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Molecular conformer generation is a fundamental task in computational chemistry. Several machine learning approaches have been developed, but none have outperformed state-of-the-art cheminformatics methods. We propose torsional diffusion, a…

With the recent advances in machine learning for quantum chemistry, it is now possible to predict the chemical properties of compounds and to generate novel molecules. Existing generative models mostly use a string- or graph-based…

A molecule's geometry, also known as conformation, is one of a molecule's most important properties, determining the reactions it participates in, the bonds it forms, and the interactions it has with other molecules. Conventional…

Virtual screening can accelerate drug discovery by identifying promising candidates for experimental evaluation. Machine learning is a powerful method for screening, as it can learn complex structure-property relationships from experimental…

Prediction of a molecule's 3D conformer ensemble from the molecular graph holds a key role in areas of cheminformatics and drug discovery. Existing generative models have several drawbacks including lack of modeling important molecular…

Chemical space is routinely explored by machine learning methods to discover interesting molecules, before time-consuming experimental synthesizing is attempted. However, these methods often rely on a graph representation, ignoring 3D…

Generating stable molecular conformations is crucial in several drug discovery applications, such as estimating the binding affinity of a molecule to a target. Recently, generative machine learning methods have emerged as a promising, more…

Reinforcement learning (RL) over text representations can be effective for finding high-value policies that can search over graphs. However, RL requires careful structuring of the search space and algorithm design to be effective in this…

Designing a network to learn a molecule structure given its physical/chemical properties is a hard problem, but is useful for drug discovery tasks. In this paper, we incorporate higher-order relational learning of Factor Graphs with strong…

We develop and test new machine learning strategies for accelerating molecular crystal structure ranking and crystal property prediction using tools from geometric deep learning on molecular graphs. Leveraging developments in graph-based…

Computer-aided design of molecules has the potential to disrupt the field of drug and material discovery. Machine learning, and deep learning, in particular, have been topics where the field has been developing at a rapid pace.…

Molecular conformation generation, a critical aspect of computational chemistry, involves producing the three-dimensional conformer geometry for a given molecule. Generating molecular conformation via diffusion requires learning to reverse…

The size and quality of chemical libraries to the drug discovery pipeline are crucial for developing new drugs or repurposing existing drugs. Existing techniques such as combinatorial organic synthesis and High-Throughput Screening usually…

We present a novel deep learning approach to approximate the solution of large, sparse, symmetric, positive-definite linear systems of equations. These systems arise from many problems in applied science, e.g., in numerical methods for…

Prediction of toxicity levels of chemical compounds is an important issue in Quantitative Structure-Activity Relationship (QSAR) modeling. Although toxicity prediction has achieved significant progress in recent times through deep learning,…

Discovering the low-energy conformations of a molecule is of great interest to computational chemists, with applications in {\em in silico} materials design and drug discovery. In this paper, we propose a variable neighbourhood search…

Traditional approaches based on finite element analyses have been successfully used to predict the macro-scale behavior of heterogeneous materials (composites, multicomponent alloys, and polycrystals) widely used in industrial applications.…

Design of new drugs is a challenging process: a candidate molecule should satisfy multiple conditions to act properly and make the least side-effect -- perfect candidates selectively attach to and influence only targets, leaving off-targets…

Computational drug discovery provides an efficient tool helping large scale lead molecules screening. One of the major tasks of lead discovery is identifying molecules with promising binding affinities towards a target, a protein in…

Artificial Neuronal Networks are models widely used for many scientific tasks. One of the well-known field of application is the approximation of high-dimensional problems via Deep Learning. In the present paper we investigate the Deep…