Related papers: BiScale-GTR: Fragment-Aware Graph Transformers for…

Deep learning is an important method for molecular design and exhibits considerable ability to predict molecular properties, including physicochemical, bioactive, and ADME/T (absorption, distribution, metabolism, excretion, and toxicity)…

Graph neural networks (GNNs) are a class of deep models that operate on data with arbitrary topology represented as graphs. We introduce an efficient memory layer for GNNs that can jointly learn node representations and coarsen the graph.…

Recent studies have highlighted the limitations of message-passing based graph neural networks (GNNs), e.g., limited model expressiveness, over-smoothing, over-squashing, etc. To alleviate these issues, Graph Transformers (GTs) have been…

As opposed to natural languages, source code understanding is influenced by grammatical relationships between tokens regardless of their identifier name. Graph representations of source code such as Abstract Syntax Tree (AST) can capture…

Graphs can model complicated interactions between entities, which naturally emerge in many important applications. These applications can often be cast into standard graph learning tasks, in which a crucial step is to learn low-dimensional…

Graph neural networks (GNNs) have emerged as a powerful model to capture critical graph patterns. Instead of treating them as black boxes in an end-to-end fashion, attempts are arising to explain the model behavior. Existing works mainly…

Graph Neural Networks (GNNs) have emerged as powerful tools for learning on graph-structured data, but often struggle to balance local and global information. While graph Transformers aim to address this by enabling long-range interactions,…

Most Graph Neural Networks (GNNs) propagate messages by treating node embeddings as holistic feature vectors, implicitly assuming uniform relevance across feature dimensions. This limits their ability to selectively transmit informative…

Graph Neural Networks (GNNs) are routinely used in molecular physics, social sciences, and economics to model many-body interactions in graph-like systems. However, GNNs are inherently local and can suffer from information flow bottlenecks.…

Graph neural networks (GNNs) are widely used as surrogates for costly experiments and first-principles simulations to study the behavior of compounds at atomistic scale, and their architectural complexity is constantly increasing to enable…

Much of the recent work on learning molecular representations has been based on Graph Convolution Networks (GCN). These models rely on local aggregation operations and can therefore miss higher-order graph properties. To remedy this, we…

Elucidating and accurately predicting the druggability and bioactivities of molecules plays a pivotal role in drug design and discovery and remains an open challenge. Recently, graph neural networks (GNN) have made remarkable advancements…

Recently many efforts have been devoted to applying graph neural networks (GNNs) to molecular property prediction which is a fundamental task for computational drug and material discovery. One of major obstacles to hinder the successful…

Graph Neural Networks (GNNs) have emerged as promising solutions for collaborative filtering (CF) through the modeling of user-item interaction graphs. The nucleus of existing GNN-based recommender systems involves recursive message passing…

Modern sequence models (e.g., Transformers, linear RNNs, etc.) emerged as dominant backbones of recent deep learning frameworks, mainly due to their efficiency, representational power, and/or ability to capture long-range dependencies.…

Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top…

Representation learning on text-attributed graphs (TAGs) has attracted significant interest due to its wide-ranging real-world applications, particularly through Graph Neural Networks (GNNs). Traditional GNN methods focus on encoding the…

The graph neural network (GNN) has been a powerful deep-learning tool in chemistry domain, due to its close connection with molecular graphs. Most GNN models collect and update atom and molecule features from the fed atom (and, in some…

Subgraph pattern detection aims to uncover complex interaction structures in graphs. However, state-of-the-art graph neural network (GNN)-based solutions assume centralized access to the entire graph. When graphs are instead distributed…

Graph convolutional networks (GCNs) allow us to learn topologically-aware node embeddings, which can be useful for classification or link prediction. However, they are unable to capture long-range dependencies between nodes without adding…