Related papers: Genarris 2.0: A Random Structure Generator for Mol…

Traditional drug discovery programs are being transformed by the advent of machine learning methods. Among these, Generative AI methods (GM) have gained attention due to their ability to design new molecules and enhance specific properties…

We propose a systematic method to construct crystal-based molecular structures often needed as input for computational chemistry studies. These structures include crystal ``slabs" with periodic boundary conditions (PBCs) and non-periodic…

We present a new computational scheme, GRIP (Geometric Random Inner Products), for testing the quality of random number generators. The GRIP formalism utilizes geometric probability techniques to calculate the average scalar products of…

Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe…

Generating molecules, both in a directed and undirected fashion, is a huge part of the drug discovery pipeline. Genetic algorithms (GAs) generate molecules by randomly modifying known molecules. In this paper we show that GAs are very…

Simulated high-dimensional data is useful for testing, validating, and improving algorithms used in dimension reduction, supervised and unsupervised learning. High-dimensional data is characterized by multiple variables that are dependent…

Computationally generating novel synthetically accessible compounds with high affinity and low toxicity is a great challenge in drug design. Machine-learning models beyond conventional pharmacophoric methods have shown promise in generating…

Graph neural networks are widely used in machine learning applied to chemistry, and in particular for material science discovery. For crystalline materials, however, generating graph-based representation from geometrical information for…

The ability to rapidly develop materials with desired properties has a transformative impact on a broad range of emerging technologies. In this work, we introduce a new framework based on the diffusion model, a recent generative machine…

Crystal Toolkit is an open source tool for viewing, analyzing and transforming crystal structures, molecules and other common forms of materials science data in an interactive way. It is intended to help beginners rapidly develop web-based…

Generative models show great promise for the inverse design of molecules and inorganic crystals, but remain largely ineffective within more complex structures such as amorphous materials. Here, we present a diffusion model that reliably…

Crystal structure prediction is now playing an increasingly important role in discovery of new materials. Global optimization methods such as genetic algorithms (GA) and particle swarm optimization (PSO) have been combined with first…

This article presents GenSQL, a probabilistic programming system for querying probabilistic generative models of database tables. By augmenting SQL with only a few key primitives for querying probabilistic models, GenSQL enables complex…

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…

Discovering new drug molecules is a pivotal yet challenging process due to the near-infinitely large chemical space and notorious demands on time and resources. Numerous generative models have recently been introduced to accelerate the drug…

Predicting properties of crystals from their structures is a fundamental yet challenging task in materials science. Unlike molecules, crystal structures exhibit infinite periodic arrangements of atoms, requiring methods capable of capturing…

Deep generative models for graph-structured data offer a new angle on the problem of chemical synthesis: by optimizing differentiable models that directly generate molecular graphs, it is possible to side-step expensive search procedures in…

Recurrent neural networks have been widely used to generate millions of de novo molecules in a known chemical space. These deep generative models are typically setup with LSTM or GRU units and trained with canonical SMILEs. In this study,…

Deep generative models, such as generative adversarial networks (GANs), have been employed for $de~novo$ molecular generation in drug discovery. Most prior studies have utilized reinforcement learning (RL) algorithms, particularly Monte…

Block2 is an open source framework to implement and perform density matrix renormalization group and matrix product state algorithms. Out-of-the-box it supports the eigenstate, time-dependent, response, and finite-temperature algorithms. In…