arXiv subjects

Yuyuan Feng

Publications and source records attributed to Yuyuan Feng.

5 recordsLinked to original sources

arXiv2026

Graph Engineering in the Era of LLM Agents: From Individual Intelligence to System Intelligence

LLMs have evolved from language generators to autonomous agents capable of complex, long-horizon tasks. This evolution has produced paradigms including Prompt Engineering to elicit model capabilities, Context Engineering to manage information access, Harness Engineering to organize external tools and resources, and Loop Engineering to support continual reflection and self-improvement. Yet as tasks grow more complex, individual intelligence faces a fundamental limit: many tasks require heterogeneous expertise, interdependent subtasks, parallel execution, independent verification, and persistent state, exceeding any single agent's organizational capacity. Augmenting one agent's capabilities or context cannot resolve this architectural mismatch; intelligence must instead be distributed across specialized agents and organized at the system level. We call this System Intelligence: an agent system's ability to organize and coordinate multiple intelligent components into a coherent, adaptive whole pursuing a shared objective. Achieving it requires more than adding agents; it demands explicit structures to organize work, coordinate heterogeneous agents, and maintain evolving execution states. We introduce Graph Engineering, an emerging paradigm for next-generation agent systems. Unlike prior paradigms that mainly optimize individual interactions or agent-level behavior, Graph Engineering constructs explicit, dynamic, evolving graph structures representing tasks, agents, and system states. These abstractions provide a unified foundation for organizing complex objectives, orchestrating heterogeneous agents, modeling system dynamics, and enabling scalable agent evolution. We systematically review the principles, methodologies, and applications of Graph Engineering for LLM agents. Related papers, open-source data, and projects are collected at https://github.com/DEEP-JLU/Awesome-Graph-Engineering.

cs.IR↗

arXiv2025

Backdoor or Manipulation? Graph Mixture of Experts Can Defend Against Various Graph Adversarial Attacks

Extensive research has highlighted the vulnerability of graph neural networks (GNNs) to adversarial attacks, including manipulation, node injection, and the recently emerging threat of backdoor attacks. However, existing defenses typically focus on a single type of attack, lacking a unified approach to simultaneously defend against multiple threats. In this work, we leverage the flexibility of the Mixture of Experts (MoE) architecture to design a scalable and unified framework for defending against backdoor, edge manipulation, and node injection attacks. Specifically, we propose an MI-based logic diversity loss to encourage individual experts to focus on distinct neighborhood structures in their decision processes, thus ensuring a sufficient subset of experts remains unaffected under perturbations in local structures. Moreover, we introduce a robustness-aware router that identifies perturbation patterns and adaptively routes perturbed nodes to corresponding robust experts. Extensive experiments conducted under various adversarial settings demonstrate that our method consistently achieves superior robustness against multiple graph adversarial attacks.

cs.LG↗

arXiv2025

Do Explanations Increase the Risk of Decision Logic Leakage? Explanation-Guided Stealing of Graph Models

Graph Neural Networks (GNNs) have become essential tools for analyzing graph-structured data in domains such as drug discovery and financial analysis, leading to a growing demand for model transparency. Recent advances in explainable GNNs have addressed this need by revealing important subgraphs that influence predictions, but these explanation mechanisms may inadvertently expose these models to security risks. This paper investigates how such explanations potentially leak critical decision logic that can be exploited for model stealing. We propose {\method}, a novel stealing framework that integrates explanation alignment for capturing decision logic with guided data augmentation for efficient training under limited queries, enabling effective replication of both the predictive behavior and underlying reasoning patterns of target models. Experiments on molecular graph datasets demonstrate that our approach shows advantages over conventional methods in model stealing. This work highlights important security considerations for the deployment of explainable GNNs in sensitive domains and suggests the need for protective measures against explanation-based attacks. Our code is available at https://github.com/beanmah/EGSteal.

cs.LG↗

arXiv2025

General Protein Pretraining or Domain-Specific Designs? Benchmarking Protein Modeling on Realistic Applications

Recently, extensive deep learning architectures and pretraining strategies have been explored to support downstream protein applications. Additionally, domain-specific models incorporating biological knowledge have been developed to enhance performance in specialized tasks. In this work, we introduce $\textbf{Protap}$, a comprehensive benchmark that systematically compares backbone architectures, pretraining strategies, and domain-specific models across diverse and realistic downstream protein applications. Specifically, Protap covers five applications: three general tasks and two novel specialized tasks, i.e., enzyme-catalyzed protein cleavage site prediction and targeted protein degradation, which are industrially relevant yet missing from existing benchmarks. For each application, Protap compares various domain-specific models and general architectures under multiple pretraining settings. Our empirical studies imply that: (i) Though large-scale pretraining encoders achieve great results, they often underperform supervised encoders trained on small downstream training sets. (ii) Incorporating structural information during downstream fine-tuning can match or even outperform protein language models pretrained on large-scale sequence corpora. (iii) Domain-specific biological priors can enhance performance on specialized downstream tasks. Code and datasets are publicly available at https://github.com/Trust-App-AI-Lab/protap.

q-bio.BM↗

arXiv2024

Adapting Amidst Degradation: Cross Domain Li-ion Battery Health Estimation via Physics-Guided Test-Time Training

Health modeling of lithium-ion batteries (LIBs) is crucial for safe and efficient energy management and carries significant socio-economic implications. Although Machine Learning (ML)-based State of Health (SOH) estimation methods have made significant progress in accuracy, the scarcity of high-quality LIB data remains a major obstacle. Existing transfer learning methods for cross-domain LIB SOH estimation have significantly alleviated the labeling burden of target LIB data, however, they still require sufficient unlabeled target data (UTD) for effective adaptation to the target domain. Collecting this UTD is challenging due to the time-consuming nature of degradation experiments. To address this issue, we introduce a practical Test-Time Training framework, BatteryTTT, which adapts the model continually using each UTD collected amidst degradation, thereby significantly reducing data collection time. To fully utilize each UTD, BatteryTTT integrates the inherent physical laws of modern LIBs into self-supervised learning, termed Physcics-Guided Test-Time Training. Additionally, we explore the potential of large language models (LLMs) in battery sequence modeling by evaluating their performance in SOH estimation through model reprogramming and prefix prompt adaptation. The combination of BatteryTTT and LLM modeling, termed GPT4Battery, achieves state-of-the-art generalization results across current LIB benchmarks. Furthermore, we demonstrate the practical value and scalability of our approach by deploying it in our real-world battery management system (BMS) for 300Ah large-scale energy storage LIBs.

cs.LG↗