Generalizable Natural Language Processing Framework for Migraine Reporting from Social Media

Migraine is a high-prevalence and disabling neurological disorder. However, information migraine management in real-world settings could be limited to traditional health information sources. In this paper, we (i) verify that there is substantial migraine-related chatter available on social media (Twitter and Reddit), self-reported by migraine sufferers; (ii) develop a platform-independent text classification system for automatically detecting self-reported migraine-related posts, and (iii) conduct analyses of the self-reported posts to assess the utility of social media for studying this problem. We manually annotated 5750 Twitter posts and 302 Reddit posts. Our system achieved an F1 score of 0.90 on Twitter and 0.93 on Reddit. Analysis of information posted by our 'migraine cohort' revealed the presence of a plethora of relevant information about migraine therapies and patient sentiments associated with them. Our study forms the foundation for conducting an in-depth analysis of migraine-related information using social media data.

Social media mining for toxicovigilance of prescription medications: End-to-end pipeline, challenges and future work

Substance use, substance use disorder, and overdoses related to substance use are major public health problems globally and in the United States. A key aspect of addressing these problems from a public health standpoint is improved surveillance. Traditional surveillance systems are laggy, and social media are potentially useful sources of timely data. However, mining knowledge from social media is challenging, and requires the development of advanced artificial intelligence, specifically natural language processing (NLP) and machine learning methods. We developed a sophisticated end-to-end pipeline for mining information about nonmedical prescription medication use from social media, namely Twitter and Reddit. Our pipeline employs supervised machine learning and NLP for filtering out noise and characterizing the chatter. In this paper, we describe our end-to-end pipeline developed over four years. In addition to describing our data mining infrastructure, we discuss existing challenges in social media mining for toxicovigilance, and possible future research directions.

Few-shot learning for medical text: A systematic review

Objective: Few-shot learning (FSL) methods require small numbers of labeled instances for training. As many medical topics have limited annotated textual data in practical settings, FSL-based natural language processing (NLP) methods hold substantial promise. We aimed to conduct a systematic review to explore the state of FSL methods for medical NLP. Materials and Methods: We searched for articles published between January 2016 and August 2021 using PubMed/Medline, Embase, ACL Anthology, and IEEE Xplore Digital Library. To identify the latest relevant methods, we also searched other sources such as preprint servers (eg., medRxiv) via Google Scholar. We included all articles that involved FSL and any type of medical text. We abstracted articles based on data source(s), aim(s), training set size(s), primary method(s)/approach(es), and evaluation method(s). Results: 31 studies met our inclusion criteria-all published after 2018; 22 (71%) since 2020. Concept extraction/named entity recognition was the most frequently addressed task (13/31; 42%), followed by text classification (10/31; 32%). Twenty-one (68%) studies reconstructed existing datasets to create few-shot scenarios synthetically, and MIMIC-III was the most frequently used dataset (7/31; 23%). Common methods included FSL with attention mechanisms (12/31; 39%), prototypical networks (8/31; 26%), and meta-learning (6/31; 19%). Discussion: Despite the potential for FSL in biomedical NLP, progress has been limited compared to domain-independent FSL. This may be due to the paucity of standardized, public datasets, and the relative underperformance of FSL methods on biomedical topics. Creation and release of specialized datasets for biomedical FSL may aid method development by enabling comparative analyses.

Towards Automatic Bot Detection in Twitter for Health-related Tasks

With the increasing use of social media data for health-related research, the credibility of the information from this source has been questioned as the posts may originate from automated accounts or "bots". While automatic bot detection approaches have been proposed, there are none that have been evaluated on users posting health-related information. In this paper, we extend an existing bot detection system and customize it for health-related research. Using a dataset of Twitter users, we first show that the system, which was designed for political bot detection, underperforms when applied to health-related Twitter users. We then incorporate additional features and a statistical machine learning classifier to significantly improve bot detection performance. Our approach obtains F_1 scores of 0.7 for the "bot" class, representing improvements of 0.339. Our approach is customizable and generalizable for bot detection in other health-related social media cohorts.

Deep Neural Networks Ensemble for Detecting Medication Mentions in Tweets

Objective: After years of research, Twitter posts are now recognized as an important source of patient-generated data, providing unique insights into population health. A fundamental step to incorporating Twitter data in pharmacoepidemiological research is to automatically recognize medication mentions in tweets. Given that lexical searches for medication names may fail due to misspellings or ambiguity with common words, we propose a more advanced method to recognize them. Methods: We present Kusuri, an Ensemble Learning classifier, able to identify tweets mentioning drug products and dietary supplements. Kusuri ("medication" in Japanese) is composed of two modules. First, four different classifiers (lexicon-based, spelling-variant-based, pattern-based and one based on a weakly-trained neural network) are applied in parallel to discover tweets potentially containing medication names. Second, an ensemble of deep neural networks encoding morphological, semantical and long-range dependencies of important words in the tweets discovered is used to make the final decision. Results: On a balanced (50-50) corpus of 15,005 tweets, Kusuri demonstrated performances close to human annotators with 93.7% F1-score, the best score achieved thus far on this corpus. On a corpus made of all tweets posted by 113 Twitter users (98,959 tweets, with only 0.26% mentioning medications), Kusuri obtained 76.3% F1-score. There is not a prior drug extraction system that compares running on such an extremely unbalanced dataset. Conclusion: The system identifies tweets mentioning drug names with performance high enough to ensure its usefulness and ready to be integrated in larger natural language processing systems.

Automatically Detecting Self-Reported Birth Defect Outcomes on Twitter for Large-scale Epidemiological Research

In recent work, we identified and studied a small cohort of Twitter users whose pregnancies with birth defect outcomes could be observed via their publicly available tweets. Exploiting social media's large-scale potential to complement the limited methods for studying birth defects, the leading cause of infant mortality, depends on the further development of automatic methods. The primary objective of this study was to take the first step towards scaling the use of social media for observing pregnancies with birth defect outcomes, namely, developing methods for automatically detecting tweets by users reporting their birth defect outcomes. We annotated and pre-processed approximately 23,000 tweets that mention birth defects in order to train and evaluate supervised machine learning algorithms, including feature-engineered and deep learning-based classifiers. We also experimented with various under-sampling and over-sampling approaches to address the class imbalance. A Support Vector Machine (SVM) classifier trained on the original, imbalanced data set, with n-grams, word clusters, and structural features, achieved the best baseline performance for the positive classes: an F1-score of 0.65 for the "defect" class and 0.51 for the "possible defect" class. Our contributions include (i) natural language processing (NLP) and supervised machine learning methods for automatically detecting tweets by users reporting their birth defect outcomes, (ii) a comparison of feature-engineered and deep learning-based classifiers trained on imbalanced, under-sampled, and over-sampled data, and (iii) an error analysis that could inform classification improvements using our publicly available corpus. Future work will focus on automating user-level analyses for cohort inclusion.

An unsupervised and customizable misspelling generator for mining noisy health-related text sources

In this paper, we present a customizable datacentric system that automatically generates common misspellings for complex health-related terms. The spelling variant generator relies on a dense vector model learned from large unlabeled text, which is used to find semantically close terms to the original/seed keyword, followed by the filtering of terms that are lexically dissimilar beyond a given threshold. The process is executed recursively, converging when no new terms similar (lexically and semantically) to the seed keyword are found. Weighting of intra-word character sequence similarities allows further problem-specific customization of the system. On a dataset prepared for this study, our system outperforms the current state-of-the-art for medication name variant generation with best F1-score of 0.69 and F1/4-score of 0.78. Extrinsic evaluation of the system on a set of cancer-related terms showed an increase of over 67% in retrieval rate from Twitter posts when the generated variants are included. Our proposed spelling variant generator has several advantages over the current state-of-the-art and other types of variant generators-(i) it is capable of filtering out lexically similar but semantically dissimilar terms, (ii) the number of variants generated is low as many low-frequency and ambiguous misspellings are filtered out, and (iii) the system is fully automatic, customizable and easily executable. While the base system is fully unsupervised, we show how supervision maybe employed to adjust weights for task-specific customization. The performance and significant relative simplicity of our proposed approach makes it a much needed misspelling generation resource for health-related text mining from noisy sources. The source code for the system has been made publicly available for research purposes.

Automated text summarisation and evidence-based medicine: A survey of two domains

The practice of evidence-based medicine (EBM) urges medical practitioners to utilise the latest research evidence when making clinical decisions. Because of the massive and growing volume of published research on various medical topics, practitioners often find themselves overloaded with information. As such, natural language processing research has recently commenced exploring techniques for performing medical domain-specific automated text summarisation (ATS) techniques-- targeted towards the task of condensing large medical texts. However, the development of effective summarisation techniques for this task requires cross-domain knowledge. We present a survey of EBM, the domain-specific needs for EBM, automated summarisation techniques, and how they have been applied hitherto. We envision that this survey will serve as a first resource for the development of future operational text summarisation techniques for EBM.

Social media mining for identification and exploration of health-related information from pregnant women

Widespread use of social media has led to the generation of substantial amounts of information about individuals, including health-related information. Social media provides the opportunity to study health-related information about selected population groups who may be of interest for a particular study. In this paper, we explore the possibility of utilizing social media to perform targeted data collection and analysis from a particular population group -- pregnant women. We hypothesize that we can use social media to identify cohorts of pregnant women and follow them over time to analyze crucial health-related information. To identify potentially pregnant women, we employ simple rule-based searches that attempt to detect pregnancy announcements with moderate precision. To further filter out false positives and noise, we employ a supervised classifier using a small number of hand-annotated data. We then collect their posts over time to create longitudinal health timelines and attempt to divide the timelines into different pregnancy trimesters. Finally, we assess the usefulness of the timelines by performing a preliminary analysis to estimate drug intake patterns of our cohort at different trimesters. Our rule-based cohort identification technique collected 53,820 users over thirty months from Twitter. Our pregnancy announcement classification technique achieved an F-measure of 0.81 for the pregnancy class, resulting in 34,895 user timelines. Analysis of the timelines revealed that pertinent health-related information, such as drug-intake and adverse reactions can be mined from the data. Our approach to using user timelines in this fashion has produced very encouraging results and can be employed for other important tasks where cohorts, for which health-related information may not be available from other sources, are required to be followed over time to derive population-based estimates.

Mining the Web for Pharmacovigilance: the Case Study of Duloxetine and Venlafaxine

Adverse reactions caused by drugs following their release into the market are among the leading causes of death in many countries. The rapid growth of electronically available health related information, and the ability to process large volumes of them automatically, using natural language processing (NLP) and machine learning algorithms, have opened new opportunities for pharmacovigilance. Survey found that more than 70% of US Internet users consult the Internet when they require medical information. In recent years, research in this area has addressed for Adverse Drug Reaction (ADR) pharmacovigilance using social media, mainly Twitter and medical forums and websites. This paper will show the information which can be collected from a variety of Internet data sources and search engines, mainly Google Trends and Google Correlate. While considering the case study of two popular Major depressive Disorder (MDD) drugs, Duloxetine and Venlafaxine, we will provide a comparative analysis for their reactions using publicly-available alternative data sources.