SUPREME: A cancer subtype prediction methodology integrating multiomics data using Graph Convolutional Neural Network

To pave the road towards precision medicine in cancer, patients with highly similar biology ought to be grouped into the same cancer subtypes. Utilizing high-dimensional multiomics datasets, several integrative computational approaches have been developed to uncover cancer subtypes. Recently, Graph Neural Networks (GNNs) was discovered to learn node embeddings while utilizing node features and node associations at the same time on graph-structured data. Although there are some commonly used architectures such as Graph Convolutional Network (GCN) for cancer subtype prediction, the existing prediction tools have some limitations in leveraging those architectures with multiomics integration on multiple networks. Addressing them, we developed SUPREME..

To learn more about our study, read the preprint version of the manuscript on BioRxiv: https://doi.org/10.1101/2022.08.03.502682.

Github link for the tool: https://github.com/ziynet/SUPREME

How to cite SUPREME

Bibtex: @article{kesimoglu2022supreme, title={SUPREME: A cancer subtype prediction methodology integrating multiomics data using Graph Convolutional Neural Network}, author={Kesimoglu, Ziynet Nesibe and Bozdag, Serdar}, journal={bioRxiv}, year={2022}, publisher={Cold Spring Harbor Laboratory} }

MLA: Kesimoglu, Ziynet Nesibe, and Serdar Bozdag. “SUPREME: A cancer subtype prediction methodology integrating multiomics data using Graph Convolutional Neural Network.” bioRxiv (2022).

APA: Kesimoglu, Z. N., & Bozdag, S. (2022). SUPREME: A cancer subtype prediction methodology integrating multiomics data using Graph Convolutional Neural Network. bioRxiv.

ISO690: KESIMOGLU, Ziynet Nesibe; BOZDAG, Serdar. SUPREME: A cancer subtype prediction methodology integrating multiomics data using Graph Convolutional Neural Network. bioRxiv, 2022.

Previous events for SUPREME

Paper @ Preprint version on BioRxiv (Paper link)

Talk @ OxML (Oxford Machine Learning) Summer School 2022 – Unconference Track – given at 10:00 am (CT) on August 3rd, 2022.

Talk and Poster Presentation @ 2022 ISMB (Intelligent Systems for Molecular Biology) – MLCSB COSI – given at 11:45 am (CT) on July 14th, 2022.

Invited Talk @ BH-BINGEN Technical University in Germany – Bits & Chips Seminar Series – given at December 8th, 2021.

Talk @ 2021 ACM-BCB (ACM Conference on Bioinformatics, Computational Biology, and Health Informatics)

Poster Presentation @ 2017 Forward Thinking Poster Session/Colloquy

For any questions/issues about SUPREME, please feel free to comment or send an email to ‘admin (at) ziynetnesibe (dot) com’

Thank you!