Adverse Drug Reaction Mentions Research Articles

A holistic AI-based approach for pharmacovigilance optimization from patients behavior on social media

In this paper, we propose a holistic AI-based pharmacovigilance optimization approach using patient’s social media data. Instead of focusing on the detection and identification of Adverse Drug Events (ADE) in social media posts in single time points, we propose a holistic approach that looks at the evolution of different user behavior indicators in time. We examine various NLP-based indicators such as word frequency, semantic similarity, Adverse Drug Reactions mentions, and sentiment analysis. We introduce a classification approach to identify normal vs. abnormal time periods based on patient comments. This approach, along with user behavior indicators, can optimize the pharmacovigilance process by flagging the need for immediate attention and further investigation. We specifically focus on the Levothyrox® case in France, which sparked media attention due to changes in the medication formula and affected patient behavior on medical forums. For classification, we propose a deep learning architecture called Word Cloud Convolutional Neural Network (WC-CNN), trained on word clouds from patient comments. We evaluate different temporal resolutions and NLP pre-processing techniques, finding that monthly resolution and the proposed indicators can effectively detect new safety signals, with an accuracy of 75%. We have made the code open source, available via github.

Artificial Neural Network and Latent Semantic Analysis for Adverse Drug Reaction Detection

Adverse drug reactions (ADR) are important information for verifying the view of the patient on a particular drug. Regular user comments and reviews have been considered during the data collection process to extract ADR mentions, when the user reported a side effect after taking a specific medication. In the literature, most researchers focused on machine learning techniques to detect ADR. These methods train the classification model using annotated medical review data. Yet, there are still many challenging issues that face ADR extraction, especially the accuracy of detection. The main aim of this study is to propose LSA with ANN classifiers for ADR detection. The findings show the effectiveness of utilizing LSA with ANN in extracting ADR.

Developing a deep learning natural language processing algorithm for automated reporting of adverse drug reactions

The detection of adverse drug reactions (ADRs) is critical to our understanding of the safety and risk-benefit profile of medications. With an incidence that has not changed over the last 30 years, ADRs are a significant source of patient morbidity, responsible for 5%–10% of acute care hospital admissions worldwide. Spontaneous reporting of ADRs has long been the standard method of reporting, however this approach is known to have high rates of under-reporting, a problem that limits pharmacovigilance efforts. Automated ADR reporting presents an alternative pathway to increase reporting rates, although this may be limited by over-reporting of other drug-related adverse events.We developed a deep learning natural language processing algorithm to identify ADRs in discharge summaries at a single academic hospital centre. Our model was developed in two stages: first, a pre-trained model (DeBERTa) was further pre-trained on 1.1 million unlabelled clinical documents; secondly, this model was fine-tuned to detect ADR mentions in a corpus of 861 annotated discharge summaries. This model was compared to a version without the pre-training step, and a previously published RoBERTa model pretrained on MIMIC III, which has demonstrated strong performance on other pharmacovigilance tasks. To ensure that our algorithm could differentiate ADRs from other drug-related adverse events, the annotated corpus was enriched for both validated ADR reports and confounding drug-related adverse events using. The final model demonstrated good performance with a ROC–AUC of 0.955 (95% CI 0.933 - 0.978) for the task of identifying discharge summaries containing ADR mentions, significantly outperforming the two comparator models.

Adverse Drug Reaction Concept Normalization in Russian-Language Reviews of Internet Users

Mapping the pharmaceutically significant entities on natural language to standardized terms/concepts is a key task in the development of the systems for pharmacovigilance, marketing, and using drugs out of the application scope. This work estimates the accuracy of mapping adverse reaction mentions to the concepts from the Medical Dictionary of Regulatory Activity (MedDRA) in the case of adverse reactions extracted from the reviews on the use of pharmaceutical products by Russian-speaking Internet users (normalization task). The solution we propose is based on a neural network approach using two neural network models: the first one for encoding concepts, and the second one for encoding mentions. Both models are pre-trained language models, but the second one is additionally tuned for the normalization task using both the Russian Drug Reviews (RDRS) corpus and a set of open English-language corpora automatically translated into Russian. Additional tuning of the model during the proposed procedure increases the accuracy of mentions of adverse drug reactions by 3% on the RDRS corpus. The resulting accuracy for the adverse reaction mentions mapping to the preferred terms of MedDRA in RDRS is 70.9% F1-micro. The paper analyzes the factors that affect the accuracy of solving the task based on a comparison of the RDRS and the CSIRO Adverse Drug Event Corpus (CADEC) corpora. It is shown that the composition of the concepts of the MedDRA and the number of examples for each concept play a key role in the task solution. The proposed model shows a comparable accuracy of 87.5% F1-micro on a subsample of RDRS and CADEC datasets with the same set of MedDRA preferred terms.

Pharmacovigilance with Transformers: A Framework to Detect Adverse Drug Reactions Using BERT Fine-Tuned with FARM.

Adverse drug reactions (ADRs) are the undesirable effects associated with the use of a drug due to some pharmacological action of the drug. During the last few years, social media has become a popular platform where people discuss their health problems and, therefore, has become a popular source to share information related to ADR in the natural language. This paper presents an end-to-end system for modelling ADR detection from the given text by fine-tuning BERT with a highly modular Framework for Adapting Representation Models (FARM). BERT overcame the predominant neural networks bringing remarkable performance gains. However, training BERT is a computationally expensive task which limits its usage for production environments and makes it difficult to determine the most important hyperparameters for the downstream task. Furthermore, developing an end-to-end ADR extraction system comprising two downstream tasks, i.e., text classification for filtering text containing ADRs and extracting ADR mentions from the classified text, is also challenging. The framework used in this work, FARM-BERT, provides support for multitask learning by combining multiple prediction heads which makes training of the end-to-end systems easier and computationally faster. In the proposed model, one prediction head is used for text classification and the other is used for ADR sequence labeling. Experiments are performed on Twitter, PubMed, TwiMed-Twitter, and TwiMed-PubMed datasets. The proposed model is compared with the baseline models and state-of-the-art techniques, and it is shown that it yields better results for the given task with the F-scores of 89.6%, 97.6%, 84.9%, and 95.9% on Twitter, PubMed, TwiMed-Twitter, and TwiMed-PubMed datasets, respectively. Moreover, training time and testing time of the proposed model are compared with BERT's, and it is shown that the proposed model is computationally faster than BERT.

Public Perspectives of Using Social Media Data to Improve Adverse Drug Reaction Reporting: A Mixed-Methods Study.

IntroductionInformation on suspected adverse drug reactions (ADRs) voluntarily submitted by patients can be a valuable source of information for improving drug safety; however, public awareness of reporting mechanisms remains low. Whilst methods to automatically detect ADR mentions from social media posts using text mining techniques have been proposed to improve reporting rates, it is unclear how acceptable these would be to social media users.ObjectiveThe objective of this study was to explore public opinion about using automated methods to detect and report mentions of ADRs on social media to enhance pharmacovigilance efforts.MethodsUsers of the online health discussion forum HealthUnlocked participated in an online survey (N = 1359) about experiences with ADRs, knowledge of pharmacovigilance methods, and opinions about using automated data mining methods to detect and report ADRs. To further explore responses, five qualitative focus groups were conducted with 20 social media users with long-term health conditions.ResultsParticipant responses indicated a low awareness of pharmacovigilance methods and ADR reporting. They showed a strong willingness to share health-related social media data about ADRs with researchers and regulators, but were cautious about automated text mining methods of detecting and reporting ADRs.ConclusionsSocial media users value public-facing pharmacovigilance schemes, even if they do not understand the current framework of pharmacovigilance within the UK. Ongoing engagement with users is essential to understand views, share knowledge and respect users’ privacy expectations to optimise future ADR reporting from online health communities.Supplementary InformationThe online version contains supplementary material available at 10.1007/s40264-021-01042-6.

DeepCADRME: A deep neural model for complex adverse drug reaction mentions extraction

Abstract Extracting mentions of Adverse Drug Reaction (ADR) from biomedical texts, aiming to support pharmacovigilance and drug safety surveillance, remains a challenging task as many ADR mentions are nested, discontinuous and overlapping. To solve these issues, in this paper, we propose a deep neural model for Complex Adverse Drug Reaction Mentions Extraction, called DeepCADRME. It first transforms the ADR mentions extraction problem as an N-level tagging sequence. Then, it feeds the sequences to an N-level model based on contextual embeddings where the output of the pre-trained model of the current level is used to build a new deep contextualized representation for the next level. This allows the DeepCADRME system to transfer knowledge between levels. Experimental results performed on the TAC 2017 ADR dataset, show the effectiveness of DeepCADRME which leads to a new state-of-the-art performance by reaching a F1 of 85.35% and 85.41% with and without mention types, respectively. The evaluation results also highlight the benefits of exploring language model to effectively extract different types of ADR mentions.

Automatic Classification of Discharge Letters to Detect Adverse Drug Reactions.

Adverse drug reactions (ADRs) are frequent and associated to significant morbidity, mortality and costs. Therefore, their early detection in the hospital context is vital. Automatic tools could be developed taking into account structured and textual data. In this paper, we present the methodology followed for the manual annotation and automatic classification of discharge letters from a tertiary hospital. The results show that ADRs and causal drugs are explicitly mentioned in the discharge letters and that machine learning algorithms are efficient for the automatic detection of documents containing mentions of ADRs.

Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels

BackgroundUse of medication can cause adverse drug reactions (ADRs), unwanted or unexpected events, which are a major safety concern. Drug labels, or prescribing information or package inserts, describe ADRs. Therefore, systematically identifying ADR information from drug labels is critical in multiple aspects; however, this task is challenging due to the nature of the natural language of drug labels.ResultsIn this paper, we present a machine learning- and rule-based system for the identification of ADR entity mentions in the text of drug labels and their normalization through the Medical Dictionary for Regulatory Activities (MedDRA) dictionary. The machine learning approach is based on a recently proposed deep learning architecture, which integrates bi-directional Long Short-Term Memory (Bi-LSTM), Convolutional Neural Network (CNN), and Conditional Random Fields (CRF) for entity recognition. The rule-based approach, used for normalizing the identified ADR mentions to MedDRA terms, is based on an extension of our in-house text-mining system, SciMiner. We evaluated our system on the Text Analysis Conference (TAC) Adverse Drug Reaction 2017 challenge test data set, consisting of 200 manually curated US FDA drug labels. Our ML-based system achieved 77.0% F1 score on the task of ADR mention recognition and 82.6% micro-averaged F1 score on the task of ADR normalization, while rule-based system achieved 67.4 and 77.6% F1 scores, respectively.ConclusionOur study demonstrates that a system composed of a deep learning architecture for entity recognition and a rule-based model for entity normalization is a promising approach for ADR extraction from drug labels.

A systematic approach for developing a corpus of patient reported adverse drug events: A case study for SSRI and SNRI medications.

"Psychiatric Treatment Adverse Reactions" (PsyTAR) corpus is an annotated corpus that has been developed using patients narrative data for psychiatric medications, particularly SSRIs (Selective Serotonin Reuptake Inhibitor) and SNRIs (Serotonin Norepinephrine Reuptake Inhibitor) medications. This corpus consists of three main components: sentence classification, entity identification, and entity normalization. We split the review posts into sentences and labeled them for presence of adverse drug reactions (ADRs) (2168 sentences), withdrawal symptoms (WDs) (438 sentences), sign/symptoms/illness (SSIs) (789 sentences), drug indications (517), drug effectiveness (EF) (1087 sentences), and drug infectiveness (INF) (337 sentences). In the entity identification phase, we identified and extracted ADRs (4813 mentions), WDs (590 mentions), SSIs (1219 mentions), and DIs (792). In the entity normalization phase, we mapped the identified entities to the corresponding concepts in both UMLS (918 unique concepts) and SNOMED CT (755 unique concepts). Four annotators double coded the sentences and the span of identified entities by strictly following guidelines rules developed for this study. We used the PsyTAR sentence classification component to automatically train a range of supervised machine learning classifiers to identifying text segments with the mentions of ADRs, WDs, DIs, SSIs, EF, and INF. SVMs classifiers had the highest performance with F-Score 0.90. We also measured performance of the cTAKES (clinical Text Analysis and Knowledge Extraction System) in identifying patients' expressions of ADRs and WDs with and without adding PsyTAR dictionary to the core dictionary of cTAKES. Augmenting cTAKES dictionary with PsyTAR improved the F-score cTAKES by 25%. The findings imply that PsyTAR has significant implications for text mining algorithms aimed to identify information about adverse drug events and drug effectiveness from patients' narratives data, by linking the patients' expressions of adverse drug events to medical standard vocabularies. The corpus is publicly available at Zolnoori et al. [30].

Detecting Adverse Drug Reactions on Twitter with Convolutional Neural Networks and Word Embedding Features.

Motivated by limitations of adverse drug reaction (ADR) detection in clinical trials and passive post-market drug safety surveillance systems, a number of researchers have examined social media data as a potential ADR information source. Twitter is a particularly attractive platform because it has a large, diverse user community. Two challenges faced in applying Twitter data are that ADR descriptions are infrequent relative to the overall number of user posts and human review of all posts is impractical. To address these challenges, we framed the ADR detection problem as a binary classification task, where our objective was to develop a computational method that can classify user posts, known as tweets, relative to the presence of an ADR description. We developed a convolutional neural network model (ConvNet) that processes tweets as represented by word vectors created using unsupervised learning on large datasets. The ConvNet model achieved an F1-score of 0.46 and sensitivity of 0.78 for tweet ADR classification on the test dataset, compared to 0.37 F1-score and 0.33 sensitivity obtained by two baseline support vector machine (SVM) models that incorporated word embedding, n-gram, and lexicon features. We attribute the superior ConvNet model performance to its ability to process arbitrary length inputs, which allows it to evaluate every word embedding in a given tweet and make better use of their semantic content as compared to the SVM models which require a fixed length, aggregated embedding input. The results presented demonstrate the feasibility of detection of infrequent ADR mentions in large-scale media data.

Frequent discussion of insomnia and weight gain with glucocorticoid therapy: an analysis of Twitter posts

In recent years, social media websites have been suggested as a novel, vast source of data which may be useful for deriving drug safety information. Despite this, there are few published reports of drug safety profiles derived in this way. The aims of this study were to detect and quantify glucocorticoid-related adverse events using a computerised system for automated detection of suspected adverse drug reactions (ADR) from narrative text in Twitter, and to compare the frequency of specific ADR mentions within Twitter to the frequency and patterns of spontaneous ADR reporting to a national drug regulatory body. Of 159,297 tweets mentioning either prednisolone or prednisone between 1st October 2012 and 30th June 2015, 20,206 tweets were deemed to contain information resembling an ADR. The top AE MedDRA® Preferred Terms were ‘insomnia’ and ‘weight increased’, both recognised non-serious but common side effects. These were proportionally over-reported in Twitter when compared to spontaneous reports in the UK regulator’s ADR reporting scheme. Serious glucocorticoid related AEs were reported less frequently. Pharmacovigilance using Twitter data has the potential to be a valuable, supplementary source of drug safety information. In particular, it can illustrate which drug side effects patients discuss most commonly, potentially because of important impacts on quality of life. This information could help clinicians to inform patients about frequent and relevant non-serious side effects as well as more serious side effects.

Recognizing Continuous and Discontinuous Adverse Drug Reaction Mentions from Social Media Using LSTM‐CRF

Social media in medicine, where patients can express their personal treatment experiences by personal computers and mobile devices, usually contains plenty of useful medical information, such as adverse drug reactions (ADRs); mining this useful medical information from social media has attracted more and more attention from researchers. In this study, we propose a deep neural network (called LSTM‐CRF) combining long short‐term memory (LSTM) neural networks (a type of recurrent neural networks) and conditional random fields (CRFs) to recognize ADR mentions from social media in medicine and investigate the effects of three factors on ADR mention recognition. The three factors are as follows: (1) representation for continuous and discontinuous ADR mentions: two novel representations, that is, “BIOHD” and “Multilabel,” are compared; (2) subject of posts: each post has a subject (i.e., drug here); and (3) external knowledge bases. Experiments conducted on a benchmark corpus, that is, CADEC, show that LSTM‐CRF achieves better F‐score than CRF; “Multilabel” is better in representing continuous and discontinuous ADR mentions than “BIOHD”; both subjects of comments and external knowledge bases are individually beneficial to ADR mention recognition. To the best of our knowledge, this is the first time to investigate deep neural networks to mine continuous and discontinuous ADRs from social media.

Сравнительный анализ нейронных сетей в задаче классификации побочных эффектов на уровне сущностей в англоязычных текстах

This paper presents our experimental work on exploring the potential of neural network models developed for aspect-based sentiment analysis for entity-level adverse drug reaction (ADR) classification. Our goal is to explore how to represent local context around ADR mentions and learn an entity representation, interacting with its context. We conducted extensive experiments on various sources of text-based information, including social media, electronic health records, and abstracts of scientific articles from PubMed. The results show that Interactive Attention Neural Network (IAN) outperformed other models on four corpora in terms of macro F-measure. This work is an abridged version of our recent paper accepted to Programming and Computer Software journal in 2019.

An Attentive Neural Sequence Labeling Model for Adverse Drug Reactions Mentions Extraction

Adverse drug reactions (ADRs) are a main cause of morbidity and mortality in patients. Extracting mentions of ADRs from the health-related text has important applications in biomedical research. Existing work mainly utilizes feature-based pipeline methods or neural network models that use only word embeddings as input features. These methods either require many efforts to design task-specific features or suffer misclassification on those words, which have not been seen before. Therefore, we propose an end-to-end neural sequence labeling model that labels words in an input sequence with ADRs membership tags. In addition to word-level embeddings, we also adopt character-level embeddings and combine them via an embedding-level attention mechanism. Through such an attention mechanism, our model can dynamically determine how much information to utilize from a word- or character-level component. In addition, we use the intermediate output of the model as an auxiliary classifier and combine it with the final output of the model to improve the overall performance. We evaluate different architectures on two ADRs labeling datasets. One is an ADRs-related Twitter corpus that includes many informal vocabularies and irregular grammar, and the other is a biomedical text extracted from PubMed abstracts with many professional terms and technical descriptions. Our model achieves approximate match F1 scores of 0.844 and 0.906 for ADRs identification on the Twitter and PubMed datasets, respectively. It presents the state-of-the-art performance on both the datasets. Our system is completely end-to-end, requires no task-specific feature engineering or hand-crafted features, and thus can be generalized to a wide range of sequence labeling tasks.

Feature Engineering for Recognizing Adverse Drug Reactions from Twitter Posts

Social media platforms are emerging digital communication channels that provide an easy way for common people to share their health and medication experiences online. With more people discussing their health information online publicly, social media platforms present a rich source of information for exploring adverse drug reactions (ADRs). ADRs are major public health problems that result in deaths and hospitalizations of millions of people. Unfortunately, not all ADRs are identified before a drug is made available in the market. In this study, an ADR event monitoring system is developed which can recognize ADR mentions from a tweet and classify its assertion. We explored several entity recognition features, feature conjunctions, and feature selection and analyzed their characteristics and impacts on the recognition of ADRs, which have never been studied previously. The results demonstrate that the entity recognition performance for ADR can achieve an F-score of 0.562 on the PSB Social Media Mining shared task dataset, which outperforms the partial-matching-based method by 0.122. After feature selection, the F-score can be further improved by 0.026. This novel technique of text mining utilizing shared online social media data will open an array of opportunities for researchers to explore various health related issues.

Pharmacovigilance from social media: mining adverse drug reaction mentions using sequence labeling with word embedding cluster features.

Objective Social media is becoming increasingly popular as a platform for sharing personal health-related information. This information can be utilized for public health monitoring tasks, particularly for pharmacovigilance, via the use of natural language processing (NLP) techniques. However, the language in social media is highly informal, and user-expressed medical concepts are often nontechnical, descriptive, and challenging to extract. There has been limited progress in addressing these challenges, and thus far, advanced machine learning-based NLP techniques have been underutilized. Our objective is to design a machine learning-based approach to extract mentions of adverse drug reactions (ADRs) from highly informal text in social media. Methods We introduce ADRMine, a machine learning-based concept extraction system that uses conditional random fields (CRFs). ADRMine utilizes a variety of features, including a novel feature for modeling words’ semantic similarities. The similarities are modeled by clustering words based on unsupervised, pretrained word representation vectors (embeddings) generated from unlabeled user posts in social media using a deep learning technique. Results ADRMine outperforms several strong baseline systems in the ADR extraction task by achieving an F-measure of 0.82. Feature analysis demonstrates that the proposed word cluster features significantly improve extraction performance. Conclusion It is possible to extract complex medical concepts, with relatively high performance, from informal, user-generated content. Our approach is particularly scalable, suitable for social media mining, as it relies on large volumes of unlabeled data, thus diminishing the need for large, annotated training data sets.