Kernel principal components based cascade forest towards disease identification with human microbiota

Background Numerous pieces of clinical evidence have shown that many phenotypic traits of human disease are related to their gut microbiome, i.e., inflammation, obesity, HIV, and diabetes. Through supervised classification, it is feasible to determine the human disease states by revealing the intestinal microbiota compositional information. However, the abundance matrix of microbiome data is so sparse, an interpretable deep model is crucial to further represent and mine the data for expansion, such as the deep forest model. What’s more, overfitting can still exist in the original deep forest model when dealing with such “large p, small n” biology data. Feature reduction is considered to improve the ensemble forest model especially towards the disease identification in the human microbiota. Methods In this work, we propose the kernel principal components based cascade forest method, so-called KPCCF, to classify the disease states of patients by using taxonomic profiles of the microbiome at the family level. In detail, the kernel principal components analysis method is first used to reduce the original dimension of human microbiota datasets. Besides, the processed data is fed into the cascade forest to preliminarily discriminate against the disease state of the samples. Results The proposed KPCCF algorithm can represent the small-scale and high-dimension human microbiota datasets with the sparse feature matrix. Systematic comparison experiments demonstrate that our method consistently outperforms the state-of-the-art methods with the comparative study on 4 datasets. Conclusion Despite sharing some common characteristics, a one-size-fits-all solution does not exist in any space. The traditional depth model has limitations in the biological application of the unbalanced scale between small samples and high dimensions. KPCCF distinguishes from the standard deep forest model for its excellent performance in the microbiota field. Additionally, compared to other dimensionality reduction methods, the kernel principal components analysis method is more suitable for microbiota datasets.