Automatic Detection of Adverse Drug Events in Geriatric Care: Study Proposal

BACKGROUND One-third of older inpatients experience adverse drug events (ADEs), which increase their mortality, morbidity, and health care use and costs. In particular, antithrombotic drugs are among the most at-risk medications for this population. Reporting systems have been implemented at the national, regional, and provider levels to monitor ADEs and design prevention strategies. Owing to their well-known limitations, automated detection technologies based on electronic medical records (EMRs) are being developed to routinely detect or predict ADEs. OBJECTIVE This study aims to develop and validate an automated detection tool for monitoring antithrombotic-related ADEs using EMRs from 4 large Swiss hospitals. We aim to assess cumulative incidences of hemorrhages and thromboses in older inpatients associated with the prescription of antithrombotic drugs, identify triggering factors, and propose improvements for clinical practice. METHODS This project is a multicenter, cross-sectional study based on 2015 to 2016 EMR data from 4 large hospitals in Switzerland: Lausanne, Geneva, and Zürich university hospitals, and Baden Cantonal Hospital. We have included inpatients aged ≥65 years who stayed at 1 of the 4 hospitals during 2015 or 2016, received at least one antithrombotic drug during their stay, and signed or were not opposed to a general consent for participation in research. First, clinical experts selected a list of relevant antithrombotic drugs along with their side effects, risks, and confounding factors. Second, administrative, clinical, prescription, and laboratory data available in the form of free text and structured data were extracted from study participants' EMRs. Third, several automated rule-based and machine learning-based algorithms are being developed, allowing for the identification of hemorrhage and thromboembolic events and their triggering factors from the extracted information. Finally, we plan to validate the developed detection tools (one per ADE type) through manual medical record review. Performance metrics for assessing internal validity will comprise the area under the receiver operating characteristic curve, F$_{1}$-score, sensitivity, specificity, and positive and negative predictive values. RESULTS After accounting for the inclusion and exclusion criteria, we will include 34,522 residents aged ≥65 years. The data will be analyzed in 2022, and the research project will run until the end of 2022 to mid-2023. CONCLUSIONS This project will allow for the introduction of measures to improve safety in prescribing antithrombotic drugs, which today remain among the drugs most involved in ADEs. The findings will be implemented in clinical practice using indicators of adverse events for risk management and training for health care professionals; the tools and methodologies developed will be disseminated for new research in this field. The increased performance of natural language processing as an important complement to structured data will bring existing tools to another level of efficiency in the detection of ADEs. Currently, such systems are unavailable in Switzerland. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/40456

Machine Learning Applications in Pharmacovigilance: Scoping Review

Background: Pharmacovigilance (PV) is the activity to identify comprehensive information on the safety characteristics of the drug after its marketing. The PV data sources are dynamic, large, structured, and unstructured; therefore, the automation of data processing is essential. Purpose: This review aims to identify the machine learning applications in PV activities. Methods: Nine (9) studies that were published within the period from 2016 to 2020 were reviewed. The studies were extracted from two databases; PubMed and web of science. The review and analysis were done in December 2020. Results: The supervised and semi-supervised learning techniques are applied in the main three PV group activities; adverse drug reactions (ADRs) and signal detection, individual case safety reports (ICSRs) identification, and ADRs prediction. Future research is needed to identify the applicability of unsupervised learning in PV and to formulate the legal framework of the false positive predicted data

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Drug-drug interactions in the hospital

Introduction Drug interaction screening programs are an important tool to check prescriptions of multiple drugs for potential drug-drug interactions (pDDIs). Several programs are available on the market. They differ in layout, update frequency, search functions, content and price. The aim of the current study was to critically appraise several interaction screening programs in the Department of Medicine of a Swiss public teaching hospital. Methods A drug interaction screening program had to fulfil minimal requirements (information on effect, severity rating, clinical management, mechanism and literature) in order to be admitted to the present evaluation. The 100 most frequently used drugs in the Cantonal Hospital of Baden, Switzerland, were used to test the comprehensiveness of the programs. Qualitative criteria were used for the assessment of the drug interaction monographs. In a precision analysis, 30 drugs with and 30 drugs without pDDIs of clinical importance were tested. In addition, 16 typical patient profiles were checked for pDDIs, using Stockley’s Drug Interactions as a reference. Results Out of nine programs included, the following four fulfilled the above mentioned criteria: Drug Interaction Facts, Drug-Reax, Lexi-Interact and Pharmavista. Drug Interaction Facts contained the lowest number of drugs and was therefore the least qualified program. Lexi-Interact condenses many DDIs into one group, resulting in less specific information, whereas Pharmavista and Drug-Reax offer excellent interaction monographs. In the precision analysis, Lexi-Interact showed the best sensitivity (1.00), followed by Drug-Reax and Pharmavista (0.83 each) and Drug Interaction Facts (0.63). The analysis of patient profiles revealed that out of 157 pDDIs found by all programs, only 18 (11%) were detected by all of them. No program found more than 50% of the total number of pDDIs. A further evaluation using Stockley’s Drug Interactions as the gold standard revealed that Pharmavista achieved a sensitivity of 0.86 (versus Drug Interaction Facts, Lexi-Interact and Drug-Reax with a sensitivity of 0.71 each) with an acceptable positive predictive value of 0.67. Conclusion In order to detect most pDDIs without causing too many false positive results, drug interaction screening programs should have a high sensitivity and a high positive predictive value. Pharmavista offers the highest sensitivity of the programs evaluated with a positive predictive value in an acceptable range. An increase in sensitivity is possible by the combination of two programs

Automatically Recognizing Medication and Adverse Event Information From Food and Drug Administration\u27s Adverse Event Reporting System Narratives

BACKGROUND: The Food and Drug Administration\u27s (FDA) Adverse Event Reporting System (FAERS) is a repository of spontaneously-reported adverse drug events (ADEs) for FDA-approved prescription drugs. FAERS reports include both structured reports and unstructured narratives. The narratives often include essential information for evaluation of the severity, causality, and description of ADEs that are not present in the structured data. The timely identification of unknown toxicities of prescription drugs is an important, unsolved problem. OBJECTIVE: The objective of this study was to develop an annotated corpus of FAERS narratives and biomedical named entity tagger to automatically identify ADE related information in the FAERS narratives. METHODS: We developed an annotation guideline and annotate medication information and adverse event related entities on 122 FAERS narratives comprising approximately 23,000 word tokens. A named entity tagger using supervised machine learning approaches was built for detecting medication information and adverse event entities using various categories of features. RESULTS: The annotated corpus had an agreement of over .9 Cohen\u27s kappa for medication and adverse event entities. The best performing tagger achieves an overall performance of 0.73 F1 score for detection of medication, adverse event and other named entities. C ONCLUSIONS: In this study, we developed an annotated corpus of FAERS narratives and machine learning based models for automatically extracting medication and adverse event information from the FAERS narratives. Our study is an important step towards enriching the FAERS data for postmarketing pharmacovigilance

GNTeam at 2018 n2c2:Feature-augmented BiLSTM-CRF for drug-related entity recognition in hospital discharge summaries

Monitoring the administration of drugs and adverse drug reactions are key parts of pharmacovigilance. In this paper, we explore the extraction of drug mentions and drug-related information (reason for taking a drug, route, frequency, dosage, strength, form, duration, and adverse events) from hospital discharge summaries through deep learning that relies on various representations for clinical named entity recognition. This work was officially part of the 2018 n2c2 shared task, and we use the data supplied as part of the task. We developed two deep learning architecture based on recurrent neural networks and pre-trained language models. We also explore the effect of augmenting word representations with semantic features for clinical named entity recognition. Our feature-augmented BiLSTM-CRF model performed with F1-score of 92.67% and ranked 4th for entity extraction sub-task among submitted systems to n2c2 challenge. The recurrent neural networks that use the pre-trained domain-specific word embeddings and a CRF layer for label optimization perform drug, adverse event and related entities extraction with micro-averaged F1-score of over 91%. The augmentation of word vectors with semantic features extracted using available clinical NLP toolkits can further improve the performance. Word embeddings that are pre-trained on a large unannotated corpus of relevant documents and further fine-tuned to the task perform rather well. However, the augmentation of word embeddings with semantic features can help improve the performance (primarily by boosting precision) of drug-related named entity recognition from electronic health records

Dual autoencoders modeling of electronic health records for adverse drug event preventability prediction

Background Elderly patients are at increased risk for Adverse Drug Events (ADEs). Proactively screening elderly people visiting the emergency department for the possibility of their hospital admission being drug-related helps to improve patient care as well as prevent potential unnecessary medical costs. Existing routine ADE assessment heavily relies on a rule-based checking process. Recently, machine learning methods have been shown to be effective in automating the detection of ADEs, however, most approaches used only either structured data or free texts for their feature engineering. How to better exploit all available EHRs data for better predictive modeling remains an important question. On the other hand, automated reasoning for the preventability of ADEs is still a nascent line of research. Methods Clinical information of 714 elderly ED-visit patients with ADE preventability labels was provided as ground truth data by Jeroen Bosch Ziekenhuis hospital, the Netherlands. Methods were developed to address the challenges of applying feature engineering to heterogeneous EHRs data. A Dual Autoencoders (2AE) model was proposed to solve the problem of imbalance embedded in the existing training data. Results Experimental results showed that 2AE can capture the patterns of the minority class without incorporating an extra process for class balancing. 2AE yields adequate performance and outperforms other more mainstream approaches, resulting in an AUPRC score of 0.481. Conclusions We have demonstrated how machine learning can be employed to analyze both structured and unstructured data from electronic health records for the purpose of preventable ADE prediction. The developed algorithm 2AE can be used to effectively learn minority group phenotype from imbalanced data

Adverse Drug Event Detection, Causality Inference, Patient Communication and Translational Research

Adverse drug events (ADEs) are injuries resulting from a medical intervention related to a drug. ADEs are responsible for nearly 20% of all the adverse events that occur in hospitalized patients. ADEs have been shown to increase the cost of health care and the length of stays in hospital. Therefore, detecting and preventing ADEs for pharmacovigilance is an important task that can improve the quality of health care and reduce the cost in a hospital setting. In this dissertation, we focus on the development of ADEtector, a system that identifies ADEs and medication information from electronic medical records and the FDA Adverse Event Reporting System reports. The ADEtector system employs novel natural language processing approaches for ADE detection and provides a user interface to display ADE information. The ADEtector employs machine learning techniques to automatically processes the narrative text and identify the adverse event (AE) and medication entities that appear in that narrative text. The system will analyze the entities recognized to infer the causal relation that exists between AEs and medications by automating the elements of Naranjo score using knowledge and rule based approaches. The Naranjo Adverse Drug Reaction Probability Scale is a validated tool for finding the causality of a drug induced adverse event or ADE. The scale calculates the likelihood of an adverse event related to drugs based on a list of weighted questions. The ADEtector also presents the user with evidence for ADEs by extracting figures that contain ADE related information from biomedical literature. A brief summary is generated for each of the figures that are extracted to help users better comprehend the figure. This will further enhance the user experience in understanding the ADE information better. The ADEtector also helps patients better understand the narrative text by recognizing complex medical jargon and abbreviations that appear in the text and providing definitions and explanations for them from external knowledge resources. This system could help clinicians and researchers in discovering novel ADEs and drug relations and also hypothesize new research questions within the ADE domain

Artificial Intelligence for Participatory Health: Applications, Impact, and Future Implications

Objective: Artificial intelligence (AI) provides people and professionals working in the field of participatory health informatics an opportunity to derive robust insights from a variety of online sources. The objective of this paper is to identify current state of the art and application areas of AI in the context of participatory health. Methods: A search was conducted across seven databases (PubMed, Embase, CINAHL, PsychInfo, ACM Digital Library, IEEExplore, and SCOPUS), covering articles published since 2013. Additionally, clinical trials involving AI in participatory health contexts registered at clinicaltrials.gov were collected and analyzed. Results: Twenty-two articles and 12 trials were selected for review. The most common application of AI in participatory health was the secondary analysis of social media data: self-reported data including patient experiences with healthcare facilities, reports of adverse drug reactions, safety and efficacy concerns about over-the-counter medications, and other perspectives on medications. Other application areas included determining which online forum threads required moderator assistance, identifying users who were likely to drop out from a forum, extracting terms used in an online forum to learn its vocabulary, highlighting contextual information that is missing from online questions and answers, and paraphrasing technical medical terms for consumers. Conclusions: While AI for supporting participatory health is still in its infancy, there are a number of important research priorities that should be considered for the advancement of the field. Further research evaluating the impact of AI in participatory health informatics on the psychosocial wellbeing of individuals would help in facilitating the wider acceptance of AI into the healthcare ecosystem