Biomedical Text Recognition Using Convolutional Neural Networks: Content Based Deep Learning

Sisir Joshi, Abeer Alsadoon, S. M. N. Arosha Senanayake, P. W. C. Prasad, Abdul Ghani Naim, Amr Elchouemi

Abstract: Named Entity Recognition (NER) targets to automatically detect the drug and disease mentions from biomedical texts and is fundamental step in the biomedical text mining. Although deep learning has been successfully implemented, the accuracy and processing time are still major issues preventing it from achieving NMR. This research aims to upgrade the accuracy of classification while decreasing the processing time, by paying more attention to significant areas of NMR. The novel proposed system consists of a Bi-Directional Long Short-Term Memory with Conditional Random Field (BiLSTM-CRF) using dropout strategy to effectively prevent overfitting and enhancing the generalization abilities. The system built includes the attention mechanism and attention fusion for redistributing the weight of samples belonging to each class in order to compensate the problem occurring from data imbalance and to focus only on the critical areas of the observed things and ignoring non-critical areas.