises the question of whether molecular LLMs can generalize beyond the local neighborhoods induced by their sequence-based representations. To systematically investigate this question, we introduce a Molecular Perturbation framework that generates syntax-valid structural variants of training molecules under controlled Graph Edit Distance (GED) to probe the manifold regularity of molecular LLMs. Our analysis shows that even a single edit can cause substantial performance drops on common molecular tasks, revealing a narrow local trust region and fragile sensitivity to structural changes. Since similar molecules tend to exhibit similar properties, In-Context Tuning (ICT), which anchors predictions on structurally similar molecules, offers a natural way to mitigate such fragility. Our experiments also examine whether ICT confers robustness under controlled structural perturbations, and the results suggest that it can partially expand the local trust region and offer a promising direction for stabilizing molecular LLMs against structural variation.

cs.LG↗

arXiv2026

Scaling the Horizon, Not the Parameters: Reaching Trillion-Parameter Performance with a 35B Agent

We introduce Agents-A1, a 35B Mixture-of-Experts Agentic Model that reaches trillion-parameter-level performance by scaling the agent horizon. We investigate agent-horizon scaling from two perspectives: scaling long-horizon trajectories and scaling heterogeneous agent abilities. To support this goal, we build a long-horizon knowledge-action infrastructure that connects external knowledge, actions, observations, and verifier outcomes, producing agentic trajectories with an average length of 45K tokens. Based on this, we train Agents-A1 with a three-stage recipe. First, we perform full-domain supervised fine-tuning to align the base model with broad agentic behaviors. Second, we train domain-level teacher models to capture specialized expertise in each domain. Third, we propose a multi-teacher domain-routed on-policy distillation with salient vocabulary alignment to improve knowledge transfer efficiency across different domains, unifying six heterogeneous domains into one deployable student model. Agents-A1 achieves strong and broad performance for long-horizon agent benchmarks. Compared with 1T-parameter model such as Kimi-K2.6 and DeepSeek-V4-pro, Agents-A1 achieves leading results on SEAL-0 (56.4), IFBench (80.6), HiPhO (46.4), FrontierScience-Olympiad (79.0), and MolBench-Bind (56.8), and remains highly competitive on SciCode (44.3), HLE (47.6) and BrowseComp (75.5). We hope this work provides the community with a practical path for scaling the horizon using a 35B agent that can reach or match the performance of 1T models on long-horizon tasks.

cs.CL↗

arXiv2026

Deep Research in Physical Sciences: A Multi-Agent Framework and Comprehensive Benchmark

Deep research agents are Large Language Model (LLM)-based systems designed for autonomous, multi-step scientific reasoning, and they hold immense potential for accelerating research in the physical sciences. However, comprehensive and in-depth evaluations of their capabilities within this domain remain lacking. To address this gap, we introduce PhySciBench, a benchmark highly relevant to physical science research, comprising 200 expert-curated questions, balanced between physics and chemistry, across six task categories that reflect real-world scientific workflows. Evaluations of state-of-the-art models and agent systems on PhySciBench reveal limited performance; even the strongest baseline, Gemini Deep Research, achieves an accuracy of only 33.5%. Analysis of failure cases identifies three recurrent deficiencies: fragility in extended reasoning chains, limited knowledge transfer across steps, and a lack of physics-grounded self-verification. Motivated by these findings, we develop DelveAgent, a modular multi-agent framework equipped with an adaptive planning loop, dual-granularity memory, and a hierarchical physics-grounded reflection mechanism. Across four scientific benchmarks, DelveAgent improves accuracy by up to 7.5 percentage points while reducing inference costs to approximately one-third of the strongest baseline. These results establish the significance of PhySciBench as a critical benchmark for evaluating AI systems in the physical sciences and demonstrate that architectural specialization can effectively enhance the reliability of autonomous scientific research. Our data and code are publicly available at https://github.com/yigengjiang/physci-deepresearch.

physics.comp-ph↗

arXiv2026

Agents-K1: Towards Agent-native Knowledge Orchestration

Current LLM-based research agents have advanced through agent orchestration, yet largely overlook scientific knowledge orchestration. Existing works often reduce papers to abstracts, surface mentions, and flat \texttt{cites} edges, omitting key entities, claims, evidence, mechanisms, and method lineages essential for scientific reasoning. To this end, we introduce \textbf{Agents-K1}, an end-to-end knowledge orchestration pipeline that converts raw documents into agent-native scientific knowledge graphs. Agents-K1 integrates three components under a unifying theoretical foundation: a multimodal parser whose five-module schema captures entities, multimodal evidence, citations, and typed inter-entity relations across the full paper rather than abstracts alone; a 4B information-extraction backbone trained with GRPO under a rule-based reward; and a graphanything CLI, a tri-source agent interface that unifies web search, multimodal graph retrieval, and cross-document traversal. On top of this, we process 2.46 million scientific papers across six subjects to produce \textbf{Scholar-KG}, of which we release a one-million-paper subset, and the full Scholar-KG is accessible via the SCP link below. The same pipeline can be extended to general-domain corpora and to schema-conformant data synthesis. Extensive experiments demonstrate that Agents-K1 achieves superior performance in scientific information extraction, knowledge graph construction, and multi-hop scientific reasoning.

cs.AI↗

arXiv2026

Step-GRPO: Internalizing Dynamic Early Exit for Efficient Reasoning

Large reasoning models that use long chain-of-thought excel at problem-solving yet waste compute on redundant checks. Curbing this overthinking is hard: training-time length penalties can cripple ability, while inference-time early-exit adds system overhead. To bridge this gap, we propose Step-GRPO, a novel post-training framework that internalizes dynamic early-exit capabilities directly into the model. Step-GRPO shifts the optimization objective from raw tokens to semantic steps by utilizing linguistic markers to structure reasoning. We introduce a Dynamic Truncated Rollout mechanism that exposes the model to concise high-confidence trajectories during exploration, synergized with a Step-Aware Relative Reward that dynamically penalizes redundancy based on group-level baselines. Extensive experiments across three model sizes on diverse benchmarks demonstrate that Step-GRPO achieves a superior accuracy-efficiency trade-off. On Qwen3-8B, our method reduces token consumption by 32.0\% compared to the vanilla model while avoiding the accuracy degradation observed in traditional length-penalty methods.

cs.AI↗

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

Equivariant Evidential Deep Learning for Interatomic Potentials

Uncertainty quantification (UQ) is critical for assessing the reliability of machine learning interatomic potentials (MLIPs) in molecular dynamics (MD) simulations, identifying extrapolation regimes and enabling uncertainty-aware workflows such as active learning for training dataset construction. Existing UQ approaches for MLIPs are often limited by high computational cost or suboptimal performance. Evidential deep learning (EDL) provides a theoretically grounded single-model alternative that determines both aleatoric and epistemic uncertainty in a single forward pass. However, extending evidential formulations from scalar targets to vector-valued quantities such as atomic forces introduces substantial challenges, particularly in maintaining statistical self-consistency under rotational transformations. To address this, we propose \textit{Equivariant Evidential Deep Learning for Interatomic Potentials} ($\text{e}^2$IP), a backbone-agnostic framework that models atomic forces and their uncertainty jointly by representing uncertainty as a full $3\times3$ symmetric positive definite covariance tensor that transforms equivariantly under rotations. Experiments on diverse molecular benchmarks show that $\text{e}^2$IP provides a stronger accuracy-efficiency-reliability balance than the non-equivariant evidential baseline and the widely used ensemble method. It also achieves better data efficiency through the fully equivariant architecture while retaining single-model inference efficiency.

cs.LG↗

arXiv2026

InternAgent-1.5: A Unified Agentic Framework for Long-Horizon Autonomous Scientific Discovery

We introduce InternAgent-1.5, a unified system designed for end-to-end scientific discovery across computational and empirical domains. The system is built on a structured architecture composed of three coordinated subsystems for generation, verification, and evolution. These subsystems are supported by foundational capabilities for deep research, solution optimization, and long horizon memory. The architecture allows InternAgent-1.5 to operate continuously across extended discovery cycles while maintaining coherent and improving behavior. It also enables the system to coordinate computational modeling and laboratory experimentation within a single unified system. We evaluate InternAgent-1.5 on scientific reasoning benchmarks such as GAIA, HLE, GPQA, and FrontierScience, and the system achieves leading performance that demonstrates strong foundational capabilities. Beyond these benchmarks, we further assess two categories of discovery tasks. In algorithm discovery tasks, InternAgent-1.5 autonomously designs competitive methods for core machine learning problems. In empirical discovery tasks, it executes complete computational or wet lab experiments and produces scientific findings in earth, life, biological, and physical domains. Overall, these results show that InternAgent-1.5 provides a general and scalable framework for autonomous scientific discovery.

cs.AI↗

arXiv2025

SciEvalKit: An Open-source Evaluation Toolkit for Scientific General Intelligence

We introduce SciEvalKit, a unified benchmarking toolkit designed to evaluate AI models for science across a broad range of scientific disciplines and task capabilities. Unlike general-purpose evaluation platforms, SciEvalKit focuses on the core competencies of scientific intelligence, including Scientific Multimodal Perception, Scientific Multimodal Reasoning, Scientific Multimodal Understanding, Scientific Symbolic Reasoning, Scientific Code Generation, Science Hypothesis Generation and Scientific Knowledge Understanding. It supports six major scientific domains, spanning from physics and chemistry to astronomy and materials science. SciEvalKit builds a foundation of expert-grade scientific benchmarks, curated from real-world, domain-specific datasets, ensuring that tasks reflect authentic scientific challenges. The toolkit features a flexible, extensible evaluation pipeline that enables batch evaluation across models and datasets, supports custom model and dataset integration, and provides transparent, reproducible, and comparable results. By bridging capability-based evaluation and disciplinary diversity, SciEvalKit offers a standardized yet customizable infrastructure to benchmark the next generation of scientific foundation models and intelligent agents. The toolkit is open-sourced and actively maintained to foster community-driven development and progress in AI4Science.

cs.AI↗

arXiv2025

VASP Agent: An Agentic Framework for Autonomous First-principles Calculations

Large Language Models (LLMs) are increasingly embedded in agentic frameworks for scientific discovery. First-principles materials computation imposes a demanding standard for autonomy: successful execution depends on internally consistent inputs, supervision of long-running calculations, and verified outputs. Here we present VASP Agent, a coding-agent-centered system that combines reusable domain skills, deterministic tools, workspace-state inspection, runtime evidence, and scientific guardrails to execute multi-step VASP calculations. The system is evaluated across multiple tasks including structural relaxation, bandgap calculation, equilibrium lattice constant determination, and CO/Pt(111) adsorption. VASP Agent completes all evaluated cases, and its computed numerical results are compared with those obtained using pymatgen and other agentic tools. When large deviations occur, the calculation parameters produced by VASP Agent are more appropriate than those produced by LLM-based workflows. Failure analysis shows that errors that terminate fixed pipelines can be diagnosed and recovered under agentic control.

cs.AI↗

arXiv2025

Probing Scientific General Intelligence of LLMs with Scientist-Aligned Workflows

Despite advances in scientific AI, a coherent framework for Scientific General Intelligence (SGI)-the ability to autonomously conceive, investigate, and reason across scientific domains-remains lacking. We present an operational SGI definition grounded in the Practical Inquiry Model (PIM: Deliberation, Conception, Action, Perception) and operationalize it via four scientist-aligned tasks: deep research, idea generation, dry/wet experiments, and experimental reasoning. SGI-Bench comprises over 1,000 expert-curated, cross-disciplinary samples inspired by Science's 125 Big Questions, enabling systematic evaluation of state-of-the-art LLMs. Results reveal gaps: low exact match (10--20%) in deep research despite step-level alignment; ideas lacking feasibility and detail; high code executability but low execution result accuracy in dry experiments; low sequence fidelity in wet protocols; and persistent multimodal comparative-reasoning challenges. We further introduce Test-Time Reinforcement Learning (TTRL), which optimizes retrieval-augmented novelty rewards at inference, enhancing hypothesis novelty without reference answer. Together, our PIM-grounded definition, workflow-centric benchmark, and empirical insights establish a foundation for AI systems that genuinely participate in scientific discovery.

cs.AI↗

arXiv2025

Chem-R: Learning to Reason as a Chemist

Although large language models (LLMs) have significant potential to advance chemical discovery, current LLMs lack core chemical knowledge, produce unreliable reasoning trajectories, and exhibit suboptimal performance across diverse chemical tasks. To address these challenges, we propose Chem-R, a generalizable Chemical Reasoning model designed to emulate the deliberative processes of chemists. Chem-R is trained through a three-phase framework that progressively builds advanced reasoning capabilities, including: 1) Chemical Foundation Training, which establishes core chemical knowledge. 2) Chemical Reasoning Protocol Distillation, incorporating structured, expert-like reasoning traces to guide systematic and reliable problem solving. 3) Multi-task Group Relative Policy Optimization that optimizes the model for balanced performance across diverse molecular- and reaction-level tasks. This structured pipeline enables Chem-R to achieve state-of-the-art performance on comprehensive benchmarks, surpassing leading large language models, including Gemini-2.5-Pro and DeepSeek-R1, by up to 32% on molecular tasks and 48% on reaction tasks. Meanwhile, Chem-R also consistently outperforms the existing chemical foundation models across both molecular and reaction level tasks. These results highlight Chem-R's robust generalization, interpretability, and potential as a foundation for next-generation AI-driven chemical discovery. The code and model are available at https://github.com/davidweidawang/Chem-R.

cs.CE↗

arXiv2025

FlowSearch: Advancing deep research with dynamic structured knowledge flow

Deep research is an inherently challenging task that demands both breadth and depth of thinking. It involves navigating diverse knowledge spaces and reasoning over complex, multi-step dependencies, which presents substantial challenges for agentic systems. To address this, we propose FlowSearch, a multi-agent framework that actively constructs and evolves a dynamic structured knowledge flow to drive subtask execution and reasoning. FlowSearch is capable of strategically planning and expanding the knowledge flow to enable parallel exploration and hierarchical task decomposition, while also adjusting the knowledge flow in real time based on feedback from intermediate reasoning outcomes and insights. FlowSearch achieves competitive performance on both general and scientific benchmarks, including GAIA, HLE, GPQA and TRQA, demonstrating its effectiveness in multi-disciplinary research scenarios and its potential to advance scientific discovery. The code is available at https://github.com/InternScience/InternAgent.

cs.AI↗

arXiv2025

Plan Then Action:High-Level Planning Guidance Reinforcement Learning for LLM Reasoning

Large language models (LLMs) demonstrate strong reasoning abilities via Chain-of-Thought (CoT), but their token-level generation encourages local decisions and lacks global planning, often leading to redundant or inaccurate reasoning. Existing methods, such as tree-based search and reinforcement learning (RL), attempt to address this issue but incur high computational costs and still struggle to produce reliable reasoning trajectories. To address these challenges, we propose Plan-Then-Action Enhanced Reasoning with Group Relative Policy Optimization (PTA-GRPO), a two-stage framework designed to jointly improve high-level planning and fine-grained CoT reasoning. Specifically, in the first stage, a given LLM is responsible for summarizing CoT reasoning into compact high-level guidance, which is then leveraged for supervised fine-tuning. Then, we introduce a guidance-aware reinforcement learning method that jointly optimizes the final output and the quality of guidance, enhancing reasoning effectiveness. We evaluate PTA-GRPO on ten reasoning benchmarks across mathematics and natural sciences, using five diverse base models spanning multiple data modalities. The results show that PTA-GRPO consistently delivers significant improvements across models and tasks, demonstrating strong effectiveness and generalization.

cs.AI↗

arXiv2025

AOT*: Efficient Synthesis Planning via LLM-Empowered AND-OR Tree Search

Retrosynthesis planning enables the discovery of viable synthetic routes for target molecules, playing a crucial role in domains like drug discovery and materials design. Multi-step retrosynthetic planning remains computationally challenging due to exponential search spaces and inference costs. While Large Language Models (LLMs) demonstrate chemical reasoning capabilities, their application to synthesis planning faces constraints on efficiency and cost. To address these challenges, we introduce AOT*, a framework that transforms retrosynthetic planning by integrating LLM-generated chemical synthesis pathways with systematic AND-OR tree search. To this end, AOT* atomically maps the generated complete synthesis routes onto AND-OR tree components, with a mathematically sound design of reward assignment strategy and retrieval-based context engineering, thus enabling LLMs to efficiently navigate in the chemical space. Experimental evaluation on multiple synthesis benchmarks demonstrates that AOT* achieves SOTA performance with significantly improved search efficiency. AOT* exhibits competitive solve rates using 3-5$\times$ fewer iterations than existing LLM-based approaches, with the efficiency advantage becoming more pronounced on complex molecular targets.

cs.AI↗

arXiv2025

ChemBOMAS: Accelerated BO in Chemistry with LLM-Enhanced Multi-Agent System

Bayesian optimization (BO) is a powerful tool for scientific discovery in chemistry, yet its efficiency is often hampered by the sparse experimental data and vast search space. Here, we introduce ChemBOMAS: a large language model (LLM)-enhanced multi-agent system that accelerates BO through synergistic data- and knowledge-driven strategies. Firstly, the data-driven strategy involves an 8B-scale LLM regressor fine-tuned on a mere 1% labeled samples for pseudo-data generation, robustly initializing the optimization process. Secondly, the knowledge-driven strategy employs a hybrid Retrieval-Augmented Generation approach to guide LLM in dividing the search space while mitigating LLM hallucinations. An Upper Confidence Bound algorithm then identifies high-potential subspaces within this established partition. Across the LLM-refined subspaces and supported by LLM-generated data, BO achieves the improvement of effectiveness and efficiency. Comprehensive evaluations across multiple scientific benchmarks demonstrate that ChemBOMAS set a new state-of-the-art, accelerating optimization efficiency by up to 5-fold compared to baseline methods.

cs.LG↗

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↗