Zhuofan Shi

Ningyuan Li, Haiyang Shen, Mugeng Liu et al.

Recent advances in large language models and tool-using agents have expanded the range of benchmarked web tasks. Yet an important class of specialized retrieval tasks remains undercharacterized. On many specialized data-retrieval websites, answer-bearing evidence becomes accessible only after establishing the correct site-specific retrieval state through filters, views, hierarchies, or scopes. We term this capability state-gated retrieval (SGR). We introduce SGR-Bench, a benchmark for this setting containing 100 expert-curated tasks spanning six source families and 12 public data ecosystems. Each task requires discovering the appropriate website and configuring its site-specific retrieval state to produce a structured answer. SGR-Bench pairs constraint-guided and goal-oriented formulations of the same underlying problems, enabling controlled comparisons between explicit and implicit guidance for state-gated retrieval. We evaluate eight CLI-based agentic LLM systems and three commercial search-agent products. On SGR-Bench, the strongest system reaches only 66.18% item-level F1, while row-level F1 remains much lower. A manual audit of 156 analyzable failed CLI trajectories shows why: agents often reach a relevant web source, but establish the wrong site-specific retrieval state. Retrieval-scope drift (37.2%) and criterion mismatch (27.6%) dominate, whereas final answer composition accounts for only 10.3%. The dataset and single-case evaluation instructions are available at https://huggingface.co/datasets/PKUAIWeb/SGR-BENCH.

Haiyang Shen, Taian Guo, Xuanzhong Chen et al.

Although LLMs have made substantial progress in reasoning, systematically producing frontier-level reasoning data remains difficult. Existing synthesis methods often have limited visibility into the structural factors that govern problem difficulty, which can result in narrow diversity and unstable difficulty control. In this work, we view the difficulty of a reasoning problem as arising from the accumulation of atomic knowledge-reasoning transformations, which we term thought modes. Building on this perspective, we propose MindLoom, a framework for synthesizing frontier-level reasoning data through compositional thought mode engineering. Given a collection of hard problems with verified solutions, MindLoom first decomposes those solutions into thought mode chains that reveal each problem's construction logic. It then trains a retrieval model that matches problem states to compatible thought modes, providing guidance on which reasoning challenges to introduce during synthesis. New problems are composed by iteratively applying retrieved thought modes to seed questions, with distribution-aligned sampling to encourage diverse reasoning coverage. Finally, a rollout-based judging stage labels generated questions by difficulty and supplies judged-correct responses for supervised fine-tuning. We evaluate MindLoom on nine benchmarks covering five STEM disciplines and four mathematical reasoning tasks across multiple model families and sizes. Models fine-tuned on MindLoom-generated data achieves favorable performances over base models, distillation, and external-data baselines across the reported benchmarks. Ablation studies indicate the contribution of each component, and further analysis suggests that MindLoom covers a broad range of reasoning patterns while maintaining useful difficulty control. We have open-sourced our implementation at https://github.com/EachSheep/MindLoom.

Ronghao Dang, Zhuofan Shi, Liuyi Wang et al.

Object navigation tasks require agents to locate specific objects in unknown environments based on visual information. Previously, graph convolutions were used to implicitly explore the relationships between objects. However, due to differences in visibility among objects, it is easy to generate biases in object attention. Thus, in this paper, we propose a directed object attention (DOA) graph to guide the agent in explicitly learning the attention relationships between objects, thereby reducing the object attention bias. In particular, we use the DOA graph to perform unbiased adaptive object attention (UAOA) on the object features and unbiased adaptive image attention (UAIA) on the raw images, respectively. To distinguish features in different branches, a concise adaptive branch energy distribution (ABED) method is proposed. We assess our methods on the AI2-Thor dataset. Compared with the state-of-the-art (SOTA) method, our method reports 7.4%, 8.1% and 17.6% increase in success rate (SR), success weighted by path length (SPL) and success weighted by action efficiency (SAE), respectively.

Zhuofan Shi, Peilun Jia, Baoqin Sun et al.

Recent deep research systems have improved the ability of large language models to produce long, grounded reports through iterative retrieval and reasoning. However, most text-centered systems rely mainly on textual evidence, while multimodal systems often retrieve images only weakly or generate charts themselves, leaving source figures underused as evidence. We present ViDR, a multimodal deep research framework that grounds long-form reports in source figures. ViDR treats source figures as retrievable, interpretable, routable, and verifiable evidence objects, while still generating analytical charts when needed. It builds an evidence-indexed outline linking claims to textual and visual evidence, refines noisy web images into source-figure evidence atoms through context-aware filtering, outline-aware reranking, and VLM-based visual analysis, and generates each section with section-specific evidence. ViDR further validates visual references to reduce hallucinated or misplaced figures. We also introduce MMR Bench+, a benchmark for evaluating visual evidence use in deep research reports, covering source-figure retrieval, placement, interpretation, verifiability, and analytical chart generation. Experiments show that ViDR improves overall report quality, source-figure integration, and verifiability over strong commercial and open-source baselines. These results suggest that source visual evidence is important for multimodal deep research, as it strengthens evidential grounding, visual support, and report verifiability.

Zhuofan Shi, Hubao A, Yufei Shao et al.

Molecular dynamics (MD) simulations are essential for understanding atomic-scale behaviors in materials science, yet writing LAMMPS scripts remains highly specialized and time-consuming tasks. Although LLMs show promise in code generation and domain-specific question answering, their performance in MD scenarios is limited by scarce domain data, the high deployment cost of state-of-the-art LLMs, and low code executability. Building upon our prior MDAgent, we present MDAgent2, the first end-to-end framework capable of performing both knowledge Q&A and code generation within the MD domain. We construct a domain-specific data-construction pipeline that yields three high-quality datasets spanning MD knowledge, question answering, and code generation. Based on these datasets, we adopt a three stage post-training strategy--continued pre-training (CPT), supervised fine-tuning (SFT), and reinforcement learning (RL)--to train two domain-adapted models, MD-Instruct and MD-Code. Furthermore, we introduce MD-GRPO, a closed-loop RL method that leverages simulation outcomes as reward signals and recycles low-reward trajectories for continual refinement. We further build MDAgent2-RUNTIME, a deployable multi-agent system that integrates code generation, execution, evaluation, and self-correction. Together with MD-EvalBench proposed in this work, the first benchmark for LAMMPS code generation and question answering, our models and system achieve performance surpassing several strong baselines.This work systematically demonstrates the adaptability and generalization capability of large language models in industrial simulation tasks, laying a methodological foundation for automatic code generation in AI for Science and industrial-scale simulations. URL: https://github.com/FredericVAN/PKU_MDAgent2

Sixiong Xie, Zhuofan Shi, Haiyang Shen et al.

Deep research, in which an agent searches the open web, collects evidence, and derives an answer through extended reasoning, is a prominent use case for frontier language models. Frontier deep research products score high on existing benchmarks, making it difficult to distinguish their capabilities from current evaluation data alone. We introduce DeepWeb-Bench, a deep research benchmark that is substantially harder than existing benchmarks for the current frontier. Difficulty comes from three properties of the data itself: each task requires massive evidence collection, cross-source reconciliation, and long-horizon multi-step derivation. We represent these three sources of difficulty as four capability families (Retrieval, Derivation, Reasoning, and Calibration) and report results sliced by family. Every reference answer is accompanied by a source-provenance record with four disclosure levels and cross-source checks where available, making scores easier to audit against the underlying evidence. We evaluate DeepWeb-Bench on nine frontier models and report three findings: (1) retrieval is not the bottleneck, as retrieval failures account for only 12-14% of errors while derivation and calibration failures account for over 70%; (2) strong and weak models fail in qualitatively different ways, with strong models' errors dominated by incomplete derivation and weak models' by hallucinated precision; and (3) models exhibit genuine specialization across domains, with cross-model agreement of only rho = 0.61 and per-case disagreement reaching 18.8 percentage points. The public benchmark release includes the data, rubrics, and evaluation code.

Zhuofan Shi, Zijie Guo, Xinjian Ma et al.

The rapid growth of multi-source, heterogeneous, and multimodal scientific data has increasingly exposed the limitations of traditional data management. Most existing DeepResearch (DR) efforts focus primarily on web search while overlooking local private data. Consequently, these frameworks exhibit low retrieval efficiency for private data and fail to comply with the FAIR principles, ultimately resulting in inefficiency and limited reusability. To this end, we propose IoDResearch (Internet of Data Research), a private data-centric Deep Research framework that operationalizes the Internet of Data paradigm. IoDResearch encapsulates heterogeneous resources as FAIR-compliant digital objects, and further refines them into atomic knowledge units and knowledge graphs, forming a heterogeneous graph index for multi-granularity retrieval. On top of this representation, a multi-agent system supports both reliable question answering and structured scientific report generation. Furthermore, we establish the IoD DeepResearch Benchmark to systematically evaluate both data representation and Deep Research capabilities in IoD scenarios. Experimental results on retrieval, QA, and report-writing tasks show that IoDResearch consistently surpasses representative RAG and Deep Research baselines. Overall, IoDResearch demonstrates the feasibility of private-data-centric Deep Research under the IoD paradigm, paving the way toward more trustworthy, reusable, and automated scientific discovery.

Sixiong Xie, Zhuofan Shi, Haiyang Shen et al.

As the capabilities of large language model (LLM) agents continue to advance, their advanced social behaviors, such as cooperation, deception, and collusion, call for systematic evaluation. However, existing benchmarks often emphasize a single capability dimension or rely solely on behavioral outcomes, overlooking rich process information from agents' decision reasoning and communicative interactions. To address this gap, we propose M3-Bench, a multi-stage benchmark for mixed-motive games, together with a process-aware evaluation framework that conducts synergistic analysis across three modules: BTA (Behavioral Trajectory Analysis), RPA (Reasoning Process Analysis), and CCA (Communication Content Analysis). Furthermore, we integrate the Big Five personality model and Social Exchange Theory to aggregate multi-dimensional evidence into interpretable social behavior portraits, thereby characterizing agents' personality traits and capability profiles beyond simple task scores or outcome-based metrics. Experimental results show that M3-Bench can reliably distinguish diverse social behavior competencies across models, and it reveals that some models achieve seemingly reasonable behavioral outcomes while exhibiting pronounced inconsistencies in their reasoning and communication.