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This paper puts forward an integrated microstructure design methodology that replaces the common existing design approaches: 1) reconstruction of microstructures, 2) analyzing and quantifying material properties, and 3) inverse design of…

Molecular dynamics is a powerful simulation tool to explore material properties. Most of the realistic material systems are too large to be simulated with first-principles molecular dynamics. Classical molecular dynamics has lower…

Molecular generation and molecular property prediction are both crucial for drug discovery, but they are often developed independently. Inspired by recent studies, which demonstrate that diffusion model, a prominent generative approach, can…

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…

Graph generation is a crucial task in many fields, including network science and bioinformatics, as it enables the creation of synthetic graphs that mimic the properties of real-world networks for various applications. Graph Generative…

Machine learning on graph-structured data has recently become a major topic in industry and research, finding many exciting applications such as recommender systems and automated theorem proving. We propose an energy-based graph embedding…

Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…

Great computational effort is invested in generating equilibrium states for molecular systems using, for example, Markov chain Monte Carlo. We present a probabilistic model that generates statistically independent samples for molecules from…

Recent advances in deep learning have accelerated its use in various applications, such as cellular image analysis and molecular discovery. In molecular discovery, a generative adversarial network (GAN), which comprises a discriminator to…

Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from…

The design of functional materials with desired properties is essential in driving technological advances in areas like energy storage, catalysis, and carbon capture. Generative models provide a new paradigm for materials design by directly…

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…

Capturing the structural changes that molecules undergo during chemical reactions in real space and time is a long-standing dream and an essential prerequisite for understanding and ultimately controlling femtochemistry. A key approach to…

Structure aware graph generation aims to generate graphs that satisfy given topological properties. It has applications in domains such as drug discovery, social network modeling, and knowledge graph construction. Unlike existing methods…

Recent advancements in deep learning-based modeling of molecules promise to accelerate in silico drug discovery. A plethora of generative models is available, building molecules either atom-by-atom and bond-by-bond or fragment-by-fragment.…

A fundamental problem in drug discovery is to design molecules that bind to specific proteins. To tackle this problem using machine learning methods, here we propose a novel and effective framework, known as GraphBP, to generate 3D…

Predicating macroscopic influences of drugs on human body, like efficacy and toxicity, is a central problem of small-molecule based drug discovery. Molecules can be represented as an undirected graph, and we can utilize graph convolution…

Molecular representation learning is vital for various downstream applications, including the analysis and prediction of molecular properties and side effects. While Graph Neural Networks (GNNs) have been a popular framework for modeling…

Deep learning has the potential to revolutionize quantum chemistry as it is ideally suited to learn representations for structured data and speed up the exploration of chemical space. While convolutional neural networks have proven to be…

Molecular representation learning has shown great success in advancing AI-based drug discovery. The core of many recent works is based on the fact that the 3D geometric structure of molecules provides essential information about their…