P. Stomma, W. R. Rudnicki. HCS—hierarchical algorithm for simulation of omics datasets, Bioinformatics, Volume 40, Issue Supplement_2, September 2024, Pages ii98–ii104, https://doi.org/10.1093/bioinformatics/btae392

Analysis of the omics data with the help of machine learning (ML) methods is limited by small sample sizes and a large number of variables. One possible approach to deal with such data is using algorithms for feature selection and reducing the dataset to include only those variables that are related to the studied phenomena. Existing simulators of the omics data were mostly developed with the goal of improving the methods for generations of high-quality data, that correspond with the highest possible fidelity to the real level of molecular markers in the biological materials. The current study aims to simulate the data on a higher level of generalization. Such datasets can then be used to perform tests of the feature selection and ML algorithms on systems that have structures mimicking those of real data, but where the ground truth may be implanted by design. They can also be used to generate contrast variables with the desired correlation structure for the feature selection. We proposed the algorithm for the reconstruction of the omic dataset that, with high fidelity, preserves the correlation structure of the original data with a reduced number of parameters. It is based on the hierarchical clustering of variables and uses principal components of the clusters. It reproduces well topological descriptors of the correlation structure. The correlation structure of the principal components of the clusters then is used to obtain datasets with correlation structures similar to the original data but not correlated with the original variables.Availability and implementation

The code and data is available at: https://github.com/p100mma/hcrs_omics.