Title: Understanding How Dimension Reduction Tools Work
Abstract: Dimension reduction (DR) techniques such as t-SNE, UMAP, and TriMap have demonstrated impressive visualization performance on many real world datasets. They are useful for understanding data and trustworthy decision-making, particularly for biological data. One tension that has always faced these methods is the trade-off between preservation of global structure and preservation of local structure: past methods can either handle one or the other, but not both. In this work, our main goal is to understand what aspects of DR methods are important for preserving both local and global structure: it is difficult to design a better method without a true understanding of the choices we make in our algorithms and their empirical impact on the lower-dimensional embeddings they produce. Towards the goal of local structure preservation, we provide several useful design principles for DR loss functions based on our new understanding of the mechanisms behind successful DR methods. Towards the goal of global structure preservation, our analysis illuminates that the choice of which components to preserve is important. We leverage these insights to design a new algorithm for DR, called Pairwise Controlled Manifold Approximation Projection (PaCMAP), which preserves both local and global structure. Our work provides several unexpected insights into what design choices both to make and avoid when constructing DR algorithms.
This talk will be based on the following papers.
Yingfan Wang, Haiyang Huang, Cynthia Rudin, Yaron Shaposhnik
Understanding How Dimension Reduction Tools Work: An Empirical Approach to Deciphering t-SNE, UMAP, TriMAP, and PaCMAP for Data Visualization
Journal of Machine Learning Research (JMLR), 2021
https://jmlr.org/papers/v22/20-1061.html
Haiyang Huang, Yingfan Wang, Cynthia Rudin, and Edward P. Browne
Towards a Comprehensive Evaluation of Dimension Reduction Methods for Transcriptomic Data Visualization
Communications Biology (Nature), 2022.
https://www.nature.com/articles/s42003-022-03628-x