Automated Detection of Adverse Drug Reactions in the Biomedical Literature Using Convolutional Neural Networks and Biomedical Word Embeddings

Monitoring the biomedical literature for cases of Adverse Drug Reactions (ADRs) is a critically important and time consuming task in pharmacovigilance. The development of computer assisted approaches to aid this process in different forms has been the subject of many recent works. One particular area that has shown promise is the use of Deep Neural Networks, in particular, Convolutional Neural Networks (CNNs), for the detection of ADR relevant sentences. Using token-level convolutions and general purpose word embeddings, this architecture has shown good performance relative to more traditional models as well as Long Short Term Memory (LSTM) models. In this work, we evaluate and compare two different CNN architectures using the ADE corpus. In addition, we show that by de-duplicating the ADR relevant sentences, we can greatly reduce overoptimism in the classification results. Finally, we evaluate the use of word embeddings specifically developed for biomedical text and show that they lead to a better performance in this task.

A Brief Introduction to the Temporal Group LASSO and its Potential Applications in Healthcare

The Temporal Group LASSO is an example of a multi-task, regularized regression approach for the prediction of response variables that vary over time. The aim of this work is to introduce the reader to the concepts behind the Temporal Group LASSO and its related methods, as well as to the type of potential applications in a healthcare setting that the method has. We argue that the method is attractive because of its ability to reduce overfitting, select predictors, learn smooth effect patterns over time, and finally, its simplicity