Generalization Boundaries of Fine-Tuned Small Language Models for Graph Structural Inference
Authors: Michal Podstawski
Organizations: NASK National Research Institute Warsaw, Poland
Abstract
Small language models fine-tuned for graph property estimation have demonstrated strong in-distribution performance, yet their generalization capabilities beyond training conditions remain poorly understood. In this work, we systematically investigate the boundaries of structural inference in fine-tuned small language models along two generalization axes - graph size and graph family distribution - and assess domain-learning capability on real-world graph benchmarks. Using a controlled experimental setup with three instruction-tuned models in the 3-4B parameter class and two graph serialization formats, we evaluate performance on graphs substantially larger than the training range and across held-out random graph families. Our results show that fine-tuned models maintain strong ordinal consistency across structurally distinct graph families and continue to rank graphs by structural properties on inputs substantially larger than those seen during training, with distinct architecture-specific degradation profiles. These findings delineate where fine-tuned small language models generalize reliably, providing empirical grounding for their use in graph-based reasoning tasks.
It remains unclear whether graph language models learn structural regularities or merely memorize training graphs; this cannot be resolved by current aggregate fidelity metrics alone. We develop a calibrated diagnostic protocol that combines frequent subgraph mining, a graph-level bootstrap baseline, and three-level frequency stratification to disentangle memorization from structural alignment. Using this framework, we show that graph language models can acquire structural regularities beyond memorization at scale, primarily in the high-frequency regime. This is supported by the following empirical evidence: On five TU benchmarks, LLaMA-style graph language models reach high subgraph-rank correlation, yet their alignment is matched or exceeded by the memorization bootstrap in most cases. At small scale, under our bootstrap diagnostic, fidelity is largely indistinguishable from verbatim recall. In contrast, at large scale with 3.75M graphs, verbatim memorization drops sharply while rank correlation remains near ceiling. Crucially, in a separate fixed-subsample analysis, frequent subgraph mining restricted to the novel-only subset closely tracks the corresponding all-generation Spearman correlation, providing evidence that the alignment is not driven solely by verbatim recall. Across all scales, high-frequency patterns are well reproduced, while rare patterns remain poorly covered, and this deficit narrows only marginally as capacity increases. We observe the same scale-dependent crossover under two distinct graph serializations (canonical DFS code and action sequences), providing evidence of robustness in our analysis.
With the rapidly improving reasoning abilities of Large Language Models (LLMs), there is also a rising demand to use them in a wide variety of domains. This brings about the need to carefully evaluate the limits of the capabilities of these models with various tests and benchmarks. Graph structures are ubiquitous in real-world data, and are often used to represent and analyze relationship patterns within data. Many benchmarks have already been proposed in the graph literature to test the reasoning ability of LLMs to follow and execute graph algorithms. However, due to the limited context length of LLMs, these benchmarks consist of very small graphs. In real-world data, the size of graphs can be significantly larger, and in many cases, not fully accessible. In this paper, we examine a class of problems that arises with very large graphs having limited accessibility. We propose a large graph benchmark dataset, EstGraph, and introduce four distinct tasks designed to estimate large graph properties. We evaluate the reasoning abilities of LLMs on these tasks using a wide variety of graph datasets. In addition, we provide task-specific prompt constructions based on random walk sampling of large graphs (up to millions of nodes) that effectively convey sufficient information to LLMs within the limits of context length.
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.