Recent Dimensionality Reduction Techniques for High-Dimensional COVID-19 Data

Abstract

We are going through the last years of the COVID-19 pandemic, where almost the entire research community has focused on the challenges that constantly arise. From the computational and mathematical perspective, we have to deal with a dataset with ultra-high volume and ultra-high dimensionality in several experimental studies. An indicative example is DNA sequencing technologies, which offer a more realistic picture of human diseases at the molecular biology level. However, these technologies produce data with high complexity and ultra-high dimensionality. On the other hand, dimensionality reduction techniques are the first choice to address this complexity, revealing the hidden data structure in the original multidimensional space. Also, such techniques can improve the efficiency of machine learning tasks such as classification and clustering. Towards this direction, we study the behavior of seven well-known and cutting-edge dimensionality reduction techniques tailored for RNA-sequencing data. Along with the study of the effect of these algorithms, we propose the extension of the Random projection and Geodesic distance t-Stochastic Neighbor Embedding (RGt-SNE) algorithm, a recent t-Stochastic Neighbor Embedding (t-SNE) improvement. We suggest a new distance criterion for the kernel matrix construction. Our results show the potential of the proposed algorithm and, at the same time, highlight the complexity of the COVID-19 data, which are not separable, creating a significant challenge that the Machine Learning field will have to face. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.