Retrieval-Augmented Generation (RAG) has significantly mitigated the hallucinations of Large Language Models (LLMs) by grounding the generation with external knowledge. Recent extensions of RAG to graph-based retrieval offer a promising direction, leveraging the structural knowledge for multi-hop reasoning. However, existing graph RAG typically decouples retrieval and reasoning processes, which prevents the retriever from adapting to the reasoning needs of the LLM. They also struggle with scalability when performing multi-hop expansion over large-scale graphs, or depend heavily on annotated ground-truth entities, which are often unavailable in open-domain settings. To address these challenges, we propose a novel graph retriever trained end-to-end with LLM, which features an attention-based growing and pruning mechanism, adaptively navigating multi-hop relevant entities while filtering out noise. Within the extracted subgraph, structural knowledge and semantic features are encoded via soft tokens and the verbalized graph, respectively, which are infused into the LLM together, thereby enhancing its reasoning capability and facilitating interactive joint training of the graph retriever and the LLM reasoner. Experimental results across three QA benchmarks show that our approach consistently achieves state-of-the-art performance, validating the strength of joint graph–LLM optimization for complex reasoning tasks. Notably, our framework eliminates the need for predefined ground-truth entities by directly optimizing the retriever using LLM logits as implicit feedback, making it especially effective in open-domain settings.

The coronavirus disease (COVID-19) has claimed the lives of over one million people and infected more than thirty-five million people worldwide. Several search engines have surfaced to provide researchers with additional tools to find and retrieve information from the rapidly growing corpora on COVID19. These engines lack extraction and visualization tools necessary to retrieve and interpret complex relations inherent to scientific literature. Moreover, because these engines mainly rely upon semantic information, their ability to capture complex global relationships across documents is limited, which reduces the quality of similarity-based article recommendations for users. In this work, we present the COVID-19 Knowledge Graph (CKG), a heterogeneous graph for extracting and visualizing complex relationships between COVID-19 scientific articles. The CKG combines semantic information with document topological information for the application of similar document retrieval. The CKG is constructed using the latent schema of the data, and then enriched with biomedical entity information extracted from the unstructured text of articles using scalable AWS technologies to form relations in the graph. Finally, we propose a document similarity engine that leverages low-dimensional graph embeddings from the CKG with semantic embeddings for similar article retrieval. Analysis demonstrates the quality of relationships in the CKG and shows that it can be used to uncover meaningful information in COVID-19 scientific articles. The CKG helps power www.cord19.aws and is publicly available.