Data reduction and data visualization for automatic diagnosis using gene expression and clinical data

Accurate diagnoses of specific diseases require, in general, the review of the whole medical history of a patient. Currently, even though many advances have been made for disease monitoring, domain experts are still requested to perform direct analyses in order to get a precise classification, thus implying significant efforts and costs. In this work we present a framework for automated diagnosis based on high-dimensional gene expression and clinical data. Given that high-dimensional data can be difficult to analyze and computationally expensive to process, we first perform data reduction to transform high-dimensional representations of data into a lower dimensional space, yet keeping them meaningful for our purposes. We used then different data visualization techniques to embed complex pieces of information in 2-D images, that are in turn used to perform diagnosis relying on deep learning approaches. Experimental analyses show that the proposed method achieves good performance, featuring a prediction Recall value between 91% and 99%.

Authors

• Pierangela Bruno
• Francesco Calimeri University of Calabria
• Alexandre Sébastien Kitanidis
• Elena De Momi

Keywords

• Classification
• Gene expression
• Heatmap
• Hot-spot map
• Convolutional neural networks