Adverse Drug Reaction Classification With Deep Neural Networks

We study the problem of detecting sentences describing adverse drug reactions (ADRs) and frame the problem as binary classification. We investigate different neural network (NN) architectures for ADR classification. In particular, we propose two new neural network models, Convolutional Recurrent Neural Network (CRNN) by concatenating convolutional neural networks with recurrent neural networks, and Convolutional Neural Network with Attention (CNNA) by adding attention weights into convolutional neural networks. We evaluate various NN architectures on a Twitter dataset containing informal language and an Adverse Drug Effects (ADE) dataset constructed by sampling from MEDLINE case reports. Experimental results show that all the NN architectures outperform the traditional maximum entropy classifiers trained from n-grams with different weighting strategies considerably on both datasets. On the Twitter dataset, all the NN architectures perform similarly. But on the ADE dataset, CNN performs better than other more complex CNN variants. Nevertheless, CNNA allows the visualisation of attention weights of words when making classification decisions and hence is more appropriate for the extraction of word subsequences describing ADRs

Big Data Transforms Discovery-Utilization Therapeutics Continuum.

Enabling omic technologies adopt a holistic view to produce unprecedented insights into the molecular underpinnings of health and disease, in part, by generating massive high-dimensional biological data. Leveraging these systems-level insights as an engine driving the healthcare evolution is maximized through integration with medical, demographic, and environmental datasets from individuals to populations. Big data analytics has accordingly emerged to add value to the technical aspects of storage, transfer, and analysis required for merging vast arrays of omic-, clinical-, and eco-datasets. In turn, this new field at the interface of biology, medicine, and information science is systematically transforming modern therapeutics across discovery, development, regulation, and utilization

Mining Adverse Drug Reactions from online healthcare forums using Hidden Markov Model

Background Adverse Drug Reactions are one of the leading causes of injury or death among patients undergoing medical treatments. Not all Adverse Drug Reactions are identified before a drug is made available in the market. Current post-marketing drug surveillance methods, which are based purely on voluntary spontaneous reports, are unable to provide the early indications necessary to prevent the occurrence of such injuries or fatalities. The objective of this research is to extract reports of adverse drug side-effects from messages in online healthcare forums and use them as early indicators to assist in post-marketing drug surveillance. Methods We treat the task of extracting adverse side-effects of drugs from healthcare forum messages as a sequence labeling problem and present a Hidden Markov Model(HMM) based Text Mining system that can be used to classify a message as containing drug side-effect information and then extract the adverse side-effect mentions from it. A manually annotated dataset from http://www.medications.comis used in the training and validation of the HMM based Text Mining system. Results A 10-fold cross-validation on the manually annotated dataset yielded on average an F-Score of 0.76 from the HMM Classifier, in comparison to 0.575 from the Baseline classifier. Without the Plain Text Filter component as a part of the Text Processing module, the F-Score of the HMM Classifier was reduced to 0.378 on average, while absence of the HTML Filter component was found to have no impact. Reducing the Drug names dictionary size by half, on average reduced the F-Score of the HMM Classifier to 0.359, while a similar reduction to the side-effects dictionary yielded an F-Score of 0.651 on average. Adverse side-effects mined from http://www.medications.comand http://www.steadyhealth.comwere found to match the Adverse Drug Reactions on the Drug Package Labels of several drugs. In addition, some novel adverse side-effects, which can be potential Adverse Drug Reactions, were also identified. Conclusions The results from the HMM based Text Miner are encouraging to pursue further enhancements to this approach. The mined novel side-effects can act as early indicators for health authorities to help focus their efforts in post-marketing drug surveillance.The authors would like to acknowledge the support from National Science Foundation awards IIS-0644366 and OIA-1028098, and KU General Research Fund GRF-2301677

Annotation analysis for testing drug safety signals using unstructured clinical notes

BackgroundThe electronic surveillance for adverse drug events is largely based upon the analysis of coded data from reporting systems. Yet, the vast majority of electronic health data lies embedded within the free text of clinical notes and is not gathered into centralized repositories. With the increasing access to large volumes of electronic medical data-in particular the clinical notes-it may be possible to computationally encode and to test drug safety signals in an active manner.ResultsWe describe the application of simple annotation tools on clinical text and the mining of the resulting annotations to compute the risk of getting a myocardial infarction for patients with rheumatoid arthritis that take Vioxx. Our analysis clearly reveals elevated risks for myocardial infarction in rheumatoid arthritis patients taking Vioxx (odds ratio 2.06) before 2005.ConclusionsOur results show that it is possible to apply annotation analysis methods for testing hypotheses about drug safety using electronic medical records

Harnessing Machine Learning to Improve Healthcare Monitoring with FAERS

This research study investigates the potential of machine learning techniques to improve healthcare monitoring through the utilization of data from the FDA Adverse Event Reporting System (FAERS). The objective is to explore specific applications of machine learning in healthcare monitoring with FAERS and highlight their findings. The study reveals several significant ways in which machine learning can contribute to enhancing healthcare monitoring using FAERS.Machine learning algorithms can detect potential safety signals at an early stage by analyzing FAERS data. By employing anomaly detection and temporal pattern analysis techniques, these models can identify emerging safety concerns that were previously unknown or underreported. This early detection enables timely action to mitigate risks associated with medications or medical products.Machine learning models can assist in pharmacovigilance triage, addressing the challenge posed by the large number of adverse event reports within FAERS. By developing ranking and classification models, adverse events can be prioritized based on severity, novelty, or potential impact. This automation of the triage process enables pharmacovigilance teams to efficiently identify and investigate critical safety concerns.Machine learning models can automate the classification and coding of adverse events, which are often present in unstructured text within FAERS reports. Through the application of Natural Language Processing (NLP) techniques, such as named entity recognition and text classification, relevant information can be extracted, enhancing the efficiency and accuracy of adverse event coding.Machine learning algorithms can refine and validate signals generated from FAERS data by incorporating additional data sources, such as electronic health records, social media, or clinical trials data. This integration provides a more comprehensive understanding of potential risks and helps filter out false positives, facilitating the identification of signals requiring further investigation.Machine learning enables real-time surveillance of FAERS data, allowing for the identification of safety concerns as they occur. Continuous monitoring and real-time analysis of incoming reports enable machine learning models to trigger alerts or notifications to relevant stakeholders, promoting timely intervention to minimize patient harm.The study demonstrates the use of machine learning models to conduct comparative safety analyses by combining FAERS data with other healthcare databases. These models assist in identifying safety differences between medications, patient populations, or dosing regimens, enabling healthcare providers and regulators to make informed decisions regarding treatment choices.While machine learning is a powerful tool in healthcare monitoring, its implementation should be complemented by human expertise and domain knowledge. The interpretation and validation of results generated by machine learning models necessitate the involvement of healthcare professionals and pharmacovigilance experts to ensure accurate and meaningful insights.This research study illustrates the diverse applications of machine learning in improving healthcare monitoring using FAERS data. The findings highlight the potential of machine learning in early safety signal detection, pharmacovigilance triage, adverse event classification and coding, signal refinement and validation, real-time surveillance and alerting, and comparative safety analysis. The study emphasizes the importance of combining machine learning with human expertise to achieve effective and reliable healthcare monitoring