BIOPSY - Biomarkers In Oncology: Pipeline for Structured Yielding (2025.emnlp-industry)
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| Challenge: | Biomarkers are crucial indicators for early cancer detection and prognosis, but extracting biomarkers from clinical texts remains a challenge. |
| Approach: | They propose a pipeline that integrates a domain-adapted biomarker entity recognition model and a relation extraction model to link biomarkers to their respective mutations. |
| Outcome: | The proposed pipeline achieves an F1 score of 0.86 for oncology and 0.87 for neuroscience domains on 5,000 clinical texts. |
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