# XGRAG: A Graph-Native Framework for Explaining KG-based Retrieval-Augmented Generation

arXiv: https://arxiv.org/abs/2604.24623 · HTML: https://mlsanity.com/paper/2604.24623/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Knowledge-graph and structured-knowledge RAG, one of 15 directions in Retrieval-augmented generation.
- Builds on 21 of its 27 references that are in the map.
- First posted on arXiv 27 Apr 2026.

## Placed in

- Retrieval-augmented generation / [Knowledge-graph and structured-knowledge RAG](https://mlsanity.com/rag/knowledge-graph-and-structured-knowledge-rag/)

## Builds on (most cited first, 21 of 21)

- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [Mistral 7B](https://mlsanity.com/paper/2310.06825/) (2023)
- [TriviaQA: A Large Scale Distantly Supervised Challenge Dataset for Reading Comprehension](https://mlsanity.com/paper/1705.03551/) (2017)
- [Retrieval-Augmented Generation for Large Language Models: A Survey](https://mlsanity.com/paper/2312.10997/) (2023)
- [Gemma 3 Technical Report](https://mlsanity.com/paper/2503.19786/) (2025)
- [From Local to Global: A Graph RAG Approach to Query-Focused Summarization](https://mlsanity.com/paper/2404.16130/) (2024)
- [The NarrativeQA Reading Comprehension Challenge](https://mlsanity.com/paper/1712.07040/) (2017)
- [Nomic Embed: Training a Reproducible Long Context Text Embedder](https://mlsanity.com/paper/2402.01613/) (2024)
- [Retrieval-Augmented Generation with Graphs (GraphRAG)](https://mlsanity.com/paper/2501.00309/) (2024)
- [Retrieval-Augmented Generation with Knowledge Graphs for Customer Service Question Answering](https://mlsanity.com/paper/2404.17723/) (2024)
- [DeepSeek-R1 Thoughtology: Let's think about LLM Reasoning](https://mlsanity.com/paper/2504.07128/) (2025)
- [Simple Is Effective: The Roles of Graphs and Large Language Models in Knowledge-Graph-Based Retrieval-Augmented Generation](https://mlsanity.com/paper/2410.20724/) (2024)
- [RAG vs. GraphRAG: A Systematic Evaluation and Key Insights](https://mlsanity.com/paper/2502.11371/) (2025)
- [Usable XAI: 10 Strategies Towards Exploiting Explainability in the LLM Era](https://mlsanity.com/paper/2403.08946/) (2024)
- [LLMs for Explainable AI: A Comprehensive Survey](https://mlsanity.com/paper/2504.00125/) (2025)
- [CausalRAG: Integrating Causal Graphs into Retrieval-Augmented Generation](https://mlsanity.com/paper/2503.19878/) (2025)
- [RAGE Against the Machine: Retrieval-Augmented LLM Explanations](https://mlsanity.com/paper/2405.13000/) (2024)
- [KGRAG-Ex: Explainable Retrieval-Augmented Generation with Knowledge Graph-based Perturbations](https://mlsanity.com/paper/2507.08443/) (2025)

## Abstract (arXiv)

Graph-based Retrieval-Augmented Generation (GraphRAG) extends traditional RAG by using knowledge graphs (KGs) to give large language models (LLMs) a structured, semantically coherent context, yielding more grounded answers. However, GraphRAG reasoning process remains a black-box, limiting our ability to understand how specific pieces of structured knowledge influence the final output. Existing explainability (XAI) methods for RAG systems, designed for text-based retrieval, are limited to interpreting an LLM response through the relational structures among knowledge components, creating a critical gap in transparency and trustworthiness. To address this, we introduce XGRAG, a novel framework that generates causally grounded explanations for GraphRAG systems by employing graph-based perturbation strategies, to quantify the contribution of individual graph components on the model answer. We conduct extensive experiments comparing XGRAG against RAG-Ex, an XAI baseline for standard RAG, and evaluate its robustness across various question types, narrative structures and LLMs. Our results demonstrate a 14.81% improvement in explanation quality over the baseline RAG-Ex across NarrativeQA, FairyTaleQA, and TriviaQA, evaluated by F1-score measuring alignment between generated explanations and original answers. Furthermore, XGRAG explanations exhibit a strong correlation with graph centrality measures, validating its ability to capture graph structure. XGRAG provides a scalable and generalizable approach towards trustworthy AI through transparent, graph-based explanations that enhance the interpretability of RAG systems.