Generalizing biomedical relation classification with neural adversarial domain adaptation

Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu

Research output: Contribution to journalArticlepeer-review

22 Scopus citations


Motivation: Creating large datasets for biomedical relation classification can be prohibitively expensive. While some datasets have been curated to extract protein-protein and drug-drug interactions (PPIs and DDIs) from text, we are also interested in other interactions including gene-disease and chemical-protein connections. Also, many biomedical researchers have begun to explore ternary relationships. Even when annotated data are available, many datasets used for relation classification are inherently biased. For example, issues such as sample selection bias typically prevent models from generalizing in the wild. To address the problem of cross-corpora generalization, we present a novel adversarial learning algorithm for unsupervised domain adaptation tasks where no labeled data are available in the target domain. Instead, our method takes advantage of unlabeled data to improve biased classifiers through learning domain-invariant features via an adversarial process. Finally, our method is built upon recent advances in neural network (NN) methods. Results: We experiment by extracting PPIs and DDIs from text. In our experiments, we show domain invariant features can be learned in NNs such that classifiers trained for one interaction type (protein-protein) can be re-purposed to others (drug-drug). We also show that our method can adapt to different source and target pairs of PPI datasets. Compared to prior convolutional and recurrent NN-based relation classification methods without domain adaptation, we achieve improvements as high as 30% in F1-score. Likewise, we show improvements over state-of-the-art adversarial methods.

Original languageEnglish
Pages (from-to)2973-2981
Number of pages9
Issue number17
StatePublished - Sep 1 2018

Bibliographical note

Funding Information:
This research is supported by the Intramural Research Programs of the National Institutes of Health, National Library of Medicine. This research was conducted when Anthony Rios was a summer intern at the NCBI/NIH. Ramakanth Kavuluru and Anthony Rios are also supported by the National Library of Medicine through grant R21LM012274. We gratefully acknowledge the support of NVIDIA Corporation with the donation of the Titan X Pascal GPU used for this research.

Publisher Copyright:
© 2018 Oxford University Press. All rights reserved.

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics


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