Graph Evidence Is Not Enough: Diagnosing Native Decoder Use in Graph-Augmented LLMs
Authors: Xiaoyu Guo, Pengcheng Chen, Jiong Yu, Yi Lu, Yaohua Wang, Ziyang Li
Organizations: School of Software, Xinjiang University, Urumqi 830002, China · School of Computer Science and Technology, Xinjiang University, Urumqi 830046, China
Abstract
Graph-augmented large language models often assume that graph evidence produced by external computation and placed in the input can be used by the native decoder. We test this assumption with HopQA, a deliberately bounded diagnostic that asks for the shortest-hop distance between two query nodes. Because the answer is a small integer and the target is purely topological, failure cannot be dismissed as open-ended generation or ambiguous evaluation. Yet existing graph-augmented baselines still fail on this setting, showing that providing graph evidence is not the same as making it usable. We introduce an intervention triangle with three matched conditions: readable graph evidence, shuffled graph evidence, and no-graph input. This separates evidence inclusion, structural readability, and decoder-usable topology. Guided by this diagnosis, we present S2GE as an instance showing that diagnosis-driven interface design can improve native decoder usability. S2GE uses query-aware sampling, endpoint and proximity-based ordering, and structure-preserving alignment. Across DBLP, Biomedical, GoodReads, and PubMed, S2GE achieves strict exact-match scores of 36.5%, 57.8%, 76.6%, and 52.0%, improving over the strongest native-generation baseline by 53.5 points on average. The interventions further reveal harmful-shuffle, shuffle-robust, and no-graph-saturated regimes.
GraphRAG conditions language models on subgraphs retrieved from knowledge graphs, encoded via message-passing GNNs. Because these encoders entangle node contributions through iterated neighborhood aggregation, there is no closed-form way to determine how much each retrieved entity influenced the encoder's output, and therefore no way to faithfully audit what structural evidence actually reached the model. We introduce Ex-GraphRAG, which replaces the GNN encoder with a Multivariate Graph Neural Additive Network (M-GNAN), an extension of additive graph models to high-dimensional embedding spaces that yields an exact decomposition of the encoder's output across individual nodes and feature groups, without post-hoc approximation. On STaRK-Prime, this auditable encoder matches black-box performance. Using it to audit evidence routing, we uncover a semantic-structural mismatch: the nodes that dominate the encoder's output are structurally disconnected in the retrieved subgraph, held together by low-attribution intermediaries whose removal degrades multi-hop QA by up to 28%. This mismatch, invisible to any opaque encoder, reveals that semantic importance and structural connectivity are governed by disjoint sets of nodes, with direct implications for retrieval pruning, context construction, and failure diagnosis in graph-augmented LLMs.
Graphs have been used to enhance large language models (LLMs) for structured reasoning, mostly as external knowledge sources are provided to models at test time. In this paper, we take a different view: the value of graphs for LLMs lie not only in supplying information, but also in organizing reasoning. Inspired by how humans use graph-structured mind maps to organize branching and converging thoughts, we ask whether graphs can serve as an internal form of reasoning assistance. We study this question on multi-hop question answering tasks, where teacher-provided reasoning traces are rewritten as graph mind maps and used to guide a student model. Our experiments reveal a clear modality gap. When graph structures are flattened into text, their benefits become limited once direct answer hints are removed. Under this abstract guidance setting, both reasoning efficiency and answer quality degrade substantially. In contrast, visual graph guidance remains effective without direct answer clues, and its advantage persists after supervised fine-tuning and KL-based distillation. The above findings support the claim that graphs should be studied not only as external knowledge structures for LLMs, but also as visual scaffolds for organizing reasoning.
With the rapid advancement of large language models (LLMs), classic graph learning tasks have greatly benefited from LLMs, including improved encoding of textual features, more efficient construction of graphs from text, and enhanced reasoning over knowledge graphs. In this paper, we ask a complementary question: How can graphs help LLMs? We address this question from three perspectives: 1) graphs provide an up-to-date knowledge source that helps reduce LLM hallucinations, 2) graph-based prompting techniques-such as Chain-of-Thought (CoT), Tree-of-Thought (ToT), and Graph-of-Thought (GoT)-enhance LLM reasoning capabilities, and 3) integrating graphs into LLMs improves their understanding of structured data, expanding their applicability to domains such as e-commerce, code, and relational databases (RDBs). We further outlook some future directions including designing sparse LLM architectures based on graphs and brain-inspired memory systems.