2026/03/30 by José Guilherme Marques dos Santos, Ricardo Yang, Rui Humberto Pereira +8 · 1 voice
Computer Science · #cs.IR #cs.AI #cs.LG
paper · pdf · doi:10.3390/app16105069
arxiv published 2026/03/30 · arxiv updated 2026/05/25
Retrieval-Augmented Generation (RAG) systems depend critically on the quality of document preprocessing, yet no prior study has evaluated PDF processing frameworks by their impact on downstream question-answering accuracy. We address this gap through a systematic comparison of four open-source PDF-to-Markdown conversion frameworks, Docling, MinerU, Marker, and DeepSeek OCR, across 21 pipeline configurations, varying the conversion tool, cleaning transformations, splitting strategy, and metadata enrichment. Evaluation was performed using a 50-question benchmark over a corpus of 36 Portuguese administrative documents (1706 pages, ~492K words), with LLM-as-judge scoring over 50 independent runs per configuration. Statistical significance was assessed via Wilcoxon signed-rank tests with Cohen's d effect sizes. Two baselines bounded the results: naïve PDFLoader (86.2%) and manually curated Markdown (91.3%). Docling with hierarchical splitting and image descriptions achieved the highest automated accuracy (94.1 +/- 1.6%), surpassing even manual curation. A per-question-type analysis revealed that table-dependent questions drive the largest accuracy differences, with a 33-percentage-point gap between basic and hierarchical splitting. Metadata enrichment and hierarchy-aware chunking contributed more to accuracy than the conversion framework alone. An exploratory GraphRAG implementation underperformed basic RAG (82% vs. 94.1%). These findings demonstrate that data preparation quality is the dominant factor in RAG system performance.