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Register a new userMultiple Sclerosis Severity Classification From Clinical Text
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Added by
Michal Malyska
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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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.
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The dominant approach to unsupervised style transfer in text is based on the idea of learning a latent representation, which is independent of the attributes specifying its style. In this paper, we show that this condition is not necessary and is not always met in practice, even with domain adversarial training that explicitly aims at learning such disentangled representations. We thus propose a new model that controls several factors of variation in textual data where this condition on disentanglement is replaced with a simpler mechanism based on back-translation. Our method allows control over multiple attributes, like gender, sentiment, product type, etc., and a more fine-grained control on the trade-off between content preservation and change of style with a pooling operator in the latent space. Our experiments demonstrate that the fully entangled model produces better generations, even when tested on new and more challenging benchmarks comprising reviews with multiple sentences and multiple attributes.
Data augmentation aims to enrich training samples for alleviating the overfitting issue in low-resource or class-imbalanced situations. Traditional methods first devise task-specific operations such as Synonym Substitute, then preset the corresponding parameters such as the substitution rate artificially, which require a lot of prior knowledge and are prone to fall into the sub-optimum. Besides, the number of editing operations is limited in the previous methods, which decreases the diversity of the augmented data and thus restricts the performance gain. To overcome the above limitations, we propose a framework named Text AutoAugment (TAA) to establish a compositional and learnable paradigm for data augmentation. We regard a combination of various operations as an augmentation policy and utilize an efficient Bayesian Optimization algorithm to automatically search for the best policy, which substantially improves the generalization capability of models. Experiments on six benchmark datasets show that TAA boosts classification accuracy in low-resource and class-imbalanced regimes by an average of 8.8% and 9.7%, respectively, outperforming strong baselines.
Clinical text classification is an important problem in medical natural language processing. Existing studies have conventionally focused on rules or knowledge sources-based feature engineering, but only a few have exploited effective feature learning capability of deep learning methods. In this study, we propose a novel approach which combines rule-based features and knowledge-guided deep learning techniques for effective disease classification. Critical Steps of our method include identifying trigger phrases, predicting classes with very few examples using trigger phrases and training a convolutional neural network with word embeddings and Unified Medical Language System (UMLS) entity embeddings. We evaluated our method on the 2008 Integrating Informatics with Biology and the Bedside (i2b2) obesity challenge. The results show that our method outperforms the state of the art methods.
We introduce BlaBla, an open-source Python library for extracting linguistic features with proven clinical relevance to neurological and psychiatric diseases across many languages. BlaBla is a unifying framework for accelerating and simplifying clinical linguistic research. The library is built on state-of-the-art NLP frameworks and supports multithreaded/GPU-enabled feature extraction via both native Python calls and a command line interface. We describe BlaBlas architecture and clinical validation of its features across 12 diseases. We further demonstrate the application of BlaBla to a task visualizing and classifying language disorders in three languages on real clinical data from the AphasiaBank dataset. We make the codebase freely available to researchers with the hope of providing a consistent, well-validated foundation for the next generation of clinical linguistic research.
In this paper, we introduce the prior knowledge, multi-scale structure, into self-attention modules. We propose a Multi-Scale Transformer which uses multi-scale multi-head self-attention to capture features from different scales. Based on the linguistic perspective and the analysis of pre-trained Transformer (BERT) on a huge corpus, we further design a strategy to control the scale distribution for each layer. Results of three different kinds of tasks (21 datasets) show our Multi-Scale Transformer outperforms the standard Transformer consistently and significantly on small and moderate size datasets.
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