ML-Net: multi-label classification of biomedical texts with deep neural networks

J Am Med Inform Assoc. 2019 Nov 1;26(11):1279-1285. doi: 10.1093/jamia/ocz085.


Objective: In multi-label text classification, each textual document is assigned 1 or more labels. As an important task that has broad applications in biomedicine, a number of different computational methods have been proposed. Many of these methods, however, have only modest accuracy or efficiency and limited success in practical use. We propose ML-Net, a novel end-to-end deep learning framework, for multi-label classification of biomedical texts.

Materials and methods: ML-Net combines a label prediction network with an automated label count prediction mechanism to provide an optimal set of labels. This is accomplished by leveraging both the predicted confidence score of each label and the deep contextual information (modeled by ELMo) in the target document. We evaluate ML-Net on 3 independent corpora in 2 text genres: biomedical literature and clinical notes. For evaluation, we use example-based measures, such as precision, recall, and the F measure. We also compare ML-Net with several competitive machine learning and deep learning baseline models.

Results: Our benchmarking results show that ML-Net compares favorably to state-of-the-art methods in multi-label classification of biomedical text. ML-Net is also shown to be robust when evaluated on different text genres in biomedicine.

Conclusion: ML-Net is able to accuractely represent biomedical document context and dynamically estimate the label count in a more systematic and accurate manner. Unlike traditional machine learning methods, ML-Net does not require human effort for feature engineering and is a highly efficient and scalable approach to tasks with a large set of labels, so there is no need to build individual classifiers for each separate label.

Keywords: biomedical literacutre; biomedical text; clinical notes; deep neural network; multi-label text classification.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural

MeSH terms

  • Benchmarking
  • Classification / methods
  • Computational Biology
  • Data Mining / methods
  • Deep Learning*
  • Machine Learning
  • Natural Language Processing*
  • Neural Networks, Computer*