skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


This content will become publicly available on March 26, 2026

Title: TopoBench: A Framework for Benchmarking Topological Deep Learning
This work introduces TopoBench, an open-source library designed to standardize benchmarking and accelerate research in topological deep learning (TDL). TopoBench decomposes TDL into a sequence of independent modules for data generation, loading, transforming and processing, as well as model training, optimization and evaluation. This modular organization provides flexibility for modifications and facilitates the adaptation and optimization of various TDL pipelines. A key feature of TopoBench is its support for transformations and lifting across topological domains. Mapping the topology and features of a graph to higher-order topological domains, such as simplicial and cell complexes, enables richer data representations and more fine-grained analyses. The applicability of TopoBench is demonstrated by benchmarking several TDL architectures across diverse tasks and datasets.  more » « less
Award ID(s):
2240158
PAR ID:
10625573
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more » ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; « less
Publisher / Repository:
Data-centric Machine Learning Research
Date Published:
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Topological deep learning (TDL) has emerged as a powerful tool for modeling higher-order interactions in relational data. However, phenomena such as over- squashing in topological message-passing remain understudied and lack theoreti- cal analysis. We propose a unifying axiomatic framework that bridges graph and topological message-passing by viewing simplicial and cellular complexes and their message-passing schemes through the lens of relational structures. This ap- proach extends graph-theoretic results and algorithms to higher-order structures, facilitating the analysis and mitigation of oversquashing in topological message- passing networks. Through theoretical analysis and empirical studies on simplicial networks, we demonstrate the potential of this framework to advance TDL. 
    more » « less
  2. Abstract The fast evolution of SARS-CoV-2 and other infectious viruses poses a grand challenge to the rapid response in terms of viral tracking, diagnostics, and design and manufacture of monoclonal antibodies (mAbs) and vaccines, which are both time-consuming and costly. This underscores the need for efficient computational approaches. Recent advancements, like topological deep learning (TDL), have introduced powerful tools for forecasting emerging dominant variants, yet they require deep mutational scanning (DMS) of viral surface proteins and associated three-dimensional (3D) protein–protein interaction (PPI) complex structures. We propose an AlphaFold 3 (AF3)-assisted multi-task topological Laplacian (MT-TopLap) strategy to address this need. MT-TopLap combines deep learning with TDA models, such as persistent Laplacians (PL) to extract detailed topological and geometric characteristics of PPIs, thereby enhancing the prediction of DMS and binding free energy (BFE) changes upon virus mutations. Validation with four experimental DMS datasets of SARS-CoV-2 spike receptor-binding domain (RBD) and the human angiotensin-converting enzyme-2 (ACE2) complexes indicates that our AF3-assisted MT-TopLap strategy maintains robust performance, with only an average 1.1% decrease in Pearson correlation coefficients (PCC) and an average 9.3% increase in root mean square errors (RMSE), compared with the use of experimental structures. Additionally, AF3-assisted MT-TopLap achieved a PCC of 0.81 when tested with a SARS-CoV-2 HK.3 variant DMS dataset, confirming its capability to accurately predict BFE changes and adapt to new experimental data, thereby showcasing its potential for rapid and effective response to fast viral evolution. 
    more » « less
  3. Abstract Over the past decade, the usefulness of quantum annealing hardware for combinatorial optimization has been the subject of much debate. Thus far, experimental benchmarking studies have indicated that quantum annealing hardware does not provide an irrefutable performance gain over state-of-the-art optimization methods. However, as this hardware continues to evolve, each new iteration brings improved performance and warrants further benchmarking. To that end, this work conducts an optimization performance assessment of D-Wave Systems’Advantage Performance Updatecomputer, which can natively solve sparse unconstrained quadratic optimization problems with over 5,000 binary decision variables and 40,000 quadratic terms. We demonstrate that classes of contrived problems exist where this quantum annealer can provide run time benefits over a collection of established classical solution methods that represent the current state-of-the-art for benchmarking quantum annealing hardware. Although this workdoes notpresent strong evidence of an irrefutable performance benefit for this emerging optimization technology, it does exhibit encouraging progress, signaling the potential impacts on practical optimization tasks in the future. 
    more » « less
  4. Topological data analysis (TDA) has proven to be a potent approach for extracting intricate topological structures from complex and high-dimensional data. In this paper, we propose a TDA-based processing pipeline for analyzing multi-channel scalp EEG data. The pipeline starts with extracting both frequency and temporal information from the signals via the Hilbert–Huang Transform. The sequences of instantaneous frequency and instantaneous amplitude across all electrode channels are treated as approximations of curves in the high-dimensional space. TDA features, which represent the local topological structure of the curves, are further extracted and used in the classification models. Three sets of scalp EEG data, including one collected in a lab and two Brain–computer Interface (BCI) competition data, were used to validate the proposed methods, and compare with other state-of-art TDA methods. The proposed TDA-based approach shows superior performance and outperform the winner of the BCI competition. Besides BCI, the proposed method can also be applied to spatial and temporal data in other domains such as computer vision, remote sensing, and medical imaging. 
    more » « less
  5. Representation learning in high-dimensional spaces faces significant robustness challenges with noisy inputs, particularly with heavy-tailed noise. Arguing that topological data analysis (TDA) offers a solution, we leverage TDA to enhance representation stability in neural networks. Our theoretical analysis establishes conditions under which incorporating topological summaries improves robustness to input noise, especially for heavy-tailed distributions. Extending these results to representation-balancing methods used in causal inference, we propose the *Topology-Aware Treatment Effect Estimation* (TATEE) framework, through which we demonstrate how topological awareness can lead to learning more robust representations. A key advantage of this approach is that it requires no ground-truth or validation data, making it suitable for observational settings common in causal inference. The method remains computationally efficient with overhead scaling linearly with data size while staying constant in input dimension. Through extensive experiments with -stable noise distributions, we validate our theoretical results, demonstrating that TATEE consistently outperforms existing methods across noise regimes. This work extends stability properties of topological summaries to representation learning via a tractable framework scalable for high-dimensional inputs, providing insights into how it can enhance robustness, with applications extending to domains facing challenges with noisy data, such as causal inference. 
    more » « less