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We challenge black-box purely deep neural approaches for molecules and graph generation, which are limited in controllability and lack formal guarantees. We introduce Neuro-Symbolic Graph Generative Modeling (NSGGM), a neurosymbolic…

This work focuses on training graph foundation models (GFMs) that have strong generalization ability in graph-level tasks such as graph classification. Effective GFM training requires capturing information consistent across different…

Stochastic process-based molecular graph generators have become the state of the art for template-free single-step retrosynthesis. However, these models are typically trained only on product-reactant pairs, thereby acquiring…

Graph Transformer has demonstrated impressive capabilities in the field of graph representation learning. However, existing approaches face two critical challenges: (1) most models suffer from exponentially increasing computational…

Advances in machine learning have led to graph neural network-based methods for drug discovery, yielding promising results in molecular design, chemical synthesis planning, and molecular property prediction. However, current graph neural…

Molecular representation learning plays a crucial role in various downstream tasks, such as molecular property prediction and drug design. To accurately represent molecules, Graph Neural Networks (GNNs) and Graph Transformers (GTs) have…

Unlike vision and language data which usually has a unique format, molecules can naturally be characterized using different chemical formulations. One can view a molecule as a 2D graph or define it as a collection of atoms located in a 3D…

Introduction: molecular geometry, the three-dimensional arrangement of atoms within a molecule, is fundamental to understanding chemical reactivity, physical properties, and biological activity. The prevailing models used to describe…

Discrete-Time Dynamic Graphs (DTDGs), which are prevalent in real-world implementations and notable for their ease of data acquisition, have garnered considerable attention from both academic researchers and industry practitioners. The…

The Transformer architecture has become a dominant choice in many domains, such as natural language processing and computer vision. Yet, it has not achieved competitive performance on popular leaderboards of graph-level prediction compared…

Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in…

Predicting molecular properties is essential for drug discovery, and computational methods can greatly enhance this process. Molecular graphs have become a focus for representation learning, with Graph Neural Networks (GNNs) widely used.…

Multimodal molecular representation learning, which jointly models molecular graphs and their textual descriptions, enhances predictive accuracy and interpretability by enabling more robust and reliable predictions of drug toxicity,…

Machine learning on graphs is an important and ubiquitous task with applications ranging from drug design to friendship recommendation in social networks. The primary challenge in this domain is finding a way to represent, or encode, graph…

In recent years, deep generative models for graphs have been used to generate new molecules. These models have produced good results, leading to several proposals in the literature. However, these models may have troubles learning some of…

Combination therapy has shown to improve therapeutic efficacy while reducing side effects. Importantly, it has become an indispensable strategy to overcome resistance in antibiotics, anti-microbials, and anti-cancer drugs. Facing enormous…

Contemporary graph learning algorithms are not well-defined for large molecules since they do not consider the hierarchical interactions among the atoms, which are essential to determine the molecular properties of macromolecules. In this…

Molecular graph neural networks (GNNs) often focus exclusively on XYZ-based geometric representations and thus overlook valuable chemical context available in public databases like PubChem. This work introduces a multimodal framework that…

GNN-based methods have achieved excellent results as a mainstream task in drug response prediction tasks in recent years. Traditional GNN methods use only the atoms in a drug molecule as nodes to obtain the representation of the molecular…

We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning…