Related papers: Learning Gradient Fields for Molecular Conformatio…

We introduce a new generative model where samples are produced via Langevin dynamics using gradients of the data distribution estimated with score matching. Because gradients can be ill-defined and hard to estimate when the data resides on…

Recent methods for molecular generation face a trade-off: they either enforce strict equivariance with costly architectures or relax it to gain scalability and flexibility. We propose a frame-based diffusion paradigm that achieves…

We study a fundamental problem in structure-based drug design -- generating molecules that bind to specific protein binding sites. While we have witnessed the great success of deep generative models in drug design, the existing methods are…

The next generation of force fields for molecular dynamics will be developed using a wealth of data. Training systematically with experimental data remains a challenge, however, especially for machine learning potentials. Differentiable…

Recently, the application of machine learning models has gained momentum in natural sciences and engineering, which is a natural fit due to the abundance of data in these fields. However, the modeling of physical processes from simulation…

The generation of 3D molecules requires simultaneously deciding the categorical features~(atom types) and continuous features~(atom coordinates). Deep generative models, especially Diffusion Models (DMs), have demonstrated effectiveness in…

Molecular dynamics (MD) simulation predicts the trajectory of atoms by solving Newton's equation of motion with a numeric integrator. Due to physical constraints, the time step of the integrator need to be small to maintain sufficient…

A molecule's 2D representation consists of its atoms, their attributes, and the molecule's covalent bonds. A 3D (geometric) representation of a molecule is called a conformer and consists of its atom types and Cartesian coordinates. Every…

Text-conditioned molecular generation aims to translate natural-language descriptions into chemical structures, enabling scientists to specify functional groups, scaffolds, and physicochemical constraints without handcrafted rules.…

We present a three-dimensional graph convolutional network (3DGCN), which predicts molecular properties and biochemical activities, based on 3D molecular graph. In the 3DGCN, graph convolution is unified with learning operations on the…

Deep learning for molecular science has so far mainly focused on 2D molecular graphs. Recently, however, there has been work to extend it to 3D molecular geometry, due to its scientific significance and critical importance in real-world…

Drug Discovery is a fundamental and ever-evolving field of research. The design of new candidate molecules requires large amounts of time and money, and computational methods are being increasingly employed to cut these costs. Machine…

Molecular dynamic simulations are important in computational physics, chemistry, material, and biology. Machine learning-based methods have shown strong abilities in predicting molecular energy and properties and are much faster than DFT…

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…

Retrosynthesis, which aims to identify viable synthetic pathways for target molecules by decomposing them into simpler precursors, is often treated as a search problem. However, its complexity arises from multi-branched tree-structured…

Neural networks are known to be susceptible to adversarial samples: small variations of natural examples crafted to deliberately mislead the models. While they can be easily generated using gradient-based techniques in digital and physical…

The simulation of geological facies in an unobservable volume is essential in various geoscience applications. Given the complexity of the problem, deep generative learning is a promising approach to overcome the limitations of traditional…

Gaussian Probability Path based Generative Models (GPPGMs) generate data by reversing a stochastic process that progressively corrupts samples with Gaussian noise. Despite state-of-the-art results in 3D molecular generation, their…

Designing molecules that bind to specific target proteins is a fundamental task in drug discovery. Recent models leverage geometric constraints to generate ligand molecules that bind cohesively with specific protein pockets. However, these…

Graph neural networks (GNNs) have emerged as powerful tools to accurately predict materials and molecular properties in computational discovery pipelines. In this article, we exploit the invertible nature of these neural networks to…