MRMD3.0: A Python Tool and Webserver for Dimensionality Reduction and Data Visualization via an Ensemble Strategy

Abstract

Dimensionality reduction is a hot topic in machine learning that can help researchers find key features from complex medical or biological data, which is crucial for biological sequence research, drug development, etc. However, when applied to specific datasets, different dimensionality reduction methods generate different results, which produces instability and makes tuning the parameters a time-consuming task. Exploring high quality features, genes, or attributes from complex data is an important task and challenge. To ensure the efficiency, robustness, and accuracy of experiments, in this work, we developed a dimensionality reduction tool MRMD3.0 based on the ensemble strategy of link analysis. It is mainly divided into two steps: first, the ensemble method is used to integrate different feature ranking algorithms to calculate feature importance, and then the forward feature search strategy combined with cross-validation is used to explore the proper feature combination. Compared with the previously developed version, MRMD3.0 has added more link-based ensemble algorithms, including PageRank, HITS, LeaderRank, and TrustRank. At the same time, more feature ranking algorithms have been added, and their effect and calculation speed have been greatly improved. In addition, the newest version provides an interface used by each feature ranking method and five kinds of charts to help users analyze features. Finally, we also provide an online webserver to help researchers analyze the data.Availability and implementationWebserver: http://lab.malab.cn/soft/MRMDv3/home.html.GitHub: https://github.com/heshida01/MRMD3.0.