Ground-Truth Subgraphs for Better Training and Evaluation of Knowledge Graph Augmented LLMs

Retrieval of information from graph-structured knowledge bases represents a promising direction for improving the factuality of LLMs. While various solutions have been proposed, a comparison of methods is difficult due to the lack of challenging QA datasets with ground-truth targets for graph retrieval. We present SynthKGQA, a framework for generating high-quality synthetic Knowledge Graph Question Answering datasets from any Knowledge Graph, providing the full set of ground-truth facts in the KG to reason over each question. We show how, in addition to enabling more informative benchmarking of KG retrievers, the data produced with SynthKGQA also allows us to train better models. We apply SynthKGQA to Wikidata to generate GTSQA, a new dataset designed to test zero-shot generalization abilities of KG retrievers with respect to unseen graph structures and relation types, and benchmark popular solutions for KG-augmented LLMs on it.

Large Language Models for Explainable Threat Intelligence

As cyber threats continue to grow in complexity, traditional security mechanisms struggle to keep up. Large language models (LLMs) offer significant potential in cybersecurity due to their advanced capabilities in text processing and generation. This paper explores the use of LLMs with retrieval-augmented generation (RAG) to obtain threat intelligence by combining real-time information retrieval with domain-specific data. The proposed system, RAGRecon, uses a LLM with RAG to answer questions about cybersecurity threats. Moreover, it makes this form of Artificial Intelligence (AI) explainable by generating and visually presenting to the user a knowledge graph for every reply. This increases the transparency and interpretability of the reasoning of the model, allowing analysts to better understand the connections made by the system based on the context recovered by the RAG system. We evaluated RAGRecon experimentally with two datasets and seven different LLMs and the responses matched the reference responses more than 91% of the time for the best combinations.

TeaRAG: A Token-Efficient Agentic Retrieval-Augmented Generation Framework

Retrieval-Augmented Generation (RAG) utilizes external knowledge to augment Large Language Models' (LLMs) reliability. For flexibility, agentic RAG employs autonomous, multi-round retrieval and reasoning to resolve queries. Although recent agentic RAG has improved via reinforcement learning, they often incur substantial token overhead from search and reasoning processes. This trade-off prioritizes accuracy over efficiency. To address this issue, this work proposes TeaRAG, a token-efficient agentic RAG framework capable of compressing both retrieval content and reasoning steps. 1) First, the retrieved content is compressed by augmenting chunk-based semantic retrieval with a graph retrieval using concise triplets. A knowledge association graph is then built from semantic similarity and co-occurrence. Finally, Personalized PageRank is leveraged to highlight key knowledge within this graph, reducing the number of tokens per retrieval. 2) Besides, to reduce reasoning steps, Iterative Process-aware Direct Preference Optimization (IP-DPO) is proposed. Specifically, our reward function evaluates the knowledge sufficiency by a knowledge matching mechanism, while penalizing excessive reasoning steps. This design can produce high-quality preference-pair datasets, supporting iterative DPO to improve reasoning conciseness. Across six datasets, TeaRAG improves the average Exact Match by 4% and 2% while reducing output tokens by 61% and 59% on Llama3-8B-Instruct and Qwen2.5-14B-Instruct, respectively. Code is available at https://github.com/Applied-Machine-Learning-Lab/TeaRAG.

Dynamic causal discovery in Alzheimer's disease through latent pseudotime modelling

The application of causal discovery to diseases like Alzheimer's (AD) is limited by the static graph assumptions of most methods; such models cannot account for an evolving pathophysiology, modulated by a latent disease pseudotime. We propose to apply an existing latent variable model to real-world AD data, inferring a pseudotime that orders patients along a data-driven disease trajectory independent of chronological age, then learning how causal relationships evolve. Pseudotime outperformed age in predicting diagnosis (AUC 0.82 vs 0.59). Incorporating minimal, disease-agnostic background knowledge substantially improved graph accuracy and orientation. Our framework reveals dynamic interactions between novel (NfL, GFAP) and established AD markers, enabling practical causal discovery despite violated assumptions.

Inter-Agent Trust Models: A Comparative Study of Brief, Claim, Proof, Stake, Reputation and Constraint in Agentic Web Protocol Design-A2A, AP2, ERC-8004, and Beyond

As the "agentic web" takes shape-billions of AI agents (often LLM-powered) autonomously transacting and collaborating-trust shifts from human oversight to protocol design. In 2025, several inter-agent protocols crystallized this shift, including Google's Agent-to-Agent (A2A), Agent Payments Protocol (AP2), and Ethereum's ERC-8004 "Trustless Agents," yet their underlying trust assumptions remain under-examined. This paper presents a comparative study of trust models in inter-agent protocol design: Brief (self- or third-party verifiable claims), Claim (self-proclaimed capabilities and identity, e.g. AgentCard), Proof (cryptographic verification, including zero-knowledge proofs and trusted execution environment attestations), Stake (bonded collateral with slashing and insurance), Reputation (crowd feedback and graph-based trust signals), and Constraint (sandboxing and capability bounding). For each, we analyze assumptions, attack surfaces, and design trade-offs, with particular emphasis on LLM-specific fragilities-prompt injection, sycophancy/nudge-susceptibility, hallucination, deception, and misalignment-that render purely reputational or claim-only approaches brittle. Our findings indicate no single mechanism suffices. We argue for trustless-by-default architectures anchored in Proof and Stake to gate high-impact actions, augmented by Brief for identity and discovery and Reputation overlays for flexibility and social signals. We comparatively evaluate A2A, AP2, ERC-8004 and related historical variations in academic research under metrics spanning security, privacy, latency/cost, and social robustness (Sybil/collusion/whitewashing resistance). We conclude with hybrid trust model recommendations that mitigate reputation gaming and misinformed LLM behavior, and we distill actionable design guidelines for safer, interoperable, and scalable agent economies.

Traceable Drug Recommendation over Medical Knowledge Graphs

Drug recommendation (DR) systems aim to support healthcare professionals in selecting appropriate medications based on patients' medical conditions. State-of-the-art approaches utilize deep learning techniques for improving DR, but fall short in providing any insights on the derivation process of recommendations -- a critical limitation in such high-stake applications. We propose TraceDR, a novel DR system operating over a medical knowledge graph (MKG), which ensures access to large-scale and high-quality information. TraceDR simultaneously predicts drug recommendations and related evidence within a multi-task learning framework, enabling traceability of medication recommendations. For covering a more diverse set of diseases and drugs than existing works, we devise a framework for automatically constructing patient health records and release DrugRec, a new large-scale testbed for DR.

LINK-KG: LLM-Driven Coreference-Resolved Knowledge Graphs for Human Smuggling Networks

Human smuggling networks are complex and constantly evolving, making them difficult to analyze comprehensively. Legal case documents offer rich factual and procedural insights into these networks but are often long, unstructured, and filled with ambiguous or shifting references, posing significant challenges for automated knowledge graph (KG) construction. Existing methods either overlook coreference resolution or fail to scale beyond short text spans, leading to fragmented graphs and inconsistent entity linking. We propose LINK-KG, a modular framework that integrates a three-stage, LLM-guided coreference resolution pipeline with downstream KG extraction. At the core of our approach is a type-specific Prompt Cache, which consistently tracks and resolves references across document chunks, enabling clean and disambiguated narratives for structured knowledge graph construction from both short and long legal texts. LINK-KG reduces average node duplication by 45.21% and noisy nodes by 32.22% compared to baseline methods, resulting in cleaner and more coherent graph structures. These improvements establish LINK-KG as a strong foundation for analyzing complex criminal networks.

Inside CORE-KG: Evaluating Structured Prompting and Coreference Resolution for Knowledge Graphs

Human smuggling networks are increasingly adaptive and difficult to analyze. Legal case documents offer critical insights but are often unstructured, lexically dense, and filled with ambiguous or shifting references, which pose significant challenges for automated knowledge graph (KG) construction. While recent LLM-based approaches improve over static templates, they still generate noisy, fragmented graphs with duplicate nodes due to the absence of guided extraction and coreference resolution. The recently proposed CORE-KG framework addresses these limitations by integrating a type-aware coreference module and domain-guided structured prompts, significantly reducing node duplication and legal noise. In this work, we present a systematic ablation study of CORE-KG to quantify the individual contributions of its two key components. Our results show that removing coreference resolution results in a 28.32% increase in node duplication and a 4.32% increase in noisy nodes, while removing structured prompts leads to a 4.34% increase in node duplication and a 73.33% increase in noisy nodes. These findings offer empirical insights for designing robust LLM-based pipelines for extracting structured representations from complex legal texts.

BambooKG: A Neurobiologically-inspired Frequency-Weight Knowledge Graph

Retrieval-Augmented Generation allows LLMs to access external knowledge, reducing hallucinations and ageing-data issues. However, it treats retrieved chunks independently and struggles with multi-hop or relational reasoning, especially across documents. Knowledge graphs enhance this by capturing the relationships between entities using triplets, enabling structured, multi-chunk reasoning. However, these tend to miss information that fails to conform to the triplet structure. We introduce BambooKG, a knowledge graph with frequency-based weights on non-triplet edges which reflect link strength, drawing on the Hebbian principle of "fire together, wire together". This decreases information loss and results in improved performance on single- and multi-hop reasoning, outperforming the existing solutions.

Conjugate Relation Modeling for Few-Shot Knowledge Graph Completion

Few-shot Knowledge Graph Completion (FKGC) infers missing triples from limited support samples, tackling long-tail distribution challenges. Existing methods, however, struggle to capture complex relational patterns and mitigate data sparsity. To address these challenges, we propose a novel FKGC framework for conjugate relation modeling (CR-FKGC). Specifically, it employs a neighborhood aggregation encoder to integrate higher-order neighbor information, a conjugate relation learner combining an implicit conditional diffusion relation module with a stable relation module to capture stable semantics and uncertainty offsets, and a manifold conjugate decoder for efficient evaluation and inference of missing triples in manifold space. Experiments on three benchmarks demonstrate that our method achieves superior performance over state-of-the-art methods.