Hannah Jauncey
2023
Using Bottleneck Adapters to Identify Cancer in Clinical Notes under Low-Resource Constraints
Omid Rohanian
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Hannah Jauncey
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Mohammadmahdi Nouriborji
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Vinod Kumar
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Bronner P. Gonalves
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Christiana Kartsonaki
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Isaric Clinical Characterisation Group
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Laura Merson
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David Clifton
The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks
Processing information locked within clinical health records is a challenging task that remains an active area of research in biomedical NLP. In this work, we evaluate a broad set of machine learning techniques ranging from simple RNNs to specialised transformers such as BioBERT on a dataset containing clinical notes along with a set of annotations indicating whether a sample is cancer-related or not. Furthermore, we specifically employ efficient fine-tuning methods from NLP, namely, bottleneck adapters and prompt tuning, to adapt the models to our specialised task. Our evaluations suggest that fine-tuning a frozen BERT model pre-trained on natural language and with bottleneck adapters outperforms all other strategies, including full fine-tuning of the specialised BioBERT model. Based on our findings, we suggest that using bottleneck adapters in low-resource situations with limited access to labelled data or processing capacity could be a viable strategy in biomedical text mining.
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