# DrKGC: Dynamic Subgraph Retrieval-Augmented LLMs for Knowledge Graph Completion across General and Biomedical Domains

arXiv: https://arxiv.org/abs/2506.00708 · HTML: https://mlsanity.com/paper/2506.00708/

## 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 15 of its 43 references that are in the map.
- First posted on arXiv 31 May 2025.

## 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, 15 of 15)

- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Modeling Relational Data with Graph Convolutional Networks](https://mlsanity.com/paper/1703.06103/) (2017)
- [Embedding Entities and Relations for Learning and Inference in Knowledge Bases](https://mlsanity.com/paper/1412.6575/) (2014)
- [Complex Embeddings for Simple Link Prediction](https://mlsanity.com/paper/1606.06357/) (2016)
- [RotatE: Knowledge Graph Embedding by Relational Rotation in Complex Space](https://mlsanity.com/paper/1902.10197/) (2019)
- [Convolutional 2D Knowledge Graph Embeddings](https://mlsanity.com/paper/1707.01476/) (2017)
- [A Survey on Knowledge Graphs: Representation, Acquisition and Applications](https://mlsanity.com/paper/2002.00388/) (2020)
- [Knowledge Graphs](https://mlsanity.com/paper/2003.02320/) (2020)
- [Composition-based Multi-Relational Graph Convolutional Networks](https://mlsanity.com/paper/1911.03082/) (2019)
- [KG-BERT: BERT for Knowledge Graph Completion](https://mlsanity.com/paper/1909.03193/) (2019)
- [A Review of Relational Machine Learning for Knowledge Graphs](https://mlsanity.com/paper/1503.00759/) (2015)
- [Modeling polypharmacy side effects with graph convolutional networks](https://mlsanity.com/paper/1802.00543/) (2018)
- [I Know What You Do Not Know: Knowledge Graph Embedding via Co-distillation Learning](https://mlsanity.com/paper/2208.09828/) (2022)
- [KGLM: Integrating Knowledge Graph Structure in Language Models for Link Prediction](https://mlsanity.com/paper/2211.02744/) (2022)

## Abstract (arXiv)

Knowledge graph completion (KGC) aims to predict missing triples in knowledge graphs (KGs) by leveraging existing triples and textual information. Recently, generative large language models (LLMs) have been increasingly employed for graph tasks. However, current approaches typically encode graph context in textual form, which fails to fully exploit the potential of LLMs for perceiving and reasoning about graph structures. To address this limitation, we propose DrKGC (Dynamic Subgraph Retrieval-Augmented LLMs for Knowledge Graph Completion). DrKGC employs a flexible lightweight model training strategy to learn structural embeddings and logical rules within the KG. It then leverages a novel bottom-up graph retrieval method to extract a subgraph for each query guided by the learned rules. Finally, a graph convolutional network (GCN) adapter uses the retrieved subgraph to enhance the structural embeddings, which are then integrated into the prompt for effective LLM fine-tuning. Experimental results on two general domain benchmark datasets and two biomedical datasets demonstrate the superior performance of DrKGC. Furthermore, a realistic case study in the biomedical domain highlights its interpretability and practical utility.