MMiDaS-AE: multi-modal missing data aware stacked autoencoder for biomedical abstract screening

Eric W. Lee, Byron C. Wallace, Karla I. Galaviz, Joyce C. Ho

View paper in the ACM journal

Abstract: Systematic review (SR) is an essential process to identify, evaluate, and summarize the findings of all relevant individual studies concerning health-related questions. However, conducting a SR is labor-intensive, as identifying relevant studies is a daunting process that entails multiple researchers screening thousands of articles for relevance. In this paper, we propose MMiDaS-AE, a Multi-modal Missing Data aware Stacked Autoencoder, for semi-automating screening for SRs. We use a multi-modal view that exploits three representations, of: 1) documents, 2) topics, and 3) citation networks. Documents that contain similar words will be nearby in the document embedding space. Models can also exploit the relationship between documents and the associated SR MeSH terms to capture article relevancy. Finally, related works will likely share the same citations, and thus closely related articles would, intuitively, be trained to be close to each other in the embedding space. However, using all three learned representations as features directly result in an unwieldy number of parameters. Thus, motivated by recent work on multi-modal auto-encoders, we adopt a multi-modal stacked autoencoder that can learn a shared representation encoding all three representations in a compressed space. However, in practice one or more of these modalities may be missing for an article (e.g., if we cannot recover citation information). Therefore, we propose to learn to impute the shared representation even when specific inputs are missing. We find this new model significantly improves performance on a dataset consisting of 15 SRs compared to existing approaches.