Papers

Machine learning and artificial intelligence will be deeply embedded in the intelligent systems humans use to automate tasking, optimize planning, and support decision-making. We present a critical review of uncertainty quantification (UQ) in large language models (LLMs), synthesizing insights from over 80 papers across leading venues (ACL, ASE, NeurIPS, ICML, AAAI, IJCAI, Nature, and others). We introduce UQ-Net, a unified probabilistic framework that combines Bayesian modeling, calibration, conformal prediction, and selective decision rules to disentangle epistemic and aleatoric uncertainty and to support reliable decision thresholds. UQ-Net integrates uncertainty estimates with calibration procedures and anomaly detection to enable safer selective deployment of LLM agents. Through case studies in medical diagnosis and code generation, we demonstrate that UQ-Net improves calibration and reduces predictive error by 15–20% relative to standard baselines. We survey existing evaluation practices and identify critical gaps: misalignment of consistency and entropy with factuality, lack of benchmarks for multi-episode interactions, and inconsistent metrics for calibration and tightness. We advocate for context-aware datasets, standardized metrics, and human-in-the-loop evaluations to better align UQ methods with deployment needs. Our review and proposed framework offer a principled foundation for operationalizing UQ in LLMs, advancing the development of trustworthy, responsible agentic AI for safety-sensitive, real-world applications.

The advancement of LLM-based agents is redefining AI for Science (AI4S) by enabling autonomous scientific research. Prominent LLMs exhibited expertise across multiple domains, catalysing constructions of domain-specialised scientific agents. Nevertheless, the profound epistemic and methodological gaps between AI and the natural sciences still impede the systematic design, training, and validation of these agents. This survey bridges the existing gap by presenting an exhaustive blueprint for scientific agents, spanning systematic construction methodologies, targeted capability enhancement, and rigorous evaluations. Anchored in the canonical scientific workflow, this paper (i) pinpoints the overview of scientific agents, starting with the development from general-purpose agents to scientific agents driven by articulated goal-orientation, then subsequently advancing a comprehensive taxonomy that organises existing agents by construction strategy and capability scope, and (ii) introduces a two-tier progressive framework, from scientific agents contrustion from scratch to targeted capability enhancement, for realizing autonomous scientific research. It is our aspiration that this survey will serve as guidance for researchers across various domains, facilitating the systematic design of domain-specific scientific agents and stimulating further innovation in AI-driven scientific research. To support long-term progress, we curate a live repository (\href{https://github.com/gudehhh666/Awesome_Scientific_Agent.git}{\textsc{Awesome\_Scientific\_Agent}}) that continuously aggregates emerging methods, benchmarks, and best practices.

This review examines the ongoing transformation of artificial intelligence applications in biomedical research, tracing the evolution from data-driven to insightdriven approaches. It synthesizes advances in AI-powered multimodal data integration techniques, including early, intermediate, late, and hybrid fusion strategies that effectively combine heterogeneous biomedical data sources. The review explores how network-based computational frameworks and single-cell technologies are revolutionizing disease mechanism analysis through multi-omics integration, enabling the identification of dysregulated pathways and potential therapeutic targets. It further evaluates AI’s role in enabling precision medicine through personalized diagnostics, treatment selection, and radiomics-based healthcare. The integration of AI with various omics disciplines has enhanced understanding of disease mechanisms at molecular, cellular, and tissue levels, creating unprecedented opportunities for early diagnosis and targeted therapeutics. The review concludes by addressing critical challenges including model explainability and data privacy considerations, while highlighting the emergence of closed-loop AI systems that actively participate in scientific discovery through continuous learning and adaptation. These developments collectively signal a paradigm shift toward AI systems that not only analyze biomedical data but generate actionable insights that advance clinical practice and scientific understanding

This comprehensive review examines the transformative role of artificial intelli- gence in biomedical research, from foundational data integration to clinical ap- plications. The paper explores how AI techniques facilitate multimodal data fu- sion across diverse biological data types, employing both traditional statistical methods and advanced deep learning architectures including variational autoen- coders, graph neural networks, and transformer models. It evaluates AI appli- cations in medical imaging, where convolutional neural networks have achieved remarkable diagnostic accuracy (up to 94% in COVID-19 detection) while en- hancing segmentation and classification tasks across multiple imaging modalities. The review further investigates generative AI’s impact on molecular design and drug discovery, highlighting transformer-based architectures like TransAntivirus that navigate vast chemical spaces to optimize therapeutic candidates. Finally, it examines AI-enabled precision medicine applications, including Clinical Deci- sion Support Systems and federated learning approaches that balance analytical power with privacy preservation. Despite significant progress, implementation challenges persist, including data heterogeneity, model explainability, and ethical concerns regarding bias and privacy. The paper underscores the importance of developing interpretable AI systems that integrate seamlessly into clinical workflows while addressing regulatory, ethical, and economic considerations to realize the full potential of AI in advancing biomedical research and healthcare delivery.

Knowledge Graphs (KGs) have long served as a fundamental infrastructure for structured knowledge representation and reasoning. With the advent of Large Language Models (LLMs), the construction of KGs has entered a new paradigm—shifting from rule-based and statistical pipelines to language-driven and generative frameworks. This survey provides a comprehensive overview of recent progress in **LLM-empowered knowledge graph construction**, systematically analyzing how LLMs reshape the classical three-layered pipeline of ontology engineering, knowledge extraction, and knowledge fusion. We first revisit traditional KG methodologies to establish conceptual foundations, and then review emerging LLM-driven approaches from two complementary perspectives: *schema-based* paradigms, which emphasize structure, normalization, and consistency; and *schema-free* paradigms, which highlight flexibility, adaptability, and open discovery. Across each stage, we synthesize representative frameworks, analyze their technical mechanisms, and identify their limitations. Finally, the survey outlines key trends and future research directions, including KG-based reasoning for LLMs, dynamic knowledge memory for agentic systems, and multimodal KG construction. Through this systematic review, we aim to clarify the evolving interplay between LLMs and knowledge graphs, bridging symbolic knowledge engineering and neural semantic understanding toward the development of adaptive, explainable, and intelligent knowledge systems.

Artificial Intelligence (AI) has great potential to transform rock mechanics by tackling its inherent complexities, such as anisotropy, nonlinearity, discontinuous, and multiphase nature. This review explores the evolution of AI, from basic neural networks like the BP model to advanced architectures such as Transformers, and their applications in areas like microstructure reconstruction, prediction of mechanical parameters, and addressing engineering challenges such as rockburst prediction and tunnel deformation. Machine learning techniques, particularly Convolutional Neural Networks (CNNs) and Generative Adversarial Networks (GANs), have been crucial in automating tasks like fracture detection and efficiently generating 3D digital rock models. However, the effectiveness of AI in rock mechanics is limited by data scarcity and the need for high-quality datasets. Hybrid approaches, such as combining physics-informed neural networks (PINNs) with traditional numerical methods, offer promising solutions for solving governing equations. Additionally, Large Language Models (LLMs) are emerging as valuable tools for code generation and decision-making support. Despite these advancements, challenges remain, including issues with reproducibility, model interpretability, and adapting AI models to specific domains. Future progress will hinge on the availability of improved datasets, greater interdisciplinary collaboration, and the integration of spatial intelligence frameworks to bridge the gap between AI’s theoretical potential and its practical application in rock engineering.

Intelligent rock mechanics represents the convergence of artificial intelligence (AI) and classical rock mechanics, providing new paradigms to understand, model, and predict the complex behaviors of geological materials. This review synthesizes recent progress from foundational AI methodologies to their practical applications in rock engineering. Traditional challenges—such as anisotropy, discontinuities, and multiphysics coupling—have been re-examined through data-driven and hybrid approaches that integrate learning algorithms with physical principles. The study traces the evolution of AI in this field, from early backpropagation and support vector machines to modern deep learning frameworks such as convolutional and transformer architectures, highlighting their roles in microstructure reconstruction, mechanical parameter estimation, constitutive modeling, and real-time hazard prediction. Emerging techniques, including physics-informed neural networks and graph-based learning, bridge data-driven inference with physical interpretability, while large language models are beginning to facilitate automated code generation and decision support in geotechnical analysis. Despite remarkable progress, key challenges remain in data quality, model generalization, and interpretability. Addressing these issues requires standardized datasets, interdisciplinary collaboration, and the establishment of transparent, reproducible AI workflows. The paper concludes by outlining a forward-looking perspective on developing next-generation intelligent frameworks capable of coupling physical knowledge, spatial reasoning, and adaptive learning, thereby advancing rock mechanics from empirical modeling toward fully intelligent, autonomous systems.