# Listwise Cross-Encoder Fine-Tuning vs. Agentic Instruction Tuning for LLM Rerankers: A Systematic Study in Medical Procedure Reranking

arXiv: https://arxiv.org/abs/2608.09650 · HTML: https://mlsanity.com/paper/2608.09650/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Medical and scientific domain agents, one of 16 directions in LLM agents and tool use.
- Builds on 5 of its 13 references that are in the map.
- First posted on arXiv 10 Aug 2026.

## Placed in

- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 5 of 5)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Qwen3 Embedding: Advancing Text Embedding and Reranking Through Foundation Models](https://mlsanity.com/paper/2506.05176/) (2025)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval](https://mlsanity.com/paper/2307.00589/) (2023)
- [Exploring the Effectiveness of Multi-stage Fine-tuning for Cross-encoder Re-rankers](https://mlsanity.com/paper/2503.22672/) (2025)

## Abstract (arXiv)

Reranking medical procedures against patient queries is a critical component of health insurance information retrieval, complicated by a substantial lexical gap between patient language and clinical nomenclature. We present a systematic comparison of two reranking paradigms for this production task: (1) small cross-encoders (MedCPT, MiniLM-L12) fine-tuned with listwise learning-to-rank objectives across layer freezing configurations, and (2) Qwen3-Reranker-4B, a 4B-parameter instruction reranker whose prompt is iteratively refined via an agentic optimization loop driven by GPT-4.1. On a purpose-built dataset of 2,647 queries across 708 insurance services, we find that a 109M-parameter cross-encoder fine-tuned with ListNet outperforms the 4B-parameter model by 2.6 percentage points on NDCG@3 and 13.3 points on Spearman correlation - at 37x fewer parameters. We report practical findings, a scalable LLM based dataset construction pipeline, and deployment trade-offs relevant to production reranking systems. We release our code and a sample dataset to support reproducibility and adaptation to other domains.