razreshili at ArchEHR-QA 2025: Contrastive Fine-Tuning for Retrieval-Augmented Biomedical QA

We present a retrieval-augmented system for the ArchEHR-QA 2025 shared task, which focuses on generating concise, medically accurate answers to clinical questions based on a patient's electronic health record (EHR).A key challenge is following a strict citation format that references relevant sentence IDs.To improve retrieval, we fine-tuned an all-MiniLM-L6-v2 embedding model using contrastive learning on over 2,300 question-sentence triplets, with DoRA for efficient adaptation.Sentences were selected using cosine similarity thresholds and passed into a quantized Mistral-7B-Instruct model along with a structured prompt.Our system achieved similar relevance to the baseline but lower overall performance (19.3 vs. 30.7),due to issues with citation formatting and generation quality.We discuss limitations such as threshold tuning, prompt-following ability, and model size, and suggest future directions for improving structured biomedical QA.

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Publication Details

Published
2025-01-01
DOI
https://doi.org/10.18653/v1/2025.bionlp-share.19
Primary Topic
Radiomics and Machine Learning in Medical Imaging
Type
article
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article

razreshili at ArchEHR-QA 2025: Contrastive Fine-Tuning for Retrieval-Augmented Biomedical QA

Arina Zemchyk
Radiomics and Machine Learning in Medical Imaging
article

razreshili at ArchEHR-QA 2025: Contrastive Fine-Tuning for Retrieval-Augmented Biomedical QA

Arina Zemchyk
article en

Abstract

We present a retrieval-augmented system for the ArchEHR-QA 2025 shared task, which focuses on generating concise, medically accurate answers to clinical questions based on a patient's electronic health record (EHR).A key challenge is following a strict citation format that references relevant sentence IDs.To improve retrieval, we fine-tuned an all-MiniLM-L6-v2 embedding model using contrastive learning on over 2,300 question-sentence triplets, with DoRA for efficient adaptation.Sentences were selected using cosine similarity thresholds and passed into a quantized Mistral-7B-Instruct model along with a structured prompt.Our system achieved similar relevance to the baseline but lower overall performance (19.3 vs. 30.7),due to issues with citation formatting and generation quality.We discuss limitations such as threshold tuning, prompt-following ability, and model size, and suggest future directions for improving structured biomedical QA.

Openalex Percentile: Top 72%
Radiomics and Machine Learning in Medical Imaging
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