Abstract
Objective. Chemical named entity recognition (NER) models have the potential to impact a wide range of downstream tasks, from identifying adverse drug reactions to general pharmacoepidemiology. However, it is unknown whether these models work the same for everyone. Performance disparities can potentially cause harm rather than the intended good. Hence, in this paper, we measure gender-related performance disparities of chemical NER systems. Materials and Methods. We develop a framework to measure gender bias in chemical NER models using synthetic data and a newly annotated dataset of over 92,405 words with self-identified gender information from Reddit. We applied and evaluated state-of-the-art biomedical NER models. Results. Our findings indicate that chemical NER models are biased. The results of the bias tests on the synthetic dataset and the real-world data multiple fairness issues. For example, for synthetic data, we find that female-related names are generally classified as chemicals, particularly in datasets containing many brand names rather than standard ones. For both datasets, we find consistent fairness issues resulting in substantial performance disparities between female- and male-related data. Discussion. Our study highlights the issue of biases in chemical NER models. For example, we find that many systems cannot detect contraceptives (e.g., birth control). Conclusion. Chemical NER models are biased and can be harmful to female-related groups. Therefore, practitioners should carefully consider the potential biases of these models and take steps to mitigate them.
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URL
https://arxiv.org/abs/2212.12799
