Representation learning on graphs is a fundamental problem that can be crucial in various tasks. Graph neural networks, the dominant approach for graph representation learning, are limited in their representation power. Therefore, it can be beneficial to explicitly extract and incorporate high-order topological and geometric information into these models. In this paper, we propose a principled approach to extract the rich connectivity information of graphs based on the theory of persistent homology. Our method utilizes the topological features to enhance the representation learning of graph neural networks and achieve state-of-the-art performance on various node classification and link prediction benchmarks. We also explore the option of end-to-end learning of the topological features, i.e., treating topological computation as a differentiable operator during learning. Our theoretical analysis and empirical study provide insights and potential guidelines for employing topological features in graph learning tasks.

Recent years have witnessed a surge of approaches to use neural networks to help tackle combinatorial optimization problems, including graph optimization problems. However, theoretical understanding of such approaches remains limited. In this paper, we consider the geometric setting, where graphs are induced by points in a fixed dimensional Euclidean space. We show that several graph optimization problems can be approximated by an algorithm that is polynomial in graph size n via a framework we propose, call the Baker-paradigm. More importantly, a key advantage of the Baker-paradigm is that it decomposes the input problem into (at most linear number of) small sub-problems of fixed sizes (independent of the size of the input). For the family of such fixed-size sub-problems, we can now design neural networks with universal approximation guarantees to solve them. This leads to a mixed algorithmic-ML framework, which we call NN-Baker that has the capacity to approximately solve a family of graph optimization problems (e.g, maximum independent set and minimum vertex cover) in time linear to input graph size, and only polynomial to approximation parameter. We instantiate our NN-Baker by a CNN version and GNN version, and demonstrate the effectiveness and efficiency of our approach via a range of experiments.

Local structural information can increase the adaptability of graph convolutional networks to large graphs with heterogeneous topology. Existing methods only use relatively simplistic topological information, such as node degrees.We present a novel approach leveraging advanced topological information, i.e., persistent homology, which measures the information flow efficiency at different parts of the graph. To fully exploit such structural information in real world graphs, we propose a new network architecture which learns to use persistent homology information to reweight messages passed between graph nodes during convolution. For node classification tasks, our network outperforms existing ones on a broad spectrum of graph benchmarks.

Recently a new feature representation and data analysis methodology based on a topological tool called persistent homology (and its persistence diagram summary) has gained much momentum. A series of methods have been developed to map a persistence diagram to a vector representation so as to facilitate the downstream use of machine learning tools. In these approaches, the importance (weight) of different persistence features are usually pre-set. However often in practice, the choice of the weight-function should depend on the nature of the specific data at hand. It is thus highly desirable to learn a best weight-function (and thus metric for persistence diagrams) from labelled data. We study this problem and develop a new weighted kernel, called WKPI, for persistence summaries, as well as an optimization framework to learn the weight (and thus kernel). We apply the learned kernel to the challenging task of graph classification, and show that our WKPI-based classification framework obtains similar or (sometimes significantly) better results than the best results from a range of previous graph classification frameworks on a collection of benchmark datasets.