Mime: A flexible machine-learning framework to construct and visualize models for clinical characteristics prediction and feature selection

The widespread use of high-throughput sequencing technologies has revolutionized the understanding of biology and cancer heterogeneity. Recently, several machine-learning models based on transcriptional data have been developed to accurately predict patients’ outcome and clinical response. However,...

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Bibliographic Details
Published in:Computational and structural biotechnology journal 2024-12, Vol.23, p.2798-2810
Main Authors: Liu, Hongwei, Zhang, Wei, Zhang, Yihao, Adegboro, Abraham Ayodeji, Fasoranti, Deborah Oluwatosin, Dai, Luohuan, Pan, Zhouyang, Liu, Hongyi, Xiong, Yi, Li, Wang, Peng, Kang, Wanggou, Siyi, Li, Xuejun
Format: Article
Language:English
Subjects:
GitHub
Machine learning
Mime
PIEZO1
Prediction models
R package
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Summary:The widespread use of high-throughput sequencing technologies has revolutionized the understanding of biology and cancer heterogeneity. Recently, several machine-learning models based on transcriptional data have been developed to accurately predict patients’ outcome and clinical response. However, an open-source R package covering state-of-the-art machine-learning algorithms for user-friendly access has yet to be developed. Thus, we proposed a flexible computational framework to construct a machine learning-based integration model with elegant performance (Mime). Mime streamlines the process of developing predictive models with high accuracy, leveraging complex datasets to identify critical genes associated with prognosis. An in silico combined model based on de novo PIEZO1-associated signatures constructed by Mime demonstrated high accuracy in predicting the outcomes of patients compared with other published models. Furthermore, the PIEZO1-associated signatures could also precisely infer immunotherapy response by applying different algorithms in Mime. Finally, SDC1 selected from the PIEZO1-associated signatures demonstrated high potential as a glioma target. Taken together, our package provides a user-friendly solution for constructing machine learning-based integration models and will be greatly expanded to provide valuable insights into current fields. The Mime package is available on GitHub (https://github.com/l-magnificence/Mime). [Display omitted]
ISSN:2001-0370
2001-0370
DOI:10.1016/j.csbj.2024.06.035