Doctoral Thesis: Leveraging Structure and Knowledge in Clinical and Biomedical Representation Learning

Matthew B.A. McDermott

Abstract:

Datasets in the machine learning for health and biomedicine domain are often noisy, irregularly sampled, only sparsely labeled, and small relative to the dimensionality of the both the data and the tasks. These problems motivate the use of \emph{representation learning} in this domain, which are a suite of techniques designed to produce representations of a dataset that are amenable to downstream modelling tasks. Representation learning in this domain can also take advantage of the significant external knowledge in the biomedical domain. In this thesis, I will explore novel pre-training and representation learning strategies for biomedical data which leverage external structure or knowledge to inform learning at both local and global scales. These techniques will be explored in 4 chapters: (1) leveraging unlabeled data to infer distributional constraints in a semi-supervised learning setting; (2) using graph convolutional neural networks over gene-gene co-regulatory networks to improve modelling of gene expression data; (3) adapting pre-training techniques from natural language processing to electronic health record data, and showing that novel methods are needed for electronic health record timeseries data; and (4) asserting global structure in pre-training applications through structure-preserving pre-training.

Thesis Supervisor: Prof. Peter Szolovits

Details

• Date: Tuesday, April 26
• Time: 12:00 pm

Additional Location Details:

To be held via zoom, contact doctoral candidate for details at

mmd@mit.edu