A Topic-modeling Based Framework for Drug-drug Interaction Classification from Biomedical Text

Dingcheng Li, Sijia Liu, Majid Rastegar-Mojarad, Yanshan Wang, Vipin Chaudhary, Terry Therneau, Hongfang Liu

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Classification of drug-drug interaction (DDI) from medical literatures is significant in preventing medication-related errors. Most of the existing machine learning approaches are based on supervised learning methods. However, the dynamic nature of drug knowledge, combined with the enormity and rapidly growing of the biomedical literatures make supervised DDI classification methods easily overfit the corpora and may not meet the needs of real-world applications. In this paper, we proposed a relation classification framework based on topic modeling (RelTM) augmented with distant supervision for the task of DDI from biomedical text. The uniqueness of RelTM lies in its two-level sampling from both DDI and drug entities. Through this design, RelTM take both relation features and drug mention features into considerations. An efficient inference algorithm for the model using Gibbs sampling is also proposed. Compared to the previous supervised models, our approach does not require human efforts such as annotation and labeling, which is its advantage in trending big data applications. Meanwhile, the distant supervision combination allows RelTM to incorporate rich existing knowledge resources provided by domain experts. The experimental results on the 2013 DDI challenge corpus reach 48% in F1 score, showing the effectiveness of RelTM.

Original languageEnglish (US)
Pages (from-to)789-798
Number of pages10
JournalAMIA ... Annual Symposium proceedings. AMIA Symposium
StatePublished - 2016

ASJC Scopus subject areas

  • General Medicine


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