9,673 research outputs found
Mining Frequency of Drug Side Effects Over a Large Twitter Dataset Using Apache Spark
Despite clinical trials by pharmaceutical companies as well as current FDA reporting systems, there are still drug side effects that have not been caught. To find a larger sample of reports, a possible way is to mine online social media. With its current widespread use, social media such as Twitter has given rise to massive amounts of data, which can be used as reports for drug side effects. To process these large datasets, Apache Spark has become popular for fast, distributed batch processing. In this work, we have improved on previous pipelines in sentimental analysis-based mining, processing, and extracting tweets with drug-caused side effects. We have also added a new ensemble classifier using a combination of sentiment analysis features to increase the accuracy of identifying drug-caused side effects. In addition, the frequency count for the side effects is also provided. Furthermore, we have also implemented the same pipeline in Apache Spark to improve the speed of processing of tweets by 2.5 times, as well as to support the process of large tweet datasets. As the frequency count of drug side effects opens a wide door for further analysis, we present a preliminary study on this issue, including the side effects of simultaneously using two drugs, and the potential danger of using less-common combination of drugs. We believe the pipeline design and the results present in this work would have great implication on studying drug side effects and on big data analysis in general
The benefits of in silico modeling to identify possible small-molecule drugs and their off-target interactions
Accepted for publication in a future issue of Future Medicinal Chemistry.The research into the use of small molecules as drugs continues to be a key driver in the development of molecular databases, computer-aided drug design software and collaborative platforms. The evolution of computational approaches is driven by the essential criteria that a drug molecule has to fulfill, from the affinity to targets to minimal side effects while having adequate absorption, distribution, metabolism, and excretion (ADME) properties. A combination of ligand- and structure-based drug development approaches is already used to obtain consensus predictions of small molecule activities and their off-target interactions. Further integration of these methods into easy-to-use workflows informed by systems biology could realize the full potential of available data in the drug discovery and reduce the attrition of drug candidates.Peer reviewe
People on Drugs: Credibility of User Statements in Health Communities
Online health communities are a valuable source of information for patients
and physicians. However, such user-generated resources are often plagued by
inaccuracies and misinformation. In this work we propose a method for
automatically establishing the credibility of user-generated medical statements
and the trustworthiness of their authors by exploiting linguistic cues and
distant supervision from expert sources. To this end we introduce a
probabilistic graphical model that jointly learns user trustworthiness,
statement credibility, and language objectivity. We apply this methodology to
the task of extracting rare or unknown side-effects of medical drugs --- this
being one of the problems where large scale non-expert data has the potential
to complement expert medical knowledge. We show that our method can reliably
extract side-effects and filter out false statements, while identifying
trustworthy users that are likely to contribute valuable medical information
Ontology of core data mining entities
In this article, we present OntoDM-core, an ontology of core data mining
entities. OntoDM-core defines themost essential datamining entities in a three-layered
ontological structure comprising of a specification, an implementation and an application
layer. It provides a representational framework for the description of mining
structured data, and in addition provides taxonomies of datasets, data mining tasks,
generalizations, data mining algorithms and constraints, based on the type of data.
OntoDM-core is designed to support a wide range of applications/use cases, such as
semantic annotation of data mining algorithms, datasets and results; annotation of
QSAR studies in the context of drug discovery investigations; and disambiguation of
terms in text mining. The ontology has been thoroughly assessed following the practices
in ontology engineering, is fully interoperable with many domain resources and
is easy to extend
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