QU-NLP at ArchEHR-QA 2026: Two-Stage QLoRA Fine-Tuning of Qwen3-4B for Patient-Oriented Clinical Question Answering and Evidence Sentence Alignment

TL;DR

This paper introduces a two-stage QLoRA fine-tuning approach for Qwen3-4B to improve clinical question answering and evidence sentence alignment, achieving competitive results on the ArchEHR-QA shared task.

Contribution

It presents a novel two-stage fine-tuning method with quantization for clinical NLP tasks and combines multiple retrieval techniques for evidence sentence identification.

Findings

The system achieved an overall score of 32.87 on the test set.

Ensemble of retrieval methods reached a micro-F1 of 67.16.

Insufficient annotated data limits relevance discrimination, suggesting data augmentation as future work.

Abstract

We present a unified system addressing both Subtask 3 (answer generation) and Subtask 4 (evidence sentence alignment) of the ArchEHR-QA Shared Task. For Subtask 3, we apply two-stage Quantised Low-Rank Adaptation (QLoRA) to Qwen3-4B loaded in 4-bit NF4 quantisation: first on 30,000 samples from the emrQA-MedSQuAD corpus to establish clinical domain competence, then on the 20 annotated development cases to learn the task-specific output style. Our system achieves an overall score of 32.87 on the official test-2026 split (BLEU = 9.42, ROUGE-L = 27.04, SARI = 55.42, BERTScore = 43.00, AlignScore = 25.28, MEDCON = 37.04). For Subtask 4, we develop a weighted ensemble of three retrieval methods - BM25 with relative thresholding, TF-IDF cosine similarity, and a fine-tuned cross-encoder - to identify note sentences supporting a given gold answer, achieving a micro-F1 of 67.16 on the 100-case test set. Experiments reveal that both subtasks expose the same fundamental challenge: 20 annotated training cases are insufficient to distinguish relevant from irrelevant clinical sentences, pointing to data augmentation as the highest-leverage future direction.