In recent years, machine learning methods have been widely used in modern electronic health record (EHR) systems, and have shown more accurate prediction performance on disease risk assessment tasks than traditional methods. However, most of the existing machine learning methods make the assessment solely based on features of the target case but ignore the cross-sample feature interactions between the target case and other similar cases, which is inconsistent with the general practice of evidence-based medicine of making diagnoses based on existing clinical experience. Moreover, current methods that focus on mining cross-sample information rely on deep neural networks to extract cross-sample feature interactions, which would suffer from the problems of data insufficiency, data heterogeneity and lack of interpretability in disease risk assessment tasks. In this work, we propose a novel retrieval-based gradient boosting decision trees (RB-GBDT) model with a cross-sample extractor to mine cross-sample information while exploiting the superiority of GBDT of robustness, generalization and interpretability. Experiments on real-world clinical datasets show the superiority and efficacy of RB-GBDT on disease risk assessment tasks. The developed software has been deployed in hospital as an auxiliary diagnosis tool for risk assessment of venous thromboembolism.

Venous thromboembolism (VTE) is the world's third most common cause of vascular mortality and a serious complication from multiple departments. Risk assessment of VTE guides clinical intervention in time and is of great importance to in-hospital patients. Traditional VTE risk assessment methods based on scaling tools, which always require rules carefully designed by human experts, are difficult to apply to large-population scenarios since the manually designed rules are not guaranteed to be accurate to all populations. In contrast, with the development of the electronic health record (EHR) datasets, data-driven machine-learning-based risk assessment methods have proven superior predictability in many studies in recent years. This paper uses the gradient boosting tree model to study the VTE risk assessment problem with multi-department data. There exist two distinct characteristics of VTE data collected at the level of the entire hospital: its wide distribution and heterogeneity across multiple departments. To this end, we consider the prediction task over multiple departments as a multi-task learning process, and introduce the algorithm of a task-aware tree-based method TSGB to tackle the multi-task prediction problem. Although the introduction of multi-task learning improves overall across-department performance, we reveal the problem of task-wise performance decline while dealing with imbalanced VTE data volume. According to the analysis, we finally propose two variants of TSGB to alleviate the problems and further boost the prediction performance. Compared with state-of-the-art rule-based and multi-task tree-based methods, the experimental results show the proposed methods not only improve the overall across-department AUC performance effectively, but also ensure the improvement of performance over every single department prediction.

Venous thromboembolism (VTE) is a common vascular disease and potentially fatal complication during hospitalization, and so the early identification of VTE risk is of significant importance. Compared with traditional scale assessments, machine learning methods provide new opportunities for precise early warning of VTE from clinical medical records. This research aimed to propose a two-stage hierarchical machine learning model for VTE risk prediction in patients from multiple departments. First, we built a machine learning prediction model that covered the entire hospital, based on all cohorts and common risk factors. Then, we took the prediction output of the first stage as an initial assessment score and then built specific models for each department. Over the duration of the study, a total of 9213 inpatients, including 1165 VTE-positive samples, were collected from four departments, which were split into developing and test datasets. The proposed model achieved an AUC of 0.879 in the department of oncology, which outperformed the first-stage model (0.730) and the department model (0.787). This was attributed to the fully usage of both the large sample size at the hospital level and variable abundance at the department level. Experimental results show that our model could effectively improve the prediction of hospital-acquired VTE risk before image diagnosis and provide decision support for further nursing and medical intervention.

In graphs with rich texts, incorporating textual information with structural information would benefit constructing expressive graph embeddings. Among various graph embedding models, random walk (RW)-based is one of the most popular and successful groups. However, it is challenged by two issues when applied on graphs with rich texts: (i) sampling efficiency: deriving from the training objective of RW-based models (e.g., DeepWalk and node2vec), we show that RW-based models are likely to generate large amounts of redundant training samples due to three main drawbacks. (ii) text utilization: these models have difficulty in dealing with zero-shot scenarios where graph embedding models have to infer graph structures directly from texts. To solve these problems, we propose a novel framework, namely Text-driven Graph Embedding with Pairs Sampling (TGE-PS). TGE-PS uses Pairs Sampling (PS) to improve the sampling strategy of RW, being able to reduce ~ 99% training samples while preserving competitive performance. TGE-PS uses Text-driven Graph Embedding (TGE), an inductive graph embedding approach, to generate node embeddings from texts. Since each node contains rich texts, TGE is able to generate high-quality embeddings and provide reasonable predictions on existence of links to unseen nodes. We evaluate TGE-PS on several real-world datasets, and experiment results demonstrate that TGE-PS produces state-of-the-art results on both traditional and zero-shot link prediction tasks.

Chinese word segmentation (CWS) trained from open source corpus faces dramatic performance drop when dealing with domain text, especially for a domain with lots of special terms and diverse writing styles, such as the biomedical domain. However, building domain-specific CWS requires extremely high annotation cost. In this paper, we propose an approach by exploiting domain-invariant knowledge from high resource to low resource domains. Extensive experiments show that our model achieves consistently higher accuracy than the single-task CWS and other transfer learning baselines, especially when there is a large disparity between source and target domains.

Zhenghui Wang, Yanru Qu, Liheng Chen, Jian Shen, Weinan Zhang, Shaodian Zhang, Yimei Gao, Gen Gu, Ken Chen, Yong Yu. Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers). 2018.

A large number of patients discuss treatments in online health communities (OHCs). One research question of interest to health researchers is whether treatments being discussed in OHCs are eventually used by community members in their real lives. In this paper, we rely on machine learning methods to automatically identify attributions of mentions of treatments from an online autism community. The context of our work is online autism communities, where parents exchange support for the care of their children with autism spectrum disorder. Our methods are able to distinguish discussions of treatments that are associated with patients, caregivers, and others, as well as identify whether a treatment is actually taken. We investigate treatments that are not just discussed but also used by patients according to two types of content analysis, cross-sectional and longitudinal. The treatments identified through our content analysis help create a catalogue of real-world treatments. This study results lay the foundation for future research to compare real-world drug usage with established clinical guidelines.

OBJECTIVE: To develop an open-source information extraction system called Eligibility Criteria Information Extraction (EliIE) for parsing and formalizing free-text clinical research eligibility criteria (EC) following Observational Medical Outcomes Partnership Common Data Model (OMOP CDM) version 5.0. MATERIALS AND METHODS: EliIE parses EC in 4 steps: (1) clinical entity and attribute recognition, (2) negation detection, (3) relation extraction, and (4) concept normalization and output structuring. Informaticians and domain experts were recruited to design an annotation guideline and generate a training corpus of annotated EC for 230 Alzheimer's clinical trials, which were represented as queries against the OMOP CDM and included 8008 entities, 3550 attributes, and 3529 relations. A sequence labeling-based method was developed for automatic entity and attribute recognition. Negation detection was supported by NegEx and a set of predefined rules. Relation extraction was achieved by a support vector machine classifier. We further performed terminology-based concept normalization and output structuring. RESULTS: In task-specific evaluations, the best F1 score for entity recognition was 0.79, and for relation extraction was 0.89. The accuracy of negation detection was 0.94. The overall accuracy for query formalization was 0.71 in an end-to-end evaluation. CONCLUSIONS: This study presents EliIE, an OMOP CDM-based information extraction system for automatic structuring and formalization of free-text EC. According to our evaluation, machine learning-based EliIE outperforms existing systems and shows promise to improve.

Objectives: The Internet and social media are revolutionizing how social support is exchanged and perceived, making online health communities (OHCs) one of the most exciting research areas in health informatics. This paper aims to provide a framework for organizing research of OHCs and help identify questions to explore for future informatics research. Based on the framework, we conceptualize OHCs from a social support standpoint and identify variables of interest in characterizing community members. For the sake of this tutorial, we focus our review on online cancer communities. Target audience: The primary target audience is informaticists interested in understanding ways to characterize OHCs, their members, and the impact of participation, and in creating tools to facilitate outcome research of OHCs. OHC designers and moderators are also among the target audience for this tutorial. Scope: The tutorial provides an informatics point of view of online cancer communities, with social support as their leading element. We conceptualize OHCs according to 3 major variables: type of support, source of support, and setting in which the support is exchanged. We summarize current research and synthesize the findings for 2 primary research questions on online cancer communities: (1) the impact of using online social support on an individual's health, and (2) the characteristics of the community, its members, and their interactions. We discuss ways in which future research in informatics in social support and OHCs can ultimately benefit patients.

Identifying topics of discussions in online health communities (OHC) is critical to various information extraction applications, but can be difficult because topics of OHC content are usually heterogeneous and domain-dependent. In this paper, we provide a multi-class schema, an annotated dataset, and supervised classifiers based on convolutional neural network (CNN) and other models for the task of classifying discussion topics. We apply the CNN classifier to the most popular breast cancer online community, and carry out cross-sectional and longitudinal analyses to show topic distributions and topic dynamics throughout members' participation. Our experimental results suggest that CNN outperforms other classifiers in the task of topic classification and identify several patterns and trajectories. For example, although members discuss mainly disease-related topics, their interest may change through time and vary with their disease severities.

Speculations represent uncertainty toward certain facts. In clinical texts, identifying speculations is a critical step of natural language processing (NLP). While it is a nontrivial task in many languages, detecting speculations in Chinese clinical notes can be particularly challenging because word segmentation may be necessary as an upstream operation. The objective of this paper is to construct a state-of-the-art speculation detection system for Chinese clinical notes and to investigate whether embedding features and word segmentations are worth exploiting toward this overall task. We propose a sequence labeling based system for speculation detection, which relies on features from bag of characters, bag of words, character embedding, and word embedding. We experiment on a novel dataset of 36,828 clinical notes with 5103 gold-standard speculation annotations on 2000 notes, and compare the systems in which word embeddings are calculated based on word segmentations given by general and by domain specific segmenters respectively. Our systems are able to reach performance as high as 92.2% measured by F score. We demonstrate that word segmentation is critical to produce high quality word embedding to facilitate downstream information extraction applications, and suggest that a domain dependent word segmenter can be vital to such a clinical NLP task in Chinese language.

Named entity recognition is a crucial component of biomedical natural language processing, enabling information extraction and ultimately reasoning over and knowledge discovery from text. Much progress has been made in the design of rule-based and supervised tools, but they are often genre and task dependent. As such, adapting them to different genres of text or identifying new types of entities requires major effort in re-annotation or rule development. In this paper, we propose an unsupervised approach to extracting named entities from biomedical text. We describe a stepwise solution to tackle the challenges of entity boundary detection and entity type classification without relying on any handcrafted rules, heuristics, or annotated data. A noun phrase chunker followed by a filter based on inverse document frequency extracts candidate entities from free text. Classification of candidate entities into categories of interest is carried out by leveraging principles from distributional semantics. Experiments show that our system, especially the entity classification step, yields competitive results on two popular biomedical datasets of clinical notes and biological literature, and outperforms a baseline dictionary match approach. Detailed error analysis provides a road map for future work.

Two main challenges of Named Entity Recognition (NER) for tweets are the insufficient information in a tweet and the lack of training data. We propose a novel method consisting of three core elements: (1) normalization of tweets; (2) combination of a K-Nearest Neighbors (KNN) classifier with a linear Conditional Random Fields (CRF) model; and (3) semisupervised learning framework. The tweet normalization preprocessing corrects common ill-formed words using a global linear model. The KNN-based classifier conducts prelabeling to collect global coarse evidence across tweets while the CRF model conducts sequential labeling to capture fine-grained information encoded in a tweet. The semisupervised learning plus the gazetteers alleviate the lack of training data. Extensive experiments show the advantages of our method over the baselines as well as the effectiveness of normalization, KNN, and semisupervised learning.