Tree Based Advanced Relative Expression Analysis [chapter]

Marcin Czajkowski, Krzysztof Jurczuk, Marek Kretowski
2020 Lecture Notes in Computer Science  
This paper presents a new concept for biomarker discovery and gene expression data classification that rises from the Relative Expression Analysis (RXA). The basic idea of RXA is to focus on simple ordering relationships between the expression of small sets of genes rather than their raw values. We propose a paradigm shift as we extend RXA concept to tree-based Advanced Relative Expression Analysis (ARXA). The main contribution is a decision tree with splitting nodes that consider relative
more » ... ion comparisons between multiple gene pairs. In addition, to face the enormous computational complexity of RXA, the most time-consuming part which is scoring all possible gene pairs in each splitting node is parallelized using GPU. This way the algorithm allows searching for more tailored interactions between sub-groups of genes in a reasonable time. Experiments carried out on 8 cancer-related datasets show not only significant improvement in accuracy and speed of our approach in comparison to various RXA solutions but also new interesting patterns between subgroups of genes.
doi:10.1007/978-3-030-50420-5_37 fatcat:ygf7xp4gyjftbk64eevltopwf4