Option B is the best fit because hierarchical chunking is designed to preserve local detail while keeping broader document context available during retrieval, which directly addresses the problem of questions spanning methodology, results, and discussion. In large scientific papers, a single answer often depends on linked paragraphs across adjacent sections. If the knowledge base retrieves only small, isolated chunks, the RAG system can cite text that is semantically close to a query term but not contextually correct, producing inconsistent answers and irrelevant citations.

With hierarchical chunking, the knowledge base creates child chunks that are small enough for high-precision vector similarity matching, such as 200 tokens, which improves the likelihood that the retrieved text is tightly related to the user’s query. At the same time, each child chunk is associated with a larger parent chunk, such as 1,000 tokens, which retains the surrounding narrative and section-level context. This structure helps the retrieval pipeline return passages that include the relevant subsection plus the explanatory framing that prevents misinterpretation, which is especially important in scientific writing where methods, results, and discussion are interdependent.

The configured overlap further reduces boundary effects where key statements split across chunks. This improves continuity for paragraphs that bridge sections, such as a results paragraph that references the methodological setup or a discussion paragraph interpreting a specific metric.

Option A can improve consistency slightly, but fixed-size chunking still risks separating related paragraphs and does not provide a built-in mechanism to retrieve broader context linked to precise matches. Option C can create more meaningful boundaries, but it does not guarantee the parent-level context that hierarchical chunking provides at retrieval time. Option D increases operational burden and is not practical at the scale of 25 million