Related papers: Simplicial Message Passing for Chemical Property P…

The recent success of graph neural networks has significantly boosted molecular property prediction, advancing activities such as drug discovery. The existing deep neural network methods usually require large training dataset for each…

The goal of this paper is to establish the fundamental tools to analyze signals defined over a topological space, i.e. a set of points along with a set of neighborhood relations. This setup does not require the definition of a metric and…

Graph Neural Networks (GNNs) excel at learning from graph-structured data but are limited to modeling pairwise interactions, insufficient for capturing higher-order relationships present in many real-world systems. Topological Deep Learning…

Message-passing graph neural networks (MPNNs) and structural features (SFs) are cornerstones for the link prediction task. However, as a common and intuitive mode of understanding, the potential of visual perception has been overlooked in…

Graph Neural Networks (GNNs) often struggle to capture the link-specific structural patterns crucial for accurate link prediction, as their node-centric message-passing schemes overlook the subgraph structures connecting a pair of nodes.…

Recent scene graph generation (SGG) frameworks have focused on learning complex relationships among multiple objects in an image. Thanks to the nature of the message passing neural network (MPNN) that models high-order interactions between…

Message-passing neural networks (MPNNs) often suffer from an information bottleneck when capturing long-range dependencies, leading to the oversquashing (OSQ) phenomenon. Alongside spatial connectivity enrichment (e.g., rewiring), recent…

We propose Dynamically Pruned Message Passing Networks (DPMPN) for large-scale knowledge graph reasoning. In contrast to existing models, embedding-based or path-based, we learn an input-dependent subgraph to explicitly model reasoning…

Explaining graph neural networks (GNNs) has become more and more important recently. Higher-order interpretation schemes, such as GNN-LRP (layer-wise relevance propagation for GNN), emerged as powerful tools for unraveling how different…

Machine learning (ML) is revolutionizing protein structural analysis, including an important subproblem of predicting protein residue contact maps, i.e., which amino-acid residues are in close spatial proximity given the amino-acid sequence…

Message Passing Neural Networks (MPNNs) are widely used for learning on graphs, but their ability to process long-range information is limited by the phenomenon of oversquashing. This limitation has led some researchers to advocate Graph…

Message passing neural networks (MPNNs) are powerful models for node classification but suffer from performance limitations under heterophily (low same-class connectivity) and structural bottlenecks in the graph. We provide a unifying…

Graph Neural Networks (GNNs) are the subject of intense focus by the machine learning community for problems involving relational reasoning. GNNs can be broadly divided into spatial and spectral approaches. Spatial approaches use a form of…

Developing methods to process irregularly structured data is crucial in applications like gene-regulatory, brain, power, and socioeconomic networks. Graphs have been the go-to algebraic tool for modeling the structure via nodes and edges…

When studying interacting systems, computing their statistical properties is a fundamental problem in various fields such as physics, applied mathematics, and machine learning. However, this task can be quite challenging due to the…

In this paper, we strive to develop an interpretable GNNs' inference paradigm, termed MSInterpreter, which can serve as a plug-and-play scheme readily applicable to various GNNs' baselines. Unlike the most existing explanation methods,…

Time series modeling, a crucial area in science, often encounters challenges when training Machine Learning (ML) models like Recurrent Neural Networks (RNNs) using the conventional mini-batch training strategy that assumes independent and…

Graph neural networks (GNNs) have been widely used to learn vector representation of graph-structured data and achieved better task performance than conventional methods. The foundation of GNNs is the message passing procedure, which…

Topological deep learning (TDL) is a rapidly growing field that seeks to leverage topological structure in data and facilitate learning from data supported on topological objects, ranging from molecules to 3D shapes. Most TDL architectures…

Molecular property prediction (MPP) is a cornerstone of drug discovery and materials science, yet conventional deep learning approaches depend on large labeled datasets that are often unavailable. Few-shot Molecular property prediction…