TREPH: A Plug-In Topological Layer for Graph Neural Networks

Abstract

Topological Data Analysis (TDA) is an approach to analyzing the shape of data using techniques from algebraic topology. The staple of TDA is Persistent Homology (PH). Recent years have seen a trend of combining PH and Graph Neural Networks (GNNs) in an end-to-end manner to capture topological features from graph data. Though effective, these methods are limited by the shortcomings of PH: incomplete topological information and irregular output format. Extended Persistent Homology (EPH), as a variant of PH, addresses these problems elegantly. In this paper, we propose a plug-in topological layer for GNNs, termed Topological Representation with Extended Persistent Homology (TREPH). Taking advantage of the uniformity of EPH, a novel aggregation mechanism is designed to collate topological features of different dimensions to the local positions determining their living processes. The proposed layer is provably differentiable and more expressive than PH-based representations, which in turn is strictly stronger than message-passing GNNs in expressive power. Experiments on real-world graph classification tasks demonstrate the competitiveness of TREPH compared with the state-of-the-art approaches.