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Bioinformatics. 2018 Dec 1;34(23):4087-4094. doi: 10.1093/bioinformatics/bty449.

Transfer learning for biomedical named entity recognition with neural networks.

Author information

Department of Computer Science, University of Toronto, Toronto, Canada.
The Donnelly Centre, University of Toronto, Toronto, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.



The explosive increase of biomedical literature has made information extraction an increasingly important tool for biomedical research. A fundamental task is the recognition of biomedical named entities in text (BNER) such as genes/proteins, diseases and species. Recently, a domain-independent method based on deep learning and statistical word embeddings, called long short-term memory network-conditional random field (LSTM-CRF), has been shown to outperform state-of-the-art entity-specific BNER tools. However, this method is dependent on gold-standard corpora (GSCs) consisting of hand-labeled entities, which tend to be small but highly reliable. An alternative to GSCs are silver-standard corpora (SSCs), which are generated by harmonizing the annotations made by several automatic annotation systems. SSCs typically contain more noise than GSCs but have the advantage of containing many more training examples. Ideally, these corpora could be combined to achieve the benefits of both, which is an opportunity for transfer learning. In this work, we analyze to what extent transfer learning improves upon state-of-the-art results for BNER.


We demonstrate that transferring a deep neural network (DNN) trained on a large, noisy SSC to a smaller, but more reliable GSC significantly improves upon state-of-the-art results for BNER. Compared to a state-of-the-art baseline evaluated on 23 GSCs covering four different entity classes, transfer learning results in an average reduction in error of approximately 11%. We found transfer learning to be especially beneficial for target datasets with a small number of labels (approximately 6000 or less).

Availability and implementation:

Source code for the LSTM-CRF is available at and links to the corpora are available at

Supplementary information:

Supplementary data are available at Bioinformatics online.

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