Identifying the Presence, Activity, and Status of Extraintestinal Manifestations of Inflammatory Bowel Disease Using Natural Language Processing of Clinical Notes.

BACKGROUND: Extraintestinal manifestations (EIMs) occur commonly in inflammatory bowel disease (IBD), but population-level understanding of EIM behavior is difficult. We present a natural language processing (NLP) system designed to identify both the presence and status of EIMs using clinical notes from patients with IBD. METHODS: In a single-center retrospective study, clinical outpatient electronic documents were collected in patients with IBD. An NLP EIM detection pipeline was designed to determine general and specific symptomatic EIM activity status descriptions using Python 3.6. Accuracy, sensitivity, and specificity, and agreement using Cohen's kappa coefficient were used to compare NLP-inferred EIM status to human documentation labels. RESULTS: The 1240 individuals identified as having at least 1 EIM consisted of 54.4% arthritis, 17.2% ocular, and 17.0% psoriasiform EIMs. Agreement between reviewers on EIM status was very good across all EIMs (κ = 0.74; 95% confidence interval [CI], 0.70-0.78). The automated NLP pipeline determining general EIM activity status had an accuracy, sensitivity, specificity, and agreement of 94.1%, 0.92, 0.95, and κ = 0.76 (95% CI, 0.74-0.79), respectively. Comparatively, prediction of EIM status using administrative codes had a poor sensitivity, specificity, and agreement with human reviewers of 0.32, 0.83, and κ = 0.26 (95% CI, 0.20-0.32), respectively. CONCLUSIONS: NLP methods can both detect and infer the activity status of EIMs using the medical document an information source. Though source document variation and ambiguity present challenges, NLP offers exciting possibilities for population-based research and decision support in IBD.

Extraintestinal manifestations of inflammatory bowel disease impact on patient experience, but are poorly captured by electronic health records. Natural language processing systems are capable of not only detecting extraintestinal manifestations, but also inferring activity information by automated analysis of clinical notes.

A Systematic Temporal Extraction Pipeline for Medical Concepts in Clinical Notes.

With increased application of natural language processing (NLP) in medicine, many NLP models are being developed for uncovering relevant clinical features from electronic health records. Temporal information plays a key role in understanding the context, significance, and interpretation of medical concepts extracted from clinical notes. This is particularly true in situations where the behavior, value, or status of a medical concept changes over time. In this paper, we introduce a systematic framework, NLP annotation-Relaxation-Generation (NRG). NRG compiles incidents of medical concept changes from status annotations and timestamps of multiple clinical notes. We demonstrate the effectiveness of the NRG pipeline by applying it to two medical concepts related to patients with inflammatory bowel disease: extra-intestinal manifestations and medications. We show that the NRG pipeline offers not only insights into medical concept changes over time, but can help convey longitudinal changes in clinical features at both individual and population level.

An Assessment of Mentions of Adverse Drug Events on Social Media With Natural Language Processing: Model Development and Analysis.

BACKGROUND: Adverse reactions to drugs attract significant concern in both clinical practice and public health monitoring. Multiple measures have been put into place to increase postmarketing surveillance of the adverse effects of drugs and to improve drug safety. These measures include implementing spontaneous reporting systems and developing automated natural language processing systems based on data from electronic health records and social media to collect evidence of adverse drug events that can be further investigated as possible adverse reactions. OBJECTIVE: While using social media for collecting evidence of adverse drug events has potential, it is not clear whether social media are a reliable source for this information. Our work aims to (1) develop natural language processing approaches to identify adverse drug events on social media and (2) assess the reliability of social media data to identify adverse drug events. METHODS: We propose a collocated long short-term memory network model with attentive pooling and aggregated, contextual representation generated by a pretrained model. We applied this model on large-scale Twitter data to identify adverse drug event-related tweets. We conducted a qualitative content analysis of these tweets to validate the reliability of social media data as a means to collect such information. RESULTS: The model outperformed a variant without contextual representation during both the validation and evaluation phases. Through the content analysis of adverse drug event tweets, we observed that adverse drug event-related discussions had 7 themes. Mental health-related, sleep-related, and pain-related adverse drug event discussions were most frequent. We also contrast known adverse drug reactions to those mentioned in tweets. CONCLUSIONS: We observed a distinct improvement in the model when it used contextual information. However, our results reveal weak generalizability of the current systems to unseen data. Additional research is needed to fully utilize social media data and improve the robustness and reliability of natural language processing systems. The content analysis, on the other hand, showed that Twitter covered a sufficiently wide range of adverse drug events, as well as known adverse reactions, for the drugs mentioned in tweets. Our work demonstrates that social media can be a reliable data source for collecting adverse drug event mentions.

Uncovering the relationship between food-related discussion on Twitter and neighborhood characteristics.

OBJECTIVE: Initiatives to reduce neighborhood-based health disparities require access to meaningful, timely, and local information regarding health behavior and its determinants. We examined the validity of Twitter as a source of information for neighborhood-level analysis of dietary choices and attitudes. MATERIALS AND METHODS: We analyzed the "healthiness" quotient and sentiment in food-related tweets at the census tract level, and associated them with neighborhood characteristics and health outcomes. We analyzed keywords driving the differences in food healthiness between the most and least-affluent tracts, and qualitatively analyzed contents of a random sample of tweets. RESULTS: Significant, albeit weak, correlations existed between healthiness and sentiment in food-related tweets and tract-level measures of affluence, disadvantage, race, age, U.S. density, and mortality from conditions associated with obesity. Analyses of keywords driving the differences in food healthiness revealed foods high in saturated fat (eg, pizza, bacon, fries) were mentioned more frequently in less-affluent tracts. Food-related discussion referred to activities (eating, drinking, cooking), locations where food was consumed, and positive (affection, cravings, enjoyment) and negative attitudes (dislike, personal struggles, complaints). DISCUSSION: Tweet-based healthiness scores largely correlated with offline phenomena in the expected directions. Social media offer less resource-intensive data collection methods than traditional surveys do. Twitter may assist in informing local health programs that focus on drivers of food consumption and could inform interventions focused on attitudes and the food environment. CONCLUSIONS: Twitter provided weak but significant signals concerning food-related behavior and attitudes at the neighborhood level, suggesting its potential usefulness for informing local health disparity reduction efforts.