298 research outputs found
A Large-Scale CNN Ensemble for Medication Safety Analysis
Revealing Adverse Drug Reactions (ADR) is an essential part of post-marketing
drug surveillance, and data from health-related forums and medical communities
can be of a great significance for estimating such effects. In this paper, we
propose an end-to-end CNN-based method for predicting drug safety on user
comments from healthcare discussion forums. We present an architecture that is
based on a vast ensemble of CNNs with varied structural parameters, where the
prediction is determined by the majority vote. To evaluate the performance of
the proposed solution, we present a large-scale dataset collected from a
medical website that consists of over 50 thousand reviews for more than 4000
drugs. The results demonstrate that our model significantly outperforms
conventional approaches and predicts medicine safety with an accuracy of 87.17%
for binary and 62.88% for multi-classification tasks
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.Comment: 9 page
Semi-Supervised Recurrent Neural Network for Adverse Drug Reaction Mention Extraction
Social media is an useful platform to share health-related information due to
its vast reach. This makes it a good candidate for public-health monitoring
tasks, specifically for pharmacovigilance. We study the problem of extraction
of Adverse-Drug-Reaction (ADR) mentions from social media, particularly from
twitter. Medical information extraction from social media is challenging,
mainly due to short and highly information nature of text, as compared to more
technical and formal medical reports.
Current methods in ADR mention extraction relies on supervised learning
methods, which suffers from labeled data scarcity problem. The State-of-the-art
method uses deep neural networks, specifically a class of Recurrent Neural
Network (RNN) which are Long-Short-Term-Memory networks (LSTMs)
\cite{hochreiter1997long}. Deep neural networks, due to their large number of
free parameters relies heavily on large annotated corpora for learning the end
task. But in real-world, it is hard to get large labeled data, mainly due to
heavy cost associated with manual annotation. Towards this end, we propose a
novel semi-supervised learning based RNN model, which can leverage unlabeled
data also present in abundance on social media. Through experiments we
demonstrate the effectiveness of our method, achieving state-of-the-art
performance in ADR mention extraction.Comment: Accepted at DTMBIO workshop, CIKM 2017. To appear in BMC
Bioinformatics. Pls cite that versio
Biomedical Information Extraction Pipelines for Public Health in the Age of Deep Learning
abstract: Unstructured texts containing biomedical information from sources such as electronic health records, scientific literature, discussion forums, and social media offer an opportunity to extract information for a wide range of applications in biomedical informatics. Building scalable and efficient pipelines for natural language processing and extraction of biomedical information plays an important role in the implementation and adoption of applications in areas such as public health. Advancements in machine learning and deep learning techniques have enabled rapid development of such pipelines. This dissertation presents entity extraction pipelines for two public health applications: virus phylogeography and pharmacovigilance. For virus phylogeography, geographical locations are extracted from biomedical scientific texts for metadata enrichment in the GenBank database containing 2.9 million virus nucleotide sequences. For pharmacovigilance, tools are developed to extract adverse drug reactions from social media posts to open avenues for post-market drug surveillance from non-traditional sources. Across these pipelines, high variance is observed in extraction performance among the entities of interest while using state-of-the-art neural network architectures. To explain the variation, linguistic measures are proposed to serve as indicators for entity extraction performance and to provide deeper insight into the domain complexity and the challenges associated with entity extraction. For both the phylogeography and pharmacovigilance pipelines presented in this work the annotated datasets and applications are open source and freely available to the public to foster further research in public health.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201
Opinion Mining and Sentiment Analysis of Online Drug Reviews as a Pharmacovigilance Technique
Pharmacovigilance is the science that focuses on identification and characterization of adverse effects of medications in populations when released to market. The focus of this paper is to study the prospects of exploiting drug related online reviews contributed by social media groups for finding the adverse effects of drugs using opinion mining and sentiment analysis. The experiences and opinions related to drug adverse reactions by patients or other contributors in these forums can be mined and analyzed as a facilitator for pharmacovigilance. This review paper highlights the usability of opinion mining and sentiment analysis as one of the approaches for pharmacovigilance.
DOI: 10.17762/ijritcc2321-8169.150711
Normalizing Spontaneous Reports into MedDRA: some Experiments with MagiCoder
Text normalization into medical dictionaries is useful to support clinical task. A typical setting is Pharmacovigilance (PV). The manual detection of suspected adverse drug reactions (ADRs) in narrative reports is time consuming and Natural Language Processing (NLP) provides a concrete help to PV experts. In this paper we carry on experiments for testing performances of MagiCoder, an NLP application designed to extract MedDRA terms from narrative clinical text. Given a narrative description, MagiCoder proposes an automatic encoding. The pharmacologist reviews, (possibly) corrects, and then validates the solution. This drastically reduces the time needed for the validation of reports with respect to a completely manual encoding. In previous work we mainly tested MagiCoder performances on Italian written spontaneous reports. In this paper, we include some new features, change the experiment design, and carry on more tests about MagiCoder. Moreover, we do a change of language, moving to English documents. In particular, we tested MagiCoder on the CADEC dataset, a corpus of manually annotated posts about ADRs collected from social media
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