Retrieval Augmented Generation enhances the response accuracy of Large Language Models (LLMs) by integrating retrieval and generation modules with external knowledge, demonstrating particular strength in real-time queries and Visual Question Answering tasks. However, the effectiveness of RAG is frequently hindered by the precision of the retriever: many retrieved samples fed into the generation phase are irrelevant or misleading, posing a critical bottleneck to LLMs’ performance. To address this challenge, we introduce \textbf{VaccineRAG}, a novel Chain-of-Thought-based retrieval-augmented generation dataset. On one hand, VaccineRAG employs a benchmark to evaluate models using data with varying positive/negative sample ratios, systematically exposing inherent weaknesses in current LLMs. On the other hand, it enhances models’ sample-discrimination capabilities by prompting LLMs to generate explicit Chain-of-Thought (CoT) analysis for each sample before producing final answers. Furthermore, to enhance the model’s ability to learn long-sequence complex CoT content, we propose \textbf{Partial-GRPO}. By modeling the outputs of LLMs as multiple components rather than a single whole, our model can make more informed preference selections for complex sequences, thereby enhancing its capacity to learn complex CoT. Comprehensive evaluations and ablation studies on VaccineRAG validate the effectiveness of the proposed scheme.

Inconsistent hallucinations remain a major challenge for large language models (LLMs), undermining the accuracy and reliability of fact-based reasoning in real-world applications. Existing approaches often rely on task-specific training or adaptation, such as hand-crafted synthetic datasets for domain tasks or solutions mainly focused on numerical reasoning, thereby limiting generalizability to broader, unseen NLP tasks. Inspired by the structural rigor and logical consistency of programming languages, we observe that fact-based texts can be mapped to programming structures due to their inherent patterns. We further propose FACT, a novel Fact-driven Alternating Code-text Training framework that alternates between text-to-code and code-to-text prediction. FACT is the first task-agnostic paradigm that embeds code and natural language in a shared semantic space, thereby transferring the logical consistency of code to LLM outputs in NLP tasks. Experiments show that with only a small subset of Wiki-40B-en for training, FACT reduces inconsistent hallucinations by 2.7%–8.0% and improves overall performance by 2.5%–6.1% in three leading LLMs and four diverse datasets covering QA and summarization tasks. This framework offers a new perspective on addressing challenging hallucinations in LLMs, contributing to more reliable AI.