Title: Modern Nonlinear Embedding Methods Unpacked
Abstract: Learning and representing low-dimensional structures from noisy, high-dimensional data is a cornerstone of modern data science. Stochastic neighbor embedding algorithms, a family of nonlinear dimensionality reduction and data visualization methods, with t-SNE and UMAP as two leading examples, have become very popular in recent years. Yet despite their wide applications, these methods remain subject to points of debate, including limited theoretical understanding, ambiguous interpretations, and sensitivity to tuning parameters. In this talk, I will present our recent efforts to decipher and improve these nonlinear embedding approaches. Our key results include a rigorous theoretical framework that uncovers the intrinsic mechanisms, large-sample limits, and fundamental principles underlying these algorithms; a set of theory-informed practical guidelines for their principled use in trustworthy biological discovery; and a collection of new algorithms that address current limitations and improve performance in areas such as bias reduction and stability. Throughout the talk, I will highlight how these advances not only deepen our theoretical understanding but also open new avenues for scientific discovery.