Contemporary approaches to assisted scientific discovery use language models to automatically generate large numbers of potential hypothesis to test, while also automatically generating code-based experiments to test those hypotheses. While hypotheses can be comparatively inexpensive to generate, automated experiments can be costly, particularly when run at scale (i.e. thousands of experiments). Developing the capacity to filter hypotheses based on their feasibility would allow discovery systems to run at scale, while increasing their likelihood of making significant discoveries. In this work we introduce Matter-of-Fact, a challenge dataset for determining the feasibility of hypotheses framed as claims. Matter-of-Fact includes 8.4k claims extracted from scientific articles spanning four high-impact contemporary materials science topics, including superconductors, semiconductors, batteries, and aerospace materials, while including qualitative and quantitative claims from theoretical, experimental, and code/simulation results. We show that strong baselines that include retrieval augmented generation over scientific literature and code generation fail to exceed 72% performance on this task (chance performance is 50%), while domain-expert verification suggests nearly all are solvable -- highlighting both the difficulty of this task for current models, and the potential to accelerate scientific discovery by making near-term progress.
Compound Al Systems (CAIS) is an emerging paradigm that integrates large language models (LLMs) with external components, such as retrievers, agents, tools, and orchestrators, to overcome the limitations of standalone models in tasks requiring memory, reasoning, real-time grounding, and multimodal understanding. These systems enable more capable and context-aware behaviors by composing multiple specialized modules into cohesive workflows. Despite growing adoption in both academia and industry, the CAIS landscape remains fragmented, lacking a unified framework for analysis, taxonomy, and evaluation. In this survey, we define the concept of CAIS, propose a multi-dimensional taxonomy based on component roles and orchestration strategies, and analyze four foundational paradigms: Retrieval-Augmented Generation (RAG), LLM Agents, Multimodal LLMs (MLLMs), and orchestration-centric architectures. We review representative systems, compare design trade-offs, and summarize evaluation methodologies across these paradigms. Finally, we identify key challenges-including scalability, interoperability, benchmarking, and coordination-and outline promising directions for future research. This survey aims to provide researchers and practitioners with a comprehensive foundation for understanding, developing, and advancing the next generation of system-level artificial intelligence.
This paper presents ThinkTank, a comprehensive and scalable framework designed to transform specialized AI agent systems into versatile collaborative intelligence platforms capable of supporting complex problem-solving across diverse domains. ThinkTank systematically generalizes agent roles, meeting structures, and knowledge integration mechanisms by adapting proven scientific collaboration methodologies. Through role abstraction, generalization of meeting types for iterative collaboration, and the integration of Retrieval-Augmented Generation with advanced knowledge storage, the framework facilitates expertise creation and robust knowledge sharing. ThinkTank enables organizations to leverage collaborative AI for knowledge-intensive tasks while ensuring data privacy and security through local deployment, utilizing frameworks like Ollama with models such as Llama3.1. The ThinkTank framework is designed to deliver significant advantages in cost-effectiveness, data security, scalability, and competitive positioning compared to cloud-based alternatives, establishing it as a universal platform for AI-driven collaborative problem-solving. The ThinkTank code is available at https://github.com/taugroup/ThinkTank
People use videos to learn new recipes, exercises, and crafts. Such videos remain difficult for blind and low vision (BLV) people to follow as they rely on visual comparison. Our observations of visual rehabilitation therapists (VRTs) guiding BLV people to follow how-to videos revealed that VRTs provide both proactive and responsive support including detailed descriptions, non-visual workarounds, and progress feedback. We propose Vid2Coach, a system that transforms how-to videos into wearable camera-based assistants that provide accessible instructions and mixed-initiative feedback. From the video, Vid2Coach generates accessible instructions by augmenting narrated instructions with demonstration details and completion criteria for each step. It then uses retrieval-augmented-generation to extract relevant non-visual workarounds from BLV-specific resources. Vid2Coach then monitors user progress with a camera embedded in commercial smart glasses to provide context-aware instructions, proactive feedback, and answers to user questions. BLV participants (N=8) using Vid2Coach completed cooking tasks with 58.5\% fewer errors than when using their typical workflow and wanted to use Vid2Coach in their daily lives. Vid2Coach demonstrates an opportunity for AI visual assistance that strengthens rather than replaces non-visual expertise.
Transforming relational databases into knowledge graphs with enriched ontologies enhances semantic interoperability and unlocks advanced graph-based learning and reasoning over data. However, previous approaches either demand significant manual effort to derive an ontology from a database schema or produce only a basic ontology. We present RIGOR, Retrieval-augmented Iterative Generation of RDB Ontologies, an LLM-driven approach that turns relational schemas into rich OWL ontologies with minimal human effort. RIGOR combines three sources via RAG, the database schema and its documentation, a repository of domain ontologies, and a growing core ontology, to prompt a generative LLM for producing successive, provenance-tagged delta ontology fragments. Each fragment is refined by a judge-LLM before being merged into the core ontology, and the process iterates table-by-table following foreign key constraints until coverage is complete. Applied to real-world databases, our approach outputs ontologies that score highly on standard quality dimensions such as accuracy, completeness, conciseness, adaptability, clarity, and consistency, while substantially reducing manual effort.
Potato functional genomics lags due to unsystematic gene information curation, gene identifier inconsistencies across reference genome versions, and the increasing volume of research publications. To address these limitations, we developed the Potato Knowledge Hub (http://www.potato-ai.top), leveraging Large Language Models (LLMs) and a systematically curated collection of over 3,200 high-quality potato research papers spanning over 120 years. This platform integrates two key modules: a functional gene database containing 2,571 literature-reported genes, meticulously mapped to the latest DMv8.1 reference genome with resolved nomenclature discrepancies and links to original publications; and a potato knowledge base. The knowledge base, built using a Retrieval-Augmented Generation (RAG) architecture, accurately answers research queries with literature citations, mitigating LLM "hallucination." Users can interact with the hub via a natural language AI agent, "Potato Research Assistant," for querying specialized knowledge, retrieving gene information, and extracting sequences. The continuously updated Potato Knowledge Hub aims to be a comprehensive resource, fostering advancements in potato functional genomics and supporting breeding programs.
The complexity of modern computing environments and the growing sophistication of cyber threats necessitate a more robust, adaptive, and automated approach to security enforcement. In this paper, we present a framework leveraging large language models (LLMs) for automating attack mitigation policy compliance through an innovative combination of in-context learning and retrieval-augmented generation (RAG). We begin by describing how our system collects and manages both tool and API specifications, storing them in a vector database to enable efficient retrieval of relevant information. We then detail the architectural pipeline that first decomposes high-level mitigation policies into discrete tasks and subsequently translates each task into a set of actionable API calls. Our empirical evaluation, conducted using publicly available CTI policies in STIXv2 format and Windows API documentation, demonstrates significant improvements in precision, recall, and F1-score when employing RAG compared to a non-RAG baseline.
Retrieval-augmented generation (RAG) systems are vulnerable to attacks that inject poisoned passages into the retrieved set, even at low corruption rates. We show that existing attacks are not designed to be stealthy, allowing reliable detection and mitigation. We formalize stealth using a distinguishability-based security game. If a few poisoned passages are designed to control the response, they must differentiate themselves from benign ones, inherently compromising stealth. This motivates the need for attackers to rigorously analyze intermediate signals involved in generation$\unicode{x2014}$such as attention patterns or next-token probability distributions$\unicode{x2014}$to avoid easily detectable traces of manipulation. Leveraging attention patterns, we propose a passage-level score$\unicode{x2014}$the Normalized Passage Attention Score$\unicode{x2014}$used by our Attention-Variance Filter algorithm to identify and filter potentially poisoned passages. This method mitigates existing attacks, improving accuracy by up to $\sim 20 \%$ over baseline defenses. To probe the limits of attention-based defenses, we craft stealthier adaptive attacks that obscure such traces, achieving up to $35 \%$ attack success rate, and highlight the challenges in improving stealth.
Modern transportation systems rely on cyber-physical systems (CPS), where cyber systems interact seamlessly with physical systems like transportation-related sensors and actuators to enhance safety, mobility, and energy efficiency. However, growing automation and connectivity increase exposure to cyber vulnerabilities. Existing threat modeling frameworks for transportation CPS are often limited in scope, resource-intensive, and dependent on significant cybersecurity expertise. To address these gaps, we present TraCR-TMF (Transportation Cybersecurity and Resiliency Threat Modeling Framework), a large language model (LLM)-based framework that minimizes expert intervention. TraCR-TMF identifies threats, potential attack techniques, and corresponding countermeasures by leveraging the MITRE ATT&CK matrix through three LLM-based approaches: (i) a retrieval-augmented generation (RAG) method requiring no expert input, (ii) an in-context learning approach requiring low expert input, and (iii) a supervised fine-tuning method requiring moderate expert input. TraCR-TMF also maps attack paths to critical assets by analyzing vulnerabilities using a customized LLM. The framework was evaluated in two scenarios. First, it identified relevant attack techniques across transportation CPS applications, with 90% precision as validated by experts. Second, using a fine-tuned LLM, it successfully predicted multiple exploitations including lateral movement, data exfiltration, and ransomware-related encryption that occurred during a major real-world cyberattack incident. These results demonstrate TraCR-TMF's effectiveness in CPS threat modeling, its reduced reliance on cybersecurity expertise, and its adaptability across CPS domains.
Retrieval-Augmented Generation (RAG) systems, which integrate Large Language Models (LLMs) with external knowledge sources, are vulnerable to a range of adversarial attack vectors. This paper examines the importance of RAG systems through recent industry adoption trends and identifies the prominent attack vectors for RAG: prompt injection, data poisoning, and adversarial query manipulation. We analyze these threats under risk management lens, and propose robust prioritized control list that includes risk-mitigating actions like input validation, adversarial training, and real-time monitoring.
This paper presents a real-time transaction monitoring framework that integrates graph-based modeling, narrative field embedding, and generative explanation to support automated financial compliance. The system constructs dynamic transaction graphs, extracts structural and contextual features, and classifies suspicious behavior using a graph neural network. A retrieval-augmented generation module generates natural language explanations aligned with regulatory clauses for each flagged transaction. Experiments conducted on a simulated stream of financial data show that the proposed method achieves superior results, with 98.2% F1-score, 97.8% precision, and 97.0% recall. Expert evaluation further confirms the quality and interpretability of generated justifications. The findings demonstrate the potential of combining graph intelligence and generative models to support explainable, audit-ready compliance in high-risk financial environments.
Graph Retrieval Augmented Generation (GraphRAG) effectively enhances external knowledge integration capabilities by explicitly modeling knowledge relationships, thereby improving the factual accuracy and generation quality of Large Language Models (LLMs) in specialized domains. However, existing methods suffer from two inherent limitations: 1) Inefficient Information Aggregation: They rely on a single agent and fixed iterative patterns, making it difficult to adaptively capture multi-level textual, structural, and degree information within graph data. 2) Rigid Reasoning Mechanism: They employ preset reasoning schemes, which cannot dynamically adjust reasoning depth nor achieve precise semantic correction. To overcome these limitations, we propose Graph Counselor, an GraphRAG method based on multi-agent collaboration. This method uses the Adaptive Graph Information Extraction Module (AGIEM), where Planning, Thought, and Execution Agents work together to precisely model complex graph structures and dynamically adjust information extraction strategies, addressing the challenges of multi-level dependency modeling and adaptive reasoning depth. Additionally, the Self-Reflection with Multiple Perspectives (SR) module improves the accuracy and semantic consistency of reasoning results through self-reflection and backward reasoning mechanisms. Experiments demonstrate that Graph Counselor outperforms existing methods in multiple graph reasoning tasks, exhibiting higher reasoning accuracy and generalization ability. Our code is available at https://github.com/gjq100/Graph-Counselor.git.
Retrieval-Augmented Generation (RAG) systems enhance Large Language Models (LLMs) by incorporating external retrieved information, mitigating issues such as hallucination and outdated knowledge. However, RAG systems are highly sensitive to retrieval noise prevalent in real-world scenarios. Existing benchmarks fail to emulate the complex and heterogeneous noise distributions encountered in real-world retrieval environments, undermining reliable robustness assessment. In this paper, we define four categories of retrieval noise based on linguistic properties and noise characteristics, aiming to reflect the heterogeneity of noise in real-world scenarios. Building on this, we introduce Magic Mushroom, a benchmark for replicating "magic mushroom" noise: contexts that appear relevant on the surface but covertly mislead RAG systems. Magic Mushroom comprises 7,468 single-hop and 3,925 multi-hop question-answer pairs. More importantly, Magic Mushroom enables researchers to flexibly configure combinations of retrieval noise according to specific research objectives or application scenarios, allowing for highly controlled evaluation setups. We evaluate LLM generators of varying parameter scales and classic RAG denoising strategies under diverse noise distributions to investigate their performance dynamics during progressive noise encroachment. Our analysis reveals that both generators and denoising strategies have significant room for improvement and exhibit extreme sensitivity to noise distributions. Magic Mushroom emerges as a promising tool for evaluating and advancing noise-robust RAG systems, accelerating their widespread deployment in real-world applications. The Magic Mushroom benchmark is available at the https://drive.google.com/file/d/1aP5kyPuk4L-L_uoI6T9UhxuTyt8oMqjT/view?usp=sharing.
Generating long-term, coherent, and realistic music-conditioned dance sequences remains a challenging task in human motion synthesis. Existing approaches exhibit critical limitations: motion graph methods rely on fixed template libraries, restricting creative generation; diffusion models, while capable of producing novel motions, often lack temporal coherence and musical alignment. To address these challenges, we propose $\textbf{MotionRAG-Diff}$, a hybrid framework that integrates Retrieval-Augmented Generation (RAG) with diffusion-based refinement to enable high-quality, musically coherent dance generation for arbitrary long-term music inputs. Our method introduces three core innovations: (1) A cross-modal contrastive learning architecture that aligns heterogeneous music and dance representations in a shared latent space, establishing unsupervised semantic correspondence without paired data; (2) An optimized motion graph system for efficient retrieval and seamless concatenation of motion segments, ensuring realism and temporal coherence across long sequences; (3) A multi-condition diffusion model that jointly conditions on raw music signals and contrastive features to enhance motion quality and global synchronization. Extensive experiments demonstrate that MotionRAG-Diff achieves state-of-the-art performance in motion quality, diversity, and music-motion synchronization accuracy. This work establishes a new paradigm for music-driven dance generation by synergizing retrieval-based template fidelity with diffusion-based creative enhancement.
Retrieval-Augmented Generation (RAG) enhances recency and factuality in answers. However, existing evaluations rarely test how well these systems cope with real-world noise, conflicting between internal and external retrieved contexts, or fast-changing facts. We introduce Retrieval-Aware Robustness Evaluation (RARE), a unified framework and large-scale benchmark that jointly stress-tests query and document perturbations over dynamic, time-sensitive corpora. One of the central features of RARE is a knowledge-graph-driven synthesis pipeline (RARE-Get) that automatically extracts single and multi-hop relations from the customized corpus and generates multi-level question sets without manual intervention. Leveraging this pipeline, we construct a dataset (RARE-Set) spanning 400 expert-level time-sensitive finance, economics, and policy documents and 48,322 questions whose distribution evolves as the underlying sources change. To quantify resilience, we formalize retrieval-conditioned robustness metrics (RARE-Met) that capture a model's ability to remain correct or recover when queries, documents, or real-world retrieval results are systematically altered. Our results show that RAG systems exhibit surprising vulnerability to perturbations, with document robustness consistently being the weakest point regardless of generator size or architecture. RAG systems consistently show lower robustness on multi-hop queries than single-hop queries across all domains.
Advancements in large language models (LLMs) have enabled the development of intelligent educational tools that support inquiry-based learning across technical domains. In cybersecurity education, where accuracy and safety are paramount, systems must go beyond surface-level relevance to provide information that is both trustworthy and domain-appropriate. To address this challenge, we introduce CyberBOT, a question-answering chatbot that leverages a retrieval-augmented generation (RAG) pipeline to incorporate contextual information from course-specific materials and validate responses using a domain-specific cybersecurity ontology. The ontology serves as a structured reasoning layer that constrains and verifies LLM-generated answers, reducing the risk of misleading or unsafe guidance. CyberBOT has been deployed in a large graduate-level course at Arizona State University (ASU), where more than one hundred students actively engage with the system through a dedicated web-based platform. Computational evaluations in lab environments highlight the potential capacity of CyberBOT, and a forthcoming field study will evaluate its pedagogical impact. By integrating structured domain reasoning with modern generative capabilities, CyberBOT illustrates a promising direction for developing reliable and curriculum-aligned AI applications in specialized educational contexts.
Retrieval-Augmented Generation (RAG) augments Large Language Models (LLMs) with external knowledge to improve factuality. However, existing RAG systems frequently underutilize the retrieved documents, failing to extract and integrate the key clues needed to support faithful and interpretable reasoning, especially in cases where relevant evidence is implicit, scattered, or obscured by noise. To address this issue, we propose ClueAnchor, a novel framework for enhancing RAG via clue-anchored reasoning exploration and optimization. ClueAnchor extracts key clues from retrieved content and generates multiple reasoning paths based on different knowledge configurations, optimizing the model by selecting the most effective one through reward-based preference optimization. Experiments show that ClueAnchor significantly outperforms prior RAG baselines in reasoning completeness and robustness. Further analysis confirms its strong resilience to noisy or partially relevant retrieved content, as well as its capability to identify supporting evidence even in the absence of explicit clue supervision during inference.
Causality detection and mining are important tasks in information retrieval due to their enormous use in information extraction, and knowledge graph construction. To solve these tasks, in existing literature there exist several solutions -- both unsupervised and supervised. However, the unsupervised methods suffer from poor performance and they often require significant human intervention for causal rule selection, leading to poor generalization across different domains. On the other hand, supervised methods suffer from the lack of large training datasets. Recently, large language models (LLMs) with effective prompt engineering are found to be effective to overcome the issue of unavailability of large training dataset. Yet, in existing literature, there does not exist comprehensive works on causality detection and mining using LLM prompting. In this paper, we present several retrieval-augmented generation (RAG) based dynamic prompting schemes to enhance LLM performance in causality detection and extraction tasks. Extensive experiments over three datasets and five LLMs validate the superiority of our proposed RAG-based dynamic prompting over other static prompting schemes.
Large language models excel at many tasks but often incur high inference costs during deployment. To mitigate hallucination, many systems use a knowledge graph to enhance retrieval-augmented generation (KG-RAG). However, the large amount of retrieved knowledge contexts increase these inference costs further. A promising solution to balance performance and cost is LLM routing, which directs simple queries to smaller LLMs and complex ones to larger LLMs. However, no dedicated routing methods currently exist for RAG, and existing training-based routers face challenges scaling to this domain due to the need for extensive training data. We observe that the score distributions produced by the retrieval scorer strongly correlate with query difficulty. Based on this, we propose a novel, training-free routing framework, the first tailored to KG-RAG that effectively balances performance and cost in a plug-and-play manner. Experiments show our method reduces calls to larger LLMs by up to 50% without sacrificing response quality, demonstrating its potential for efficient and scalable LLM deployment.
As Large Language Models (LLMs) continue to exhibit increasingly human-like capabilities, aligning them with human values has become critically important. Contemporary advanced techniques, such as prompt learning and reinforcement learning, are being deployed to better align LLMs with human values. However, while these approaches address broad ethical considerations and helpfulness, they rarely focus on simulating individualized human value systems. To address this gap, we present ValueSim, a framework that simulates individual values through the generation of personal backstories reflecting past experiences and demographic information. ValueSim converts structured individual data into narrative backstories and employs a multi-module architecture inspired by the Cognitive-Affective Personality System to simulate individual values based on these narratives. Testing ValueSim on a self-constructed benchmark derived from the World Values Survey demonstrates an improvement in top-1 accuracy by over 10% compared to retrieval-augmented generation methods. Further analysis reveals that performance enhances as additional user interaction history becomes available, indicating the model's ability to refine its persona simulation capabilities over time.