Comparative Evaluation of Advanced Chunking for Retrieval-Augmented Generation in Large Language Models for Clinical Decision Support

Abstract

Retrieval-augmented generation (RAG) quality depends on how source documents are segmented before indexing; fixed-length chunks can split concepts or add noise, reducing precision. We evaluated whether proposition, semantic, and adaptive chunking improve accuracy and relevance for safer clinical decision support. Using a curated domain knowledge base with Gemini 1.0 Pro, we built four otherwise identical RAG pipelines that differed only in the chunking strategy: adaptive length, proposition, semantic, and a fixed token-dependent baseline. Thirty common postoperative rhinoplasty questions were submitted to each pipeline. Outcomes included medical accuracy and clinical relevance (3-point Likert scale) and retrieval precision, recall, and F1; group differences were tested with ANOVA and Tukey post hoc analyses. Adaptive chunking achieved the highest accuracy-87% (Likert 2.37 ± 0.72) versus baseline 50% (1.63 ± 0.72; <i>p</i> = 0.001)-and the highest relevance (93%, 2.90 ± 0.40). Retrieval metrics were strongest with adaptive (precision 0.50, recall 0.88, F1 0.64) versus baseline (0.17, 0.40, 0.24). Proposition and semantic strategies improved all metrics relative to baseline, though less than adaptive. Aligning chunks to logical topic boundaries yielded more accurate, relevant answers without modifying the language model, offering a model-agnostic, data-source-neutral lever to enhance the safety and utility of LLM-based clinical decision support.

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