Evaluating Chunking Strategies for Retrieval-Augmented Generation on Academic Texts

Retrieval-Augmented Generation (RAG) systems depend critically on document chunking quality for retrieving relevant context. Fixed chunking segments documents into uniform units irrespective of semantics or user intent, producing a precision-recall trade-off unresolvable by tuning chunk size alone. Semantic and agentic methods partially address these limitations but do not integrate user queries at the chunking stage. We present Query-Adaptive Semantic Chunking (QASC), which dynamically constructs chunks by integrating queries into segmentation through three mechanisms: cosine similarity scoring between sentence and query embeddings to identify seed sentences, contextual window expansion around seeds to preserve coherence, and chunk-level score aggregation to ensure holistic relevance. We evaluate QASC on 100 technical documents across 200 queries spanning four types, comparing against fixed chunking at five granularities, recursive splitting, semantic chunking, and agentic chunking. QASC achieves an F1-score of 0.85, a relative improvement of 18-27% over fixed chunking and 8-12% over semantic and agentic alternatives. Ablation studies confirm each component contributes meaningfully. Human evaluation by three annotators (Cohen kappa = 0.82) corroborates that QASC produces more relevant and coherent chunks than existing methods.

Retrieval-Augmented Generation (RAG) systems are often evaluated using final answer accuracy, even though their failures can originate from preprocessing, retrieval, context packing, or generation. This paper presents a controlled empirical study of RAG sensitivity, robustness, and stability across 56 experimental runs. We evaluate how chunk size, retrieval depth (top k), embedding-based reranking, probabilistic retrieval noise, and repeated seeded runs affect retrieval, context packing, and generation behavior. Using a fixed 500-question QA subset mapped to 20,958 unique corpus contexts, we analyze both final answer metrics and intermediate failure modes. Across these experiments, retrieval-oriented metrics improved under broader retrieval settings, while downstream exact-match and F1 scores often behaved non-monotonically. We also observe preprocessing-induced answer loss under smaller chunk sizes, progressive degradation under retrieval corruption, and higher observed variance in broader retrieval regimes. These findings suggest that RAG evaluation should include sensitivity, robustness, stability, and multi-stage failure analysis rather than relying only on final answer accuracy.

Retrieval-Augmented Generation (RAG) has demonstrated significant capabilities in enhancing the performance of Large Language Models (LLMs). One of the key tasks in RAG systems is the chunking process. Traditionally, fixed-size chunking and semantic chunking have been the standard approaches. However, interest in chunking strategies has been increasing, leading to a growing number of proposed methods that often claim improved performance over these conventional techniques. Many of these approaches are tailored to specific use cases and data types, with limited evidence of their effectiveness across diverse scenarios. As a result, it remains challenging to directly compare different techniques and assess their relative strengths. To the best of our knowledge, this study is the first to systematically evaluate the effectiveness of a wide range of chunking methods and emphasize the underlying challenges of chunking strategies in RAG systems. While chunking is commonly treated as a simple preprocessing step, we show that it introduces a range of impactful and often overlooked issues.