Structured output from large language models (LLMs) has enhanced efficiency in processing generated information and is increasingly adopted in industrial applications. Prior studies have investigated the impact of structured output on LLMs’ generation quality, often presenting one-way findings. Some suggest that structured format enhances completeness and factual accuracy, while others argue that it restricts the reasoning capacity of LLMs and leads to reductions in standard evaluation metrics. Potential limitations of these assessments include restricted testing scenarios, weakly controlled comparative settings, and reliance on coarse metrics. In this work, we present a refined analysis using causal inference. Based on one assumed and two guaranteed constraints, we derive five potential causal structures characterizing the influence of structured output on LLMs’ generation: (1) collider without m-bias, (2) collider with m-bias, (3) single cause from instruction, (4) single cause from output format, and (5) independence. Across seven public and one developed reasoning tasks, we find that coarse metrics report positive, negative, or neutral effects of structured output on GPT-4o’s generation. However, causal inference reveals no causal impact in 43 out of 48 scenarios. In the remaining 5, 3 involve multifaceted causal structures influenced by concrete instructions. Further experiments show that OpenAI-o3 are more resilient to output formats than general-purpose GPT-4o and GPT-4.1, highlighting an unaware advantage of reasoning models.

Large language models (LLMs) are widely used, but they often generate subtle factual errors, especially in long-form text. These errors are fatal in some specialized domains such as medicine. Existing fact-checking with grounding documents methods face two main challenges: (1) they struggle to understand complex multihop relations in long documents, often overlooking subtle factual errors; (2) most specialized methods rely on pairwise comparisons, requiring multiple model calls, leading to high resource and computational costs. To address these challenges, we propose GraphCheck, a fact-checking framework that uses extracted knowledge graphs to enhance text representation. Graph Neural Networks further process these graphs as a soft prompt, enabling LLMs to incorporate structured knowledge more effectively. Enhanced with graph-based reasoning, GraphCheck captures multihop reasoning chains that are often overlooked by existing methods, enabling precise and efficient fact-checking in a single inference call. Experimental results on seven benchmarks spanning both general and medical domains demonstrate up to a 7.1% overall improvement over baseline models. Notably, GraphCheck outperforms existing specialized fact-checkers and achieves comparable performance with state-of-the-art LLMs, such as DeepSeek-V3 and OpenAI-o1, with significantly fewer parameters.