arXiv subjects

Zekun Guo

Publications and source records attributed to Zekun Guo.

11 recordsLinked to original sources

arXiv2026

AgentRadio: Passive Awareness for Long-Horizon Multi-Agent Collaboration

Understanding large codebases is a long-horizon task for Large Language Model (LLM) agents: answering a single question can require building and running the software, tracing execution across files, and synthesizing evidence over tens of minutes. On SWE-Atlas QnA, a benchmark of long-horizon questions over production repositories, a single Claude Code agent (Opus 4.6) resolves only 32.3% of tasks. Dividing the work among agents with clean contexts mitigates this limitation. However, the subtasks of code comprehension are interdependent. One agent's findings can rewrite another's task, so agents must coordinate during execution, not only at phase boundaries. Existing multi-agent systems support such exchange only between phases, through staged handoffs or synchronized rounds. Communication and work remain mutually exclusive. A discovery made mid-execution cannot be shared until the next boundary. We present AgentRadio, an asynchronous message-passing layer that equips coding-agent harnesses with three primitives: threads, messages, and waiting for mentions. The last runs as a background task, surfacing teammates' messages without interrupting foreground work, so each agent remains passively aware of its peers and folds new findings into its ongoing task. Under a five-phase protocol of division of labor and negotiation, four agents organized by AgentRadio resolve 62.1% of tasks, 29.8 points above a single agent and above Claude Code with the newer Opus 4.8 (57.2%). Rubric-level analysis shows the gain growing with task difficulty, consistent with mid-course correction as the underlying mechanism. Our code is available at https://github.com/Coral-Protocol/AgentRadio.

cs.MA↗

arXiv2026

Deciphering Scientific Reasoning Steps from Outcome Data for Molecule Optimization

Emerging reasoning models hold promise for automating scientific discovery. However, their training is hindered by a critical supervision gap: experimental outcomes are abundant, whereas intermediate reasoning steps are rarely documented at scale. To bridge this gap, we propose DESRO, a framework for deciphering scientific reasoning from outcomes. By analyzing shared patterns and key differences within grouped data, a large language model (LLM) can recover the underlying logic. We instantiate this framework in molecule optimization, a pivotal stage in drug discovery that traditionally relies on the iterative reasoning of medicinal chemists. Across 2.3 million molecular property records, our framework infers optimization rationales by grouping molecules with shared fragments, then using an LLM to analyze how structural variations correlate with property differences. Based on the derived data, we train a model that conducts molecule optimization through an interpretable reasoning process. DESRO achieves the highest success rates on 15 out of 18 tasks, spanning both single- and multi-property optimization of bioactivity and ADMET properties. The reasoning process enables robust generalization to out-of-distribution scenarios, including novel property combinations, unseen biological targets, and unseen properties defined solely by natural language descriptions. In retrospective case studies under strict temporal splits, the model autonomously reconstructs expert-level lead optimization trajectories. Additionally, our framework extends beyond molecule optimization to reaction ligand selection. Our results establish deciphering reasoning steps from outcome data as a viable paradigm for enabling scientific reasoning, providing a scalable approach to accelerate scientific discovery.

q-bio.BM↗

arXiv2026

Beyond Rule-Based Workflows: An Information-Flow-Orchestrated Multi-Agents Paradigm via Agent-to-Agent Communication from CORAL

Most existing Large Language Model (LLM)-based Multi-Agent Systems (MAS) rely on predefined workflows, where human engineers enumerate task states in advance and specify routing rules and contextual injections accordingly. Such workflow-driven designs are essentially rule-based decision trees, which suffer from two fundamental limitations: they require substantial manual effort to anticipate and encode possible task states, and they cannot exhaustively cover the state space of complex real-world tasks. To address these issues, we propose an Information-Flow-Orchestrated Multi-Agent Paradigm via Agent-to-Agent (A2A) Communication from CORAL, in which a dedicated information flow orchestrator continuously monitors task progress and dynamically coordinates other agents through the A2A toolkit using natural language, without relying on predefined workflows. We evaluate our approach on the general-purpose benchmark GAIA, using the representative workflow-based MAS OWL as the baseline while controlling for agent roles and underlying models. Under the pass@1 setting, our method achieves 63.64% accuracy, outperforming OWL's 55.15% by 8.49 percentage points with comparable token consumption. Further case-level analysis shows that our paradigm enables more flexible task monitoring and more robust handling of edge cases. Our implementation is publicly available at: https://github.com/Coral-Protocol/Beyond-Rule-Based-Workflows

cs.AI↗

arXiv2025

MolChord: Structure-Sequence Alignment for Protein-Guided Drug Design

Structure-based drug design (SBDD), which maps target proteins to candidate molecular ligands, is a fundamental task in drug discovery. Effectively aligning protein structural representations with molecular representations, and ensuring alignment between generated drugs and their pharmacological properties, remains a critical challenge. To address these challenges, we propose MolChord, which integrates two key techniques: (1) to align protein and molecule structures with their textual descriptions and sequential representations (e.g., FASTA for proteins and SMILES for molecules), we leverage NatureLM, an autoregressive model unifying text, small molecules, and proteins, as the molecule generator, alongside a diffusion-based structure encoder; and (2) to guide molecules toward desired properties, we curate a property-aware dataset by integrating preference data and refine the alignment process using Direct Preference Optimization (DPO). Experimental results on CrossDocked2020 demonstrate that our approach achieves state-of-the-art performance on key evaluation metrics, highlighting its potential as a practical tool for SBDD.

cs.AI↗

arXiv2025

Anemoi: A Semi-Centralized Multi-agent System Based on Agent-to-Agent Communication MCP server from Coral Protocol

Recent advances in generalist multi-agent systems (MAS) have largely followed a context-engineering plus centralized paradigm, where a planner agent coordinates multiple worker agents through unidirectional prompt passing. While effective under strong planner models, this design suffers from two critical limitations: (1) strong dependency on the planner's capability, which leads to degraded performance when a smaller LLM powers the planner; and (2) limited inter-agent communication, where collaboration relies on prompt concatenation rather than genuine refinement through structured discussions. To address these challenges, we propose Anemoi, a semi-centralized MAS built on the Agent-to-Agent (A2A) communication MCP server from Coral Protocol. Unlike traditional designs, Anemoi enables structured and direct inter-agent collaboration, allowing all agents to monitor progress, assess results, identify bottlenecks, and propose refinements in real time. This paradigm reduces reliance on a single planner, supports adaptive plan updates, and minimizes redundant context passing, resulting in more scalable execution. Evaluated on the GAIA benchmark, Anemoi achieved 52.73% accuracy with a small LLM (GPT-4.1-mini) as the planner, surpassing the strongest open-source baseline OWL (43.63%) by +9.09% under identical LLM settings. Our implementation is publicly available at https://github.com/Coral-Protocol/Anemoi.

cs.MA↗

arXiv2025

SimuGen: Multi-modal Agentic Framework for Constructing Block Diagram-Based Simulation Models

Recent advances in large language models (LLMs) have shown impressive performance in mathematical reasoning and code generation. However, LLMs still struggle in the simulation domain, particularly in generating Simulink models, which are essential tools in engineering and scientific research. Our preliminary experiments indicate that LLM agents often fail to produce reliable and complete Simulink simulation code from text-only inputs, likely due to the lack of Simulink-specific data in their pretraining. To address this challenge, we propose SimuGen, a multimodal agent-based framework that automatically generates accurate Simulink simulation code by leveraging both the visual Simulink diagram and domain knowledge. SimuGen coordinates several specialized agents, including an investigator, unit test reviewer, code generator, executor, debug locator, and report writer, supported by a domain-specific knowledge base. This collaborative and modular design enables interpretable, robust, and reproducible Simulink simulation generation. Our source code is publicly available at https://github.com/renxinxing123/SimuGen_beta.

cs.LG↗

arXiv2025

Nature Language Model: Deciphering the Language of Nature for Scientific Discovery

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, RNA and even cells. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) top performance across different domains, matching or surpassing state-of-the-art specialist models. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

cs.AI↗

arXiv2025

Can AI automatically analyze public opinion? A LLM agents-based agentic pipeline for timely public opinion analysis

This study proposes and implements the first LLM agents based agentic pipeline for multi task public opinion analysis. Unlike traditional methods, it offers an end-to-end, fully automated analytical workflow without requiring domain specific training data, manual annotation, or local deployment. The pipeline integrates advanced LLM capabilities into a low-cost, user-friendly framework suitable for resource constrained environments. It enables timely, integrated public opinion analysis through a single natural language query, making it accessible to non-expert users. To validate its effectiveness, the pipeline was applied to a real world case study of the 2025 U.S. China tariff dispute, where it analyzed 1,572 Weibo posts and generated a structured, multi part analytical report. The results demonstrate some relationships between public opinion and governmental decision-making. These contributions represent a novel advancement in applying generative AI to public governance, bridging the gap between technical sophistication and practical usability in public opinion monitoring.

cs.CY↗

arXiv2025

Can Large Language Model Agents Balance Energy Systems?

This paper presents a hybrid approach that integrates Large Language Models (LLMs) with a multi-scenario Stochastic Unit Commitment (SUC) framework to enhance both efficiency and reliability under high wind generation uncertainties. In a 10-trial study on the test energy system, the traditional SUC approach incurs an average total cost of 187.68 million dollars, whereas the LLM-assisted SUC (LLM-SUC) achieves a mean cost of 185.58 million dollars (range: 182.61 to 188.65 million dollars), corresponding to a cost reduction of 1.1 to 2.7 percent. Furthermore, LLM-SUC reduces load curtailment by 26.3 percent (2.24 plus/minus 0.31 GWh versus 3.04 GWh for SUC), while both methods maintain zero wind curtailment. Detailed temporal analysis shows that LLM-SUC achieves lower costs in the majority of time intervals and consistently outperforms SUC in 90 percent of cases, with solutions clustering in a favorable cost-reliability region (Coefficient of Variation = 0.93 percent for total cost and 13.8 percent for load curtailment). By leveraging an LLM agent to guide generator commitment decisions and dynamically adjust to stochastic conditions, the proposed framework improves demand fulfillment and operational resilience.

eess.SY↗

arXiv2024

Regulator-Manufacturer AI Agents Modeling: Mathematical Feedback-Driven Multi-Agent LLM Framework

The increasing complexity of regulatory updates from global authorities presents significant challenges for medical device manufacturers, necessitating agile strategies to sustain compliance and maintain market access. Concurrently, regulatory bodies must effectively monitor manufacturers' responses and develop strategic surveillance plans. This study employs a multi-agent modeling approach, enhanced with Large Language Models (LLMs), to simulate regulatory dynamics and examine the adaptive behaviors of key actors, including regulatory bodies, manufacturers, and competitors. These agents operate within a simulated environment governed by regulatory flow theory, capturing the impacts of regulatory changes on compliance decisions, market adaptation, and innovation strategies. Our findings illuminate the influence of regulatory shifts on industry behaviour and identify strategic opportunities for improving regulatory practices, optimizing compliance, and fostering innovation. By leveraging the integration of multi-agent systems and LLMs, this research provides a novel perspective and offers actionable insights for stakeholders navigating the evolving regulatory landscape of the medical device industry.

cs.AI↗

arXiv2023

NTIRE 2023 Quality Assessment of Video Enhancement Challenge

This paper reports on the NTIRE 2023 Quality Assessment of Video Enhancement Challenge, which will be held in conjunction with the New Trends in Image Restoration and Enhancement Workshop (NTIRE) at CVPR 2023. This challenge is to address a major challenge in the field of video processing, namely, video quality assessment (VQA) for enhanced videos. The challenge uses the VQA Dataset for Perceptual Video Enhancement (VDPVE), which has a total of 1211 enhanced videos, including 600 videos with color, brightness, and contrast enhancements, 310 videos with deblurring, and 301 deshaked videos. The challenge has a total of 167 registered participants. 61 participating teams submitted their prediction results during the development phase, with a total of 3168 submissions. A total of 176 submissions were submitted by 37 participating teams during the final testing phase. Finally, 19 participating teams submitted their models and fact sheets, and detailed the methods they used. Some methods have achieved better results than baseline methods, and the winning methods have demonstrated superior prediction performance.

cs.CV↗