Applied Topology Seminar

Using persistent homology to guide optimization has emerged as a novel application of topological data analysis. Existing methods treat persistence calculation as a black box and backpropagate gradients only onto the simplices involved in particular pairs. We show how the cycles and chains used in the persistence calculation can be used to prescribe gradients to larger subsets of the domain. In particular, we show that in a special case, which serves as a building block for general losses, the problem can be solved exactly in linear time. We present empirical experiments that show the practical benefits of our algorithm: the number of steps required for the optimization is reduced by an order of magnitude. (Joint work with Arnur Nigmetov.)

Simulating diffusion computationally allows to predict the diffusivity of materials, understand diffusion mechanisms, and to tailor-make materials such as solid-state electrolytes with desired properties aiming at developing new batteries. By studying the geometry and topology of 3-periodic scalar fields (e.g. the potential of ions in the electrolyte), we develop a cost-efficient multi-scale model for diffusion in crystalline materials. This project is a typical example of a collaboration in the overlap of topology and materials science that started as a persistent homology project and turned into something else.

There are several ways of defining the persistence diagram, but the definition using the Möbius inversion formula (for posets) offers the greatest amount of flexibility. There are now many variations of the so called Generalized Persistence Diagrams by many people.  In this talk, I will focus on the approach I am developing. I will cover the state-of-the-art and where I see this work going.

In this talk I explain the fertile relationship between the foundations of inference and learning and combinatorial geometry.

My presentation contains several powerful examples where famous theorems in discrete geometry answered natural  questions from machine learning and statistical inference:

In this tasting tour I will include the problem of deciding the existence of Maximum likelihood estimator in multiclass logistic regression, the variability of behavior of k-means algorithms with distinct random initializations and the shapes of the clusters, and the estimation of the number of samples in chance-constrained optimization models. These obviously only scratch the surface of what one could do with extra free time. Along the way we will see fascinating connections to the coupon collector problem, topological data analysis, measures of separability of data, and to the computation of Tukey centerpoints of data clouds (a high-dimensional generalization of median). All new theorems are joint work with subsets of the following wonderful folks: T. Hogan, D. Oliveros, E. Jaramillo-Rodriguez, and A. Torres-Hernandez.

Two relevant papers published/ to appear are

https://arxiv.org/abs/1907.09698https://arxiv.org/abs/1907.09698

https://arxiv.org/abs/2205.05743https://arxiv.org/abs/2205.05743

At the intersection of Topological Data Analysis and machine learning, the field of cellular signal processing has advanced rapidly in recent years. In this context, each signal on the cells of a complex is processed using the combinatorial Laplacian and the resulting Hodge decomposition. Meanwhile, discrete Morse theory has been widely used to speed up computations by reducing the size of complexes while preserving their global topological properties. In this talk, we introduce an approach to signal compression and reconstruction on complexes that leverages the tools of discrete Morse theory. The main goal is to reduce and reconstruct a cell complex together with a set of signals on its cells while preserving their global topological structure as much as possible. This is joint work with Stefania Ebli and Kelly Maggs.

The tumor microenvironment (TME) is a complex milieu around the tumor, whereby cancer cells interact with stromal, immune, vascular, and extracellular components. The TME is being increasingly recognized as a key determinant of tumor growth, disease progression, and response to therapies. We build a generalizable and robust tensor-based framework capable of integrating dissociated single-cell and spatially resolved RNA-seq data for a comprehensive analysis of the TME. Tensors are a generalization of matrices to higher dimensions. Tensor methods are known to be able to successfully incorporate data from multiple sources and perform a joint analysis of heterogeneous high-dimensional data sets. The methodologies developed as part of this effort will advance our understanding of the TME in multiple directions. These include cellular heterogeneity within the TME, crosstalks between cells, and tumor-intrinsic pathways stimulating tumor growth and immune evasion.

Here is the program.