# Reliable Graph-RAG for Codebases: AST-Derived Graphs vs LLM-Extracted Knowledge Graphs

arXiv: https://arxiv.org/abs/2601.08773 · HTML: https://mlsanity.com/paper/2601.08773/

## Key facts

- Cited by 4 papers in the map (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 30 references that are in the map.
- First posted on arXiv 13 Jan 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)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Evaluating Large Language Models Trained on Code](https://mlsanity.com/paper/2107.03374/) (2021)
- [Dense Passage Retrieval for Open-Domain Question Answering](https://mlsanity.com/paper/2004.04906/) (2020)
- [Program Synthesis with Large Language Models](https://mlsanity.com/paper/2108.07732/) (2021)
- [SWE-bench: Can Language Models Resolve Real-World GitHub Issues?](https://mlsanity.com/paper/2310.06770/) (2023)
- [Retrieval-Augmented Generation for Large Language Models: A Survey](https://mlsanity.com/paper/2312.10997/) (2023)
- [From Local to Global: A Graph RAG Approach to Query-Focused Summarization](https://mlsanity.com/paper/2404.16130/) (2024)
- [Atlas: Few-shot Learning with Retrieval Augmented Language Models](https://mlsanity.com/paper/2208.03299/) (2022)
- [RepoCoder: Repository-Level Code Completion Through Iterative Retrieval and Generation](https://mlsanity.com/paper/2303.12570/) (2023)
- [RepoBench: Benchmarking Repository-Level Code Auto-Completion Systems](https://mlsanity.com/paper/2306.03091/) (2023)
- [LightRAG: Simple and Fast Retrieval-Augmented Generation](https://mlsanity.com/paper/2410.05779/) (2024)
- [Agentic Retrieval-Augmented Generation: A Survey on Agentic RAG](https://mlsanity.com/paper/2501.09136/) (2025)
- [A Survey of Graph Retrieval-Augmented Generation for Customized Large Language Models](https://mlsanity.com/paper/2501.13958/) (2025)
- [Measuring memorization in language models via probabilistic extraction](https://mlsanity.com/paper/2410.19482/) (2024)
- [Code Graph Model (CGM): A Graph-Integrated Large Language Model for Repository-Level Software Engineering Tasks](https://mlsanity.com/paper/2505.16901/) (2025)
- [Retrieval-Augmented Code Generation: A Survey with Focus on Repository-Level Approaches](https://mlsanity.com/paper/2510.04905/) (2025)
- [An Empirical Study of Retrieval-Augmented Code Generation: Challenges and Opportunities](https://mlsanity.com/paper/2501.13742/) (2025)
- [cAST: Enhancing Code Retrieval-Augmented Generation with Structural Chunking via Abstract Syntax Tree](https://mlsanity.com/paper/2506.15655/) (2025)
- [Think Inside the JSON: Reinforcement Strategy for Strict LLM Schema Adherence](https://mlsanity.com/paper/2502.14905/) (2025)
- [Large Language Models Versus Static Code Analysis Tools: A Systematic Benchmark for Vulnerability Detection](https://mlsanity.com/paper/2508.04448/) (2025)

## Built on by (most cited first, 4 of 4)

- [Externalization in LLM Agents: A Unified Review of Memory, Skills, Protocols and Harness Engineering](https://mlsanity.com/paper/2604.08224/) (2026)
- [DeepDiscovery: A Location-Inference Framework for Task-Level Repository Understanding](https://mlsanity.com/paper/2606.22906/) (2026)
- [Seed-Anchored Budget-Bounded Graph Rendering for Question Answering on Industry-Standard Power-Grid Information and Exchange Models](https://mlsanity.com/paper/2609.02011/) (2026)
- [Beyond Vector Similarity: Hierarchical Context-Aware Graph RAG vs Standard RAG in Enterprise Code Migration](https://mlsanity.com/paper/2609.12464/) (2026)

## Abstract (arXiv)

Retrieval-Augmented Generation for software engineering often relies on vector similarity search, which captures topical similarity but can fail on multi-hop architectural reasoning such as controller to service to repository chains, interface-driven wiring, and inheritance. This paper benchmarks three retrieval pipelines on Java codebases (Shopizer, with additional runs on ThingsBoard and OpenMRS Core): (A) vector-only No-Graph RAG, (B) an LLM-generated knowledge graph RAG (LLM-KB), and (C) a deterministic AST-derived knowledge graph RAG (DKB) built with Tree-sitter and bidirectional traversal. Using 15 architecture and code-tracing queries per repository, we measure indexing time, query latency, corpus coverage, cost, and answer correctness. DKB builds its graph in seconds, while LLM-KB requires much longer graph generation. LLM-KB also shows indexing incompleteness: on Shopizer, 377 files are skipped or missed, reducing embedded chunk coverage and graph size compared to DKB. End-to-end cost is modest for DKB relative to the vector-only baseline but much higher for LLM-KB, especially as repository scale increases. Query latency is similar for No-Graph and DKB, while LLM-KB is slower and more variable. On the Shopizer question suite, DKB achieves the highest correctness, LLM-KB is close behind, and the vector-only baseline performs worst on upstream architectural queries and has the highest hallucination risk. Overall, deterministic AST-derived graphs provide more reliable coverage and multi-hop grounding than LLM-extracted graphs at substantially lower indexing cost.