Related papers: Graph Kernels exploiting Weisfeiler-Lehman Graph I…
Graph Neural Networks (GNNs), despite achieving remarkable performance across different tasks, are theoretically bounded by the 1-Weisfeiler-Lehman test, resulting in limitations in terms of graph expressivity. Even though prior works on…
Line graph transformation has been widely studied in graph theory, where each node in a line graph corresponds to an edge in the original graph. This has inspired a series of graph neural networks (GNNs) applied to transformed line graphs,…
Subgraph isomorphism counting is known as #P-complete and requires exponential time to find the accurate solution. Utilizing representation learning has been shown as a promising direction to represent substructures and approximate the…
Accurate RNA secondary structure prediction is vital for understanding cellular regulation and disease mechanisms. Deep learning (DL) methods have surpassed traditional algorithms by predicting complex features like pseudoknots and…
As a classical approach on graph learning, the propagation-aggregation methodology is widely exploited by many of Graph Neural Networks (GNNs), wherein the representation of a node is updated by aggregating representations from itself and…
Graph kernels have been successfully applied to many graph classification problems. Typically, a kernel is first designed, and then an SVM classifier is trained based on the features defined implicitly by this kernel. This two-stage…
We introduce a family of multilayer graph kernels and establish new links between graph convolutional neural networks and kernel methods. Our approach generalizes convolutional kernel networks to graph-structured data, by representing…
Graph Neural Networks (GNNs) are limited in their expressive power, struggle with long-range interactions and lack a principled way to model higher-order structures. These problems can be attributed to the strong coupling between the…
We present a unified framework to study graph kernels, special cases of which include the random walk graph kernel \citep{GaeFlaWro03,BorOngSchVisetal05}, marginalized graph kernel \citep{KasTsuIno03,KasTsuIno04,MahUedAkuPeretal04}, and…
In recent years, algorithms and neural architectures based on the Weisfeiler-Leman algorithm, a well-known heuristic for the graph isomorphism problem, emerged as a powerful tool for (supervised) machine learning with graphs and relational…
We introduce $r$-loopy Weisfeiler-Leman ($r$-$\ell{}$WL), a novel hierarchy of graph isomorphism tests and a corresponding GNN framework, $r$-$\ell{}$MPNN, that can count cycles up to length $r + 2$. Most notably, we show that…
The color refinement algorithm is mainly known as a heuristic method for graph isomorphism testing. It has surprising but natural characterizations in terms of, for example, homomorphism counts from trees and solutions to a system of linear…
Message passing graph neural networks (GNNs) are known to have their expressiveness upper-bounded by 1-dimensional Weisfeiler-Leman (1-WL) algorithm. To achieve more powerful GNNs, existing attempts either require ad hoc features, or…
The Weisfeiler-Leman algorithm ($1$-WL) is a well-studied heuristic for the graph isomorphism problem. Recently, the algorithm has played a prominent role in understanding the expressive power of message-passing graph neural networks…
Recently, the Weisfeiler-Lehman (WL) graph isomorphism test was used to measure the expressive power of graph neural networks (GNN). It was shown that the popular message passing GNN cannot distinguish between graphs that are…
Our starting point is the observation that if graphs in a class C have low descriptive complexity in first order logic, then the isomorphism problem for C is solvable by a fast parallel algorithm (essentially, by a simple combinatorial…
Graph kernels have attracted a lot of attention during the last decade, and have evolved into a rapidly developing branch of learning on structured data. During the past 20 years, the considerable research activity that occurred in the…
In recent years, kernel methods are widespread in tasks of similarity measuring. Specifically, graph kernels are widely used in fields of bioinformatics, chemistry and financial data analysis. However, existing methods, especially entropy…
In recent years, Graph Neural Network (GNN) has bloomly progressed for its power in processing graph-based data. Most GNNs follow a message passing scheme, and their expressive power is mathematically limited by the discriminative ability…
We propose a new graph-theoretic benchmark in this paper. The benchmark is developed to address shortcomings of an existing widely-used graph benchmark. We thoroughly studied a large number of traditional and contemporary graph algorithms…