Simon Lin

Xianlong Zeng, Simon Lin, Chang Liu

The adoption of electronic health records (EHR) has become universal during the past decade, which has afforded in-depth data-based research. By learning from the large amount of healthcare data, various data-driven models have been built to predict future events for different medical tasks, such as auto diagnosis and heart-attack prediction. Although EHR is abundant, the population that satisfies specific criteria for learning population-specific tasks is scarce, making it challenging to train data-hungry deep learning models. This study presents the Claim Pre-Training (Claim-PT) framework, a generic pre-training model that first trains on the entire pediatric claims dataset, followed by a discriminative fine-tuning on each population-specific task. The semantic meaning of medical events can be captured in the pre-training stage, and the effective knowledge transfer is completed through the task-aware fine-tuning stage. The fine-tuning process requires minimal parameter modification without changing the model architecture, which mitigates the data scarcity issue and helps train the deep learning model adequately on small patient cohorts. We conducted experiments on a real-world claims dataset with more than one million patient records. Experimental results on two downstream tasks demonstrated the effectiveness of our method: our general task-agnostic pre-training framework outperformed tailored task-specific models, achieving more than 10\% higher in model performance as compared to baselines. In addition, our framework showed a great generalizability potential to transfer learned knowledge from one institution to another, paving the way for future healthcare model pre-training across institutions.

Xiang Yue, Xinliang Frederick Zhang, Ziyu Yao et al.

Clinical question answering (QA) aims to automatically answer questions from medical professionals based on clinical texts. Studies show that neural QA models trained on one corpus may not generalize well to new clinical texts from a different institute or a different patient group, where large-scale QA pairs are not readily available for model retraining. To address this challenge, we propose a simple yet effective framework, CliniQG4QA, which leverages question generation (QG) to synthesize QA pairs on new clinical contexts and boosts QA models without requiring manual annotations. In order to generate diverse types of questions that are essential for training QA models, we further introduce a seq2seq-based question phrase prediction (QPP) module that can be used together with most existing QG models to diversify the generation. Our comprehensive experiment results show that the QA corpus generated by our framework can improve QA models on the new contexts (up to 8% absolute gain in terms of Exact Match), and that the QPP module plays a crucial role in achieving the gain.

Zhen Wang, Jennifer Lee, Simon Lin et al.

Nowadays, the interpretability of machine learning models is becoming increasingly important, especially in the medical domain. Aiming to shed some light on how to rationalize medical relation prediction, we present a new interpretable framework inspired by existing theories on how human memory works, e.g., theories of recall and recognition. Given the corpus-level statistics, i.e., a global co-occurrence graph of a clinical text corpus, to predict the relations between two entities, we first recall rich contexts associated with the target entities, and then recognize relational interactions between these contexts to form model rationales, which will contribute to the final prediction. We conduct experiments on a real-world public clinical dataset and show that our framework can not only achieve competitive predictive performance against a comprehensive list of neural baseline models, but also present rationales to justify its prediction. We further collaborate with medical experts deeply to verify the usefulness of our model rationales for clinical decision making.

Manirupa Das, Juanxi Li, Eric Fosler-Lussier et al.

Novel contexts may often arise in complex querying scenarios such as in evidence-based medicine (EBM) involving biomedical literature, that may not explicitly refer to entities or canonical concept forms occurring in any fact- or rule-based knowledge source such as an ontology like the UMLS. Moreover, hidden associations between candidate concepts meaningful in the current context, may not exist within a single document, but within the collection, via alternate lexical forms. Therefore, inspired by the recent success of sequence-to-sequence neural models in delivering the state-of-the-art in a wide range of NLP tasks, we develop a novel sequence-to-set framework with neural attention for learning document representations that can effect term transfer within the corpus, for semantically tagging a large collection of documents. We demonstrate that our proposed method can be effective in both a supervised multi-label classification setup for text categorization, as well as in a unique unsupervised setting with no human-annotated document labels that uses no external knowledge resources and only corpus-derived term statistics to drive the training. Further, we show that semi-supervised training using our architecture on large amounts of unlabeled data can augment performance on the text categorization task when limited labeled data is available. Our approach to generate document encodings employing our sequence-to-set models for inference of semantic tags, gives to the best of our knowledge, the state-of-the-art for both, the unsupervised query expansion task for the TREC CDS 2016 challenge dataset when evaluated on an Okapi BM25--based document retrieval system; and also over the MLTM baseline (Soleimani et al, 2016), for both supervised and semi-supervised multi-label prediction tasks on the del.icio.us and Ohsumed datasets. We will make our code and data publicly available.

Xianlong Zeng, Soheil Moosavinasab, En-Ju D Lin et al.

Efficient representation of patients is very important in the healthcare domain and can help with many tasks such as medical risk prediction. Many existing methods, such as diagnostic Cost Groups (DCG), rely on expert knowledge to build patient representation from medical data, which is resource consuming and non-scalable. Unsupervised machine learning algorithms are a good choice for automating the representation learning process. However, there is very little research focusing on onpatient-level representation learning directly from medical claims. In this paper, weproposed a novel patient vector learning architecture that learns high quality,fixed-length patient representation from claims data. We conducted several experiments to test the quality of our learned representation, and the empirical results show that our learned patient vectors are superior to vectors learned through other methods including a popular commercial model. Lastly, we provide potential clinical interpretation for using our representation on predictive tasks, as interpretability is vital in the healthcare domain