R-PathCluster: Identifying cancer subtype of glioblastoma multiforme using pathway-based Restricted Boltzmann Machine Conference Paper
| Authors: | Mallavarapu, T.; Kim, Y.; Oh, J. H.; Kang, M. |
| Editors: | Hu, X.; Shyu, C. R.; Bromberg, Y.; Gao, J.; Gong, Y.; Korkin, D.; Yoo, I.; Zheng, J. H. |
| Title: | R-PathCluster: Identifying cancer subtype of glioblastoma multiforme using pathway-based Restricted Boltzmann Machine |
| Conference Title: | 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) |
| Abstract: | Glioblastoma multiforme (GBM) is the most fatal malignant type of brain tumor with a very poor prognosis with a median survival of around one year. Numerous studies have reported tumor subtypes that consider different characteristics on individual patients, which may play important roles in determining the survival rates in GBM. In this study, we present a pathway-based clustering method using Restricted Boltzmann Machine (RBM), called R-PathCluster, for identifying unknown subtypes with pathway markers of gene expressions. In order to assess the performance of R-PathCluster, we conducted experiments with several clustering methods such as k-means, hierarchical clustering, and RBM models with different input data. R-PathCluster showed the best performance in clustering long-term and short-term survivals, although its clustering score was not the highest among them in experiments. R-PathCluster provides a solution to interpret the model in biological sense, since it takes pathway markers that represent biological process of pathways. We discussed that our findings from R-PathCluster are supported by many biological literatures. © 2017 IEEE. |
| Keywords: | cluster analysis; gene expression; tumors; diagnosis; glioblastoma multiforme; bioinformatics; biological process; clustering; tumor subtypes; clustering methods; restricted boltzmann machine; biological literatures; hier-archical clustering |
| Journal Title | Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine |
| Conference Dates: | 2017 Nov 13-16 |
| Conference Location: | Kansas City, MO |
| ISBN: | 978-1-5090-3049-1 |
| Publisher: | IEEE |
| Date Published: | 2017-01-01 |
| Start Page: | 1183 |
| End Page: | 1188 |
| Language: | English |
| DOI: | 10.1109/BIBM.2017.8217825 |
| PROVIDER: | scopus |
| DOI/URL: | |
| Notes: | Conference Paper -- Export Date: 1 June 2018 -- Source: Scopus |
