MSc Thesis Proposal of Narinder Pal Singh:"Structuring gene expression data for classification of disease subtypes in Deep Neural Networks "

 

Date: Monday April 19th 2021 

Time:  12:30 PM to 02:30 PM 

Meeting URL:  https://zoom.us/j/94371113926?from=addon 

Passcode:      If interested in attending this event, contact the graduate secretary at csgradinfo@uwindsor.ca

 

 

The introduction of genetic testing has profoundly enhanced the prospects of early detection of diseases and techniques to suggest precision medicines. The subtyping of critical diseases has proven to be an essential part of the development of individualized therapies and has led to deeper insights into the heterogeneity of the disease. Studies suggest that variants in particular genes have significant effects on certain types of immune system cells and are also involved in the risk of certain critical illnesses like cancer. By analyzing the genetic sequence of a patient, disease types and subtypes can be predicted. Recent research work has shown that the CNN's prediction quality within this context using gene intensity features could be improved when the input is structured into 2D images via transformations like kPCA, t-SNE, etc., to express certain types of relationships among the intensity features. Considering the increased computational complexity in transforming 1D data to images, we propose to induce similar relationships among the gene intensity features by way of 1D ordering to preserve the simplicity inherent to original gene data. The heterogeneity between the gene data and the clinical data is handled by feeding the latter directly into the fully connected layers. We will get more insight into the impact of different structuring techniques on the prediction quality in terms of CNN, RNN, and their combination. We will be applying our approach to The Cancer Genome Atlas (TCGA) dataset for cancer subtypes and compare our method with the state-of-the-art. 

 

Keywords: Convolutional neural networks, cancer subtype classification, HGNC data, RNA Seq, precision medicine 

 

Internal Reader: Dr. Ahmad Biniaz            

External Reader: Dr. Balakumar Balasingan           

Advisor: Dr. Jessica Chen