Exploration of Augmentation Strategies in Multi-modal Retrieval-Augmented Generation for the Biomedical Domain: A Case Study Evaluating Question Answering in Glycobiology

Primož Kocbek; Azra Frkatović-Hodžić; Dora Lalić; Vivian Hui; Gordan Lauc; Gregor Štiglic

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arXiv · 2512.16802

Exploration of Augmentation Strategies in Multi-modal Retrieval-Augmented Generation for the Biomedical Domain: A Case Study Evaluating Question Answering in Glycobiology

Primož Kocbek·Azra Frkatović-Hodžić·Dora Lalić·Vivian Hui·Gordan Lauc·Gregor Štiglic

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Abstract

Multi-modal retrieval-augmented generation (MM-RAG) promises grounded biomedical QA, but it is unclear when to (i) convert figures/tables into text versus (ii) use optical character recognition (OCR)-free visual retrieval that returns page images and leaves interpretation to the generator. We study this trade-off in glycobiology, a visually dense domain. We built a benchmark of 120 multiple-choice questions (MCQs) from 25 papers, stratified by retrieval difficulty (easy text, medium figures/tables, hard cross-evidence). We implemented four augmentations-None, Text RAG, Multi-modal conversion, and late-interaction visual retrieval (ColPali)-using Docling parsing and Qdrant indexing. We evaluated mid-size open-source and frontier proprietary models (e.g., Gemma-3-27B-IT, GPT-4o family). Additional testing used the GPT-5 family and multiple visual retrievers (ColPali/ColQwen/ColFlor). Accuracy with Agresti-Coull 95% confidence intervals (CIs) was computed over 5 runs per configuration. With Gemma-3-27B-IT, Text and Multi-modal augmentation outperformed OCR-free retrieval (0.722-0.740 vs. 0.510 average accuracy). With GPT-4o, Multi-modal achieved 0.808, with Text 0.782 and ColPali 0.745 close behind; within-model differences were small. In follow-on experiments with the GPT-5 family, the best results with ColPali and ColFlor improved by ~2% to 0.828 in both cases. In general, across the GPT-5 family, ColPali, ColQwen, and ColFlor were statistically indistinguishable. GPT-5-nano trailed larger GPT-5 variants by roughly 8-10%. Pipeline choice is capacity-dependent: converting visuals to text lowers the reader burden and is more reliable for mid-size models, whereas OCR-free visual retrieval becomes competitive under frontier models. Among retrievers, ColFlor offers parity with heavier options at a smaller footprint, making it an efficient default when strong generators are available.

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Primož Kocbek, Azra Frkatović-Hodžić, Dora Lalić, Vivian Hui, Gordan Lauc, Gregor Štiglic. 2025-12-18. Exploration of Augmentation Strategies in Multi-modal Retrieval-Augmented Generation for the Biomedical Domain: A Case Study Evaluating Question Answering in Glycobiology. https://arxiv.org/abs/2512.16802

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