Multiple Sclerosis (MS) is a chronic, inflammatory and degenerative neurological disease, which is monitored by a specialist using the Expanded Disability Status Scale (EDSS) and recorded in unstructured text in the form of a neurology consult note. An EDSS measurement contains an overall ‘EDSS’ score and several functional subscores. Typically, expert knowledge is required to interpret consult notes and generate these scores. Previous approaches used limited context length Word2Vec embeddings and keyword searches to predict scores given a consult note, but often failed when scores were not explicitly stated. In this work, we present MS-BERT, the first publicly available transformer model trained on real clinical data other than MIMIC. Next, we present MSBC, a classifier that applies MS-BERT to generate embeddings and predict EDSS and functional subscores. Lastly, we explore combining MSBC with other models through the use of Snorkel to generate scores for unlabelled consult notes. MSBC achieves state-of-the-art performance on all metrics and prediction tasks and outperforms the models generated from the Snorkel ensemble. We improve Macro-F1 by 0.12 (to 0.88) for predicting EDSS and on average by 0.29 (to 0.63) for predicting functional subscores over previous Word2Vec CNN and rule-based approaches.

Models that perform well on a training domain often fail to generalize to out-of-domain (OOD) examples. Data augmentation is a common method used to prevent overfitting and improve OOD generalization. However, in natural language, it is difficult to generate new examples that stay on the underlying data manifold. We introduce SSMBA, a data augmentation method for generating synthetic training examples by using a pair of corruption and reconstruction functions to move randomly on a data manifold. We investigate the use of SSMBA in the natural language domain, leveraging the manifold assumption to reconstruct corrupted text with masked language models. In experiments on robustness benchmarks across 3 tasks and 9 datasets, SSMBA consistently outperforms existing data augmentation methods and baseline models on both in-domain and OOD data, achieving gains of 0.8% on OOD Amazon reviews, 1.8% accuracy on OOD MNLI, and 1.4 BLEU on in-domain IWSLT14 German-English.