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

Graph Neural Networks (GNNs) have received considerable attention since its introduction. It has been widely applied in various fields due to its ability to represent graph structured data. However, the application of GNNs is constrained by…

Generating molecules with high binding affinities to target proteins (a.k.a. structure-based drug design) is a fundamental and challenging task in drug discovery. Recently, deep generative models have achieved remarkable success in…

Structure-based drug design (SBDD) leverages the three-dimensional geometry of proteins to identify potential drug candidates. Traditional approaches, rooted in physicochemical modeling and domain expertise, are often resource-intensive.…

Although recent advances in higher-order Graph Neural Networks (GNNs) improve the theoretical expressiveness and molecular property predictive performance, they often fall short of the empirical performance of models that explicitly use…

3D generative models have shown significant promise in structure-based drug design (SBDD), particularly in discovering ligands tailored to specific target binding sites. Existing algorithms often focus primarily on ligand-target binding,…

Generative methods for graphs need to be sufficiently flexible to model complex dependencies between sets of nodes. At the same time, the generated graphs need to satisfy domain-dependent feasibility conditions, that is, they should not…

The fundamental goal of generative drug design is to propose optimized molecules that meet predefined activity, selectivity, and pharmacokinetic criteria. Despite recent progress, we argue that existing generative methods are limited in…

Graph Neural Networks (GNNs) have achieved remarkable success in various applications, but their performance can be sensitive to specific data properties of the graph datasets they operate on. Current literature on understanding the…

We investigate a relatively underexplored class of hybrid neurosymbolic models integrating symbolic learning with neural reasoning to construct data generators meeting formal correctness criteria. In \textit{Symbolic Neural Generators}…

Graph Neural Networks (GNNs) are exemplary deep models designed for graph data. Message passing mechanism enables GNNs to effectively capture graph topology and push the performance boundaries across various graph tasks. However, the trend…

Graph neural networks (GNNs) are powerful graph-based machine-learning models that are popular in various domains, e.g., social media, transportation, and drug discovery. However, owing to complex data representations, GNNs do not easily…

Drug synergy arises when the combined impact of two drugs exceeds the sum of their individual effects. While single-drug effects on cell lines are well-documented, the scarcity of data on drug synergy, considering the vast array of…

In image generation, generative models can be evaluated naturally by visually inspecting model outputs. However, this is not always the case for graph generative models (GGMs), making their evaluation challenging. Currently, the standard…

Efficient and effective drug-target binding affinity (DTBA) prediction is a challenging task due to the limited computational resources in practical applications and is a crucial basis for drug screening. Inspired by the good representation…

Synthesizability in small molecule generative design remains a bottleneck. Existing works that do consider synthesizability can output predicted synthesis routes for generated molecules. However, there has been minimal attention in…

In genome-scale constraint-based metabolic models, gene deletion strategies are essential for achieving growth-coupled production, where cell growth and target metabolite synthesis occur simultaneously. Despite the inherently networked…

Structure-based drug design involves finding ligand molecules that exhibit structural and chemical complementarity to protein pockets. Deep generative methods have shown promise in proposing novel molecules from scratch (de-novo design),…

Graph generative models have been extensively studied in the data mining literature. While traditional techniques are based on generating structures that adhere to a pre-decided distribution, recent techniques have shifted towards learning…

One of the major applications of generative models for drug Discovery targets the lead-optimization phase. During the optimization of a lead series, it is common to have scaffold constraints imposed on the structure of the molecules…

Training generative models that capture rich semantics of the data and interpreting the latent representations encoded by such models are very important problems in un-/self-supervised learning. In this work, we provide a simple algorithm…