CaresAI at BioCreative IX Track 1 -- LLM for Biomedical QA
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| Format: | Preprint |
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2025
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| _version_ | 1866908511946932224 |
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| author | Abdel-Salam, Reem Adewunmi, Mary Abayomi, Modinat A. |
| author_facet | Abdel-Salam, Reem Adewunmi, Mary Abayomi, Modinat A. |
| contents | Large language models (LLMs) are increasingly evident for accurate question answering across various domains. However, rigorous evaluation of their performance on complex question-answering (QA) capabilities is essential before deployment in real-world biomedical and healthcare applications. This paper presents our approach to the MedHopQA track of the BioCreative IX shared task, which focuses on multi-hop biomedical question answering involving diseases, genes, and chemicals. We adopt a supervised fine-tuning strategy leveraging LLaMA 3 8B, enhanced with a curated biomedical question-answer dataset compiled from external sources including BioASQ, MedQuAD, and TREC. Three experimental setups are explored: fine-tuning on combined short and long answers, short answers only, and long answers only. While our models demonstrate strong domain understanding, achieving concept-level accuracy scores of up to 0.8, their Exact Match (EM) scores remain significantly lower, particularly in the test phase. We introduce a two-stage inference pipeline for precise short-answer extraction to mitigate verbosity and improve alignment with evaluation metrics. Despite partial improvements, challenges persist in generating strictly formatted outputs. Our findings highlight the gap between semantic understanding and exact answer evaluation in biomedical LLM applications, motivating further research in output control and post-processing strategies. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2509_00806 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | CaresAI at BioCreative IX Track 1 -- LLM for Biomedical QA Abdel-Salam, Reem Adewunmi, Mary Abayomi, Modinat A. Computation and Language Artificial Intelligence Machine Learning Large language models (LLMs) are increasingly evident for accurate question answering across various domains. However, rigorous evaluation of their performance on complex question-answering (QA) capabilities is essential before deployment in real-world biomedical and healthcare applications. This paper presents our approach to the MedHopQA track of the BioCreative IX shared task, which focuses on multi-hop biomedical question answering involving diseases, genes, and chemicals. We adopt a supervised fine-tuning strategy leveraging LLaMA 3 8B, enhanced with a curated biomedical question-answer dataset compiled from external sources including BioASQ, MedQuAD, and TREC. Three experimental setups are explored: fine-tuning on combined short and long answers, short answers only, and long answers only. While our models demonstrate strong domain understanding, achieving concept-level accuracy scores of up to 0.8, their Exact Match (EM) scores remain significantly lower, particularly in the test phase. We introduce a two-stage inference pipeline for precise short-answer extraction to mitigate verbosity and improve alignment with evaluation metrics. Despite partial improvements, challenges persist in generating strictly formatted outputs. Our findings highlight the gap between semantic understanding and exact answer evaluation in biomedical LLM applications, motivating further research in output control and post-processing strategies. |
| title | CaresAI at BioCreative IX Track 1 -- LLM for Biomedical QA |
| topic | Computation and Language Artificial Intelligence Machine Learning |
| url | https://arxiv.org/abs/2509.00806 |