Objective This article methodically reviews the literature on deep learning (DL) for natural language processing (NLP) in the clinical domain, providing quantitative analysis to answer 3 research questions concerning methods, scope, and context of current research. Materials and Methods We searched MEDLINE, EMBASE, Scopus, the Association for Computing Machinery Digital Library, and the Association for Computational Linguistics Anthology for articles using DL-based approaches to NLP problems in electronic health records. After screening 1,737 articles, we collected data on 25 variables across 212 papers. Results DL in clinical NLP publications more than doubled each year, through 2018. Recurrent neural networks (60.8%) and word2vec embeddings (74.1%) were the most popular methods; the information extraction tasks of text classification, named entity recognition, and relation extraction were dominant (89.2%). However, there was a “long tail” of other methods and specific tasks. Most contributions were methodological variants or applications, but 20.8% were new methods of some kind. The earliest adopters were in the NLP community, but the medical informatics community was the most prolific. Discussion Our analysis shows growing acceptance of deep learning as a baseline for NLP research, and of DL-based NLP in the medical community. A number of common associations were substantiated (eg, the preference of recurrent neural networks for sequence-labeling named entity recognition), while others were surprisingly nuanced (eg, the scarcity of French language clinical NLP with deep learning). Conclusion Deep learning has not yet fully penetrated clinical NLP and is growing rapidly. This review highlighted both the popular and unique trends in this active field.

The major challenge for Question Retrieval (QR) in Community Question Answering (CQA) is the lexical gap between the queried question and the historical questions. This paper proposes a novel Question-Answer Topic Model (QATM) to learn the latent topics aligned across the question-answer pairs to alleviate the lexical gap problem, with the assumption that a question and its paired answer share the same topic distribution. Experiments conducted on a real world CQA dataset from Yahoo! Answers show that combining both parts properly can get more knowledge than each part or both parts in a simple mixing way and combining our QATM with the state-of-the-art translation-based language model, where the topic and translation information is learned from the question-answer pairs at two different grained semantic levels respectively, can significantly improve the QR performance.

Objective This article presents our approaches to extraction of medications and associated adverse drug events (ADEs) from clinical documents, which is the second track of the 2018 National NLP Clinical Challenges (n2c2) shared task. Materials and Methods The clinical corpus used in this study was from the MIMIC-III database and the organizers annotated 303 documents for training and 202 for testing. Our system consists of 2 components: a named entity recognition (NER) and a relation classification (RC) component. For each component, we implemented deep learning-based approaches (eg, BI-LSTM-CRF) and compared them with traditional machine learning approaches, namely, conditional random fields for NER and support vector machines for RC, respectively. In addition, we developed a deep learning-based joint model that recognizes ADEs and their relations to medications in 1 step using a sequence labeling approach. To further improve the performance, we also investigated different ensemble approaches to generating optimal performance by combining outputs from multiple approaches. Results Our best-performing systems achieved F1 scores of 93.45% for NER, 96.30% for RC, and 89.05% for end-to-end evaluation, which ranked #2, #1, and #1 among all participants, respectively. Additional evaluations show that the deep learning-based approaches did outperform traditional machine learning algorithms in both NER and RC. The joint model that simultaneously recognizes ADEs and their relations to medications also achieved the best performance on RC, indicating its promise for relation extraction. Conclusion In this study, we developed deep learning approaches for extracting medications and their attributes such as ADEs, and demonstrated its superior performance compared with traditional machine learning algorithms, indicating its uses in broader NER and RC tasks in the medical domain.

Human computer conversation is regarded as one of the most difficult problems in artificial intelligence. In this paper, we address one of its key sub-problems, referred to as short text conversation, in which given a message from human, the computer returns a reasonable response to the message. We leverage the vast amount of short conversation data available on social media to study the issue. We propose formalizing short text conversation as a search problem at the first step, and employing state-of-the-art information retrieval (IR) techniques to carry out the task. We investigate the significance as well as the limitation of the IR approach. Our experiments demonstrate that the retrieval-based model can make the system behave rather "intelligently", when combined with a huge repository of conversation data from social media.

Many users casually reveal their locations such as restaurants, landmarks, and shops in their tweets. Recognizing such fine-grained locations from tweets and then linking the location mentions to well-defined location profiles (e.g., with formal name, detailed address, and geo-coordinates etc.) offer a tremendous opportunity for many applications. Different from existing solutions which perform location recognition and linking as two sub-tasks sequentially in a pipeline setting, in this paper, we propose a novel joint framework to perform location recognition and location linking simultaneously in a joint search space. We formulate this end-to-end location linking problem as a structured prediction problem and propose a beamsearch based algorithm. Based on the concept of multi-view learning, we further enable the algorithm to learn from unlabeled data to alleviate the dearth of labeled data. Extensive experiments are conducted to recognize locations mentioned in tweets and link them to location profiles in Foursquare. Experimental results show that the proposed joint learning algorithm outperforms the state-of-theart solutions, and learning from unlabeled data improves both the recognition and linking accuracy.

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This paper focuses on the problem of Question Routing (QR) in Community Question Answering (CQA), which aims to route newly posted questions to the potential answerers who are most likely to answer them. Traditional methods to solve this problem only consider the text similarity features between the newly posted question and the user profile, while ignoring the important statistical features, including the question-specific statistical feature and the user-specific statistical features. Moreover, traditional methods are based on unsupervised learning, which is not easy to introduce the rich features into them. This paper proposes a general framework based on the learning to rank concepts for QR. Training sets consist of triples (q, asker, answerers) are first collected. Then, by introducing the intrinsic relationships between the asker and the answerers in each CQA session to capture the intrinsic labels/orders of the users about their expertise degree of the question q, two different methods, including the SVM-based and RankingSVM-based methods, are presented to learn the models with different example creation processes from the training set. Finally, the potential answerers are ranked using the trained models. Extensive experiments conducted on a real world CQA dataset from Stack Overflow show that our proposed two methods can both outperform the traditional query likelihood language model (QLLM) as well as the state-of-the-art Latent Dirichlet Allocation based model (LDA). Specifically, the RankingSVMbased method achieves statistical significant improvements over the SVM-based method and has gained the best performance.