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

Currently, the field of structure-based drug design is dominated by three main types of algorithms: search-based algorithms, deep generative models, and reinforcement learning. While existing works have typically focused on comparing models…

Deep graph generative modeling has proven capable of learning the distribution of complex, multi-scale structures characterizing real-world graphs. However, one of the main limitations of existing methods is their large output space, which…

Graph representation learning has now become the de facto standard when handling graph-structured data, with the framework of message-passing graph neural networks (MPNN) being the most prevailing algorithmic tool. Despite its popularity,…

Subgraph GNNs enhance message-passing GNNs expressivity by representing graphs as sets of subgraphs, demonstrating impressive performance across various tasks. However, their scalability is hindered by the need to process large numbers of…

Graph neural networks (GNNs) are powerful graph-based deep-learning models that have gained significant attention and demonstrated remarkable performance in various domains, including natural language processing, drug discovery, and…

Graph neural networks (GNNs) have emerged as powerful tools for learning protein structures by capturing spatial relationships at the residue level. However, existing GNN-based methods often face challenges in learning multiscale…

Recently, deep generative models for molecular graphs are gaining more and more attention in the field of de novo drug design. A variety of models have been developed to generate topological structures of drug-like molecules, but…

Structure-based drug design (SBDD) focuses on designing small-molecule ligands that bind to specific protein pockets. Computational methods are integral in modern SBDD workflows and often make use of virtual screening methods via docking or…

Structure-Based drug design (SBDD) has emerged as a popular approach in drug discovery, leveraging three-dimensional protein structures to generate drug ligands. However, existing generative models encounter several key challenges: (1)…

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…

Graph Neural Networks (GNNs) have emerged as a promising approach for ``learning to branch'' in Mixed-Integer Linear Programming (MILP). While standard Message-Passing GNNs (MPNNs) are efficient, they theoretically lack the expressive power…

Structure-based drug design (SBDD) is a critical task in drug discovery, requiring the generation of molecular information across two distinct modalities: discrete molecular graphs and continuous 3D coordinates. However, existing SBDD…

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…

Graph neural networks (GNNs) are effective machine learning models for various graph learning problems. Despite their empirical successes, the theoretical limitations of GNNs have been revealed recently. Consequently, many GNN models have…

Structure-based drug design (SBDD) faces a fundamental scaling fidelity dilemma: rich pocket-aware conditioning captures interaction geometry but can be costly, often scales quadratically ($O(L^2)$) or worse with protein length ($L$), while…

Drug discovery aims to find novel compounds with specified chemical property profiles. In terms of generative modeling, the goal is to learn to sample molecules in the intersection of multiple property constraints. This task becomes…

Designing expressive Graph Neural Networks (GNNs) is a fundamental topic in the graph learning community. So far, GNN expressiveness has been primarily assessed via the Weisfeiler-Lehman (WL) hierarchy. However, such an expressivity measure…

Graph neural networks (GNNs) have been demonstrated to be powerful in modeling graph-structured data. However, training GNNs usually requires abundant task-specific labeled data, which is often arduously expensive to obtain. One effective…

Subgraph-enhanced graph neural networks (SGNN) can increase the expressive power of the standard message-passing framework. This model family represents each graph as a collection of subgraphs, generally extracted by random sampling or with…

Structure-based drug design (SBDD), which aims to generate molecules that can bind tightly to the target protein, is an essential problem in drug discovery, and previous approaches have achieved initial success. However, most existing…