MLOmics: Cancer Multi-Omics Database for Machine Learning

Ziwei Yang; Rikuto Kotoge; Xihao Piao; Zheng Chen; Lingwei Zhu; Peng Gao; Yasuko Matsubara; Yasushi Sakurai; Jimeng Sun

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arXiv · 2409.02143

MLOmics: Cancer Multi-Omics Database for Machine Learning

Ziwei Yang·Rikuto Kotoge·Xihao Piao·Zheng Chen·Lingwei Zhu·Peng Gao·Yasuko Matsubara·Yasushi Sakurai·Jimeng Sun

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Abstract

Framing the investigation of diverse cancers as a machine learning problem has recently shown significant potential in multi-omics analysis and cancer research. Empowering these successful machine learning models are the high-quality training datasets with sufficient data volume and adequate preprocessing. However, while there exist several public data portals, including The Cancer Genome Atlas (TCGA) multi-omics initiative or open-bases such as the LinkedOmics, these databases are not off-the-shelf for existing machine learning models. In this paper, we introduce MLOmics, an open cancer multi-omics database aiming at serving better the development and evaluation of bioinformatics and machine learning models. MLOmics contains 8,314 patient samples covering all 32 cancer types with four omics types, stratified features, and extensive baselines. Complementary support for downstream analysis and bio-knowledge linking are also included to support interdisciplinary analysis.

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Ziwei Yang, Rikuto Kotoge, Xihao Piao, Zheng Chen, Lingwei Zhu, Peng Gao, Yasuko Matsubara, Yasushi Sakurai, Jimeng Sun. 2025-06-16. MLOmics: Cancer Multi-Omics Database for Machine Learning. https://arxiv.org/abs/2409.02143

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