Related papers: What Ails Generative Structure-based Drug Design: …

This letter proposes a graph neural network (GNN)-based framework for statistical precoder design that leverages model-based insights to compactly represent statistical knowledge, resulting in efficient, lightweight architectures. The…

Drug Discovery is a fundamental and ever-evolving field of research. The design of new candidate molecules requires large amounts of time and money, and computational methods are being increasingly employed to cut these costs. Machine…

Symbolic regression (SR) with genetic programming (GP) aims to discover interpretable mathematical expressions directly from data. Despite its strong empirical success, the theoretical understanding of why GP-based SR generalizes beyond the…

Generative models for structure-based drug design (SBDD) have shown promising results in recent years. Existing works mainly focus on how to generate molecules with higher binding affinity, ignoring the feasibility prerequisites for…

Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…

Graph diffusion generative models (GDGMs) have emerged as powerful tools for generating high-quality graphs. However, their broader adoption faces challenges in \emph{scalability and size generalization}. GDGMs struggle to scale to large…

Structure-based drug design (SBDD) stands at the forefront of drug discovery, emphasizing the creation of molecules that target specific binding pockets. Recent advances in this area have witnessed the adoption of deep generative models and…

Recently, there have been some breakthroughs in graph analysis by applying the graph neural networks (GNNs) following a neighborhood aggregation scheme, which demonstrate outstanding performance in many tasks. However, we observe that the…

Predicting drug-gene associations is crucial for drug development and disease treatment. While graph neural networks (GNN) have shown effectiveness in this task, they face challenges with data sparsity and efficient contrastive learning…

Discrete graph generation has emerged as a powerful paradigm for modeling graph data, often relying on highly expressive neural backbones such as transformers or higher-order architectures. We revisit this design choice by introducing…

To design a drug given a biological molecule by using deep learning methods, there are many successful models published recently. People commonly used generative models to design new molecules given certain protein. LiGAN was regarded as…

Predicting drug side-effects before they occur is a key task in keeping the number of drug-related hospitalizations low and to improve drug discovery processes. Automatic predictors of side-effects generally are not able to process the…

Predicting interactions between structured entities lies at the core of numerous tasks such as drug regimen and new material design. In recent years, graph neural networks have become attractive. They represent structured entities as graphs…

As powerful tools for representation learning on graphs, graph neural networks (GNNs) have facilitated various applications from drug discovery to recommender systems. Nevertheless, the effectiveness of GNNs is immensely challenged by…

This extended abstract describes a framework for analyzing the expressiveness, learning, and (structural) generalization of hypergraph neural networks (HyperGNNs). Specifically, we focus on how HyperGNNs can learn from finite datasets and…

In this work, we introduce a method to fine-tune a Transformer-based generative model for molecular de novo design. Leveraging the superior sequence learning capacity of Transformers over Recurrent Neural Networks (RNNs), our model can…

Research on the theoretical expressiveness of Graph Neural Networks (GNNs) has developed rapidly, and many methods have been proposed to enhance the expressiveness. However, most methods do not have a uniform expressiveness measure except…

Graph Neural Networks (GNNs) have attracted increasing attention in recent years and have achieved excellent performance in semi-supervised node classification tasks. The success of most GNNs relies on one fundamental assumption, i.e., the…

Graph Neural Networks (GNNs) have achieved remarkable performance in a wide range of graph-related learning tasks. However, explaining their predictions remains a challenging problem, especially due to the mismatch between the graphs used…

Incorporating spectral information to enhance Graph Neural Networks (GNNs) has shown promising results but raises a fundamental challenge due to the inherent ambiguity of eigenvectors. Various architectures have been proposed to address…