# Ranking-Aware Prompt Optimization for Multimodal Clinical Diagnosis

arXiv: https://arxiv.org/abs/2609.40361 · HTML: https://mlsanity.com/paper/2609.40361/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Medical vision-language models, one of 16 directions in Multimodal LLMs / vision-language models.
- Builds on 21 of its 34 references that are in the map.
- First posted on arXiv 30 Sep 2026.

## Placed in

- Multimodal LLMs / vision-language models / [Medical vision-language models](https://mlsanity.com/mllm/medical-vision-language-models/)

## Builds on (most cited first, 21 of 21)

- [QLoRA: Efficient Finetuning of Quantized LLMs](https://mlsanity.com/paper/2305.14314/) (2023)
- [Qwen3-VL Technical Report](https://mlsanity.com/paper/2511.21631/) (2025)
- [Language Models (Mostly) Know What They Know](https://mlsanity.com/paper/2207.05221/) (2022)
- [Gemma 3 Technical Report](https://mlsanity.com/paper/2503.19786/) (2025)
- [LlamaFactory: Unified Efficient Fine-Tuning of 100+ Language Models](https://mlsanity.com/paper/2403.13372/) (2024)
- [CheXpert: A Large Chest Radiograph Dataset with Uncertainty Labels and Expert Comparison](https://mlsanity.com/paper/1901.07031/) (2019)
- [LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Day](https://mlsanity.com/paper/2306.00890/) (2023)
- [SGLang: Efficient Execution of Structured Language Model Programs](https://mlsanity.com/paper/2312.07104/) (2023)
- [DSPy: Compiling Declarative Language Model Calls into Self-Improving Pipelines](https://mlsanity.com/paper/2310.03714/) (2023)
- [Automatic Prompt Optimization with "Gradient Descent" and Beam Search](https://mlsanity.com/paper/2305.03495/) (2023)
- [Promptbreeder: Self-Referential Self-Improvement Via Prompt Evolution](https://mlsanity.com/paper/2309.16797/) (2023)
- [GEPA: Reflective Prompt Evolution Can Outperform Reinforcement Learning](https://mlsanity.com/paper/2507.19457/) (2025)
- [MedGemma Technical Report](https://mlsanity.com/paper/2507.05201/) (2025)
- [Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine](https://mlsanity.com/paper/2311.16452/) (2023)
- [Towards Generalist Biomedical AI](https://mlsanity.com/paper/2307.14334/) (2023)
- [Surface Form Competition: Why the Highest Probability Answer Isn't Always Right](https://mlsanity.com/paper/2104.08315/) (2021)
- [BiomedGPT: A Generalist Vision-Language Foundation Model for Diverse Biomedical Tasks](https://mlsanity.com/paper/2305.17100/) (2023)
- [CheXpert Plus: Augmenting a Large Chest X-ray Dataset with Text Radiology Reports, Patient Demographics and Additional Image Formats](https://mlsanity.com/paper/2405.19538/) (2024)
- [Large-scale Robust Deep AUC Maximization: A New Surrogate Loss and Empirical Studies on Medical Image Classification](https://mlsanity.com/paper/2012.03173/) (2020)
- [PeFoMed: Parameter Efficient Fine-tuning of Multimodal Large Language Models for Medical Imaging](https://mlsanity.com/paper/2401.02797/) (2024)
- [ReXVQA: A Large-scale Visual Question Answering Benchmark for Generalist Chest X-ray Understanding](https://mlsanity.com/paper/2506.04353/) (2025)

## Abstract (arXiv)

Multimodal large language models (MLLMs) are rapidly advancing clinical diagnosis, yet their adaptation pipelines remain anchored to accuracy-based objectives. Clinical data are heavily class-imbalanced: a constant-majority predictor can score above 90% accuracy while being clinically useless. We therefore evaluate and optimize for AUROC, a threshold-free score that ranks positives above negatives and is invariant to class balance. We focus on prompt optimization in MLLMs. Reflective methods such as GEPA use a binary scores matrix with one row per evaluation instance and one column per candidate prompt; cells record per-instance correctness, so the column average is accuracy and drives candidate selection. We introduce pair-level Pareto prompt evolution (Ranking-PE), which replaces each correctness row with a pairwise-ordering row over (positive, negative) instance pairs: the cell is 1 if the candidate scores the positive higher than the paired negative. The column average then equals empirical AUROC (by the Wilcoxon-Mann-Whitney identity). We apply this swap at all three layers the prompt evolution search reads from - the scores matrix that decides Pareto dominance, the per-example feedback to the reflection LM, and final candidate selection - at no extra model calls and with no surrogate loss. Across three diseases on MIMIC, accuracy-based prompt evolution can degrade ranking; Ranking-PE reverses this, beating the accuracy-based recipe by +5.8 AUROC pp on fine-tuned Qwen3-VL-8B and +16.2 pp on MedGemma-4B. Ablations examine each design component and show that a medical-grade visual backbone - via vision-encoder-tuned SFT or medical pretraining - is a prerequisite that prompt search cannot replace - our recipe extends reflective prompt evolution from text-only data to multimodal clinical decision-making.