Related papers: Structure-Aware E(3)-Invariant Molecular Conformer…

Most machine learning models for molecular property prediction rely on a single molecular representation (either a sequence, a graph, or a 3D structure) and treat molecular geometry as static. We present MolFM-Lite, a multi-modal model that…

Artificial intelligence for scientific discovery has recently generated significant interest within the machine learning and scientific communities, particularly in the domains of chemistry, biology, and material discovery. For these…

Transformers have become methods of choice in many applications thanks to their ability to represent complex interactions between elements. However, extending the Transformer architecture to non-sequential data such as molecules and…

Graph neural networks are emerging as promising methods for modeling molecular graphs, in which nodes and edges correspond to atoms and chemical bonds, respectively. Recent studies show that when 3D molecular geometries, such as bond…

How can diffusion models process 3D geometries in a coarse-to-fine manner, akin to our multiscale view of the world? In this paper, we address the question by focusing on a fundamental biochemical problem of generating 3D molecular…

In this work, we propose a simple transformer-based baseline for multimodal molecular representation learning, integrating three distinct modalities: SMILES strings, 2D graph representations, and 3D conformers of molecules. A key aspect of…

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…

Graph neural networks (GNNs) have achieved remarkable success in molecular property prediction. However, traditional graph representations struggle to effectively encode the inherent 3D spatial structures of molecules, as molecular…

In recent years, molecular graph representation learning (GRL) has drawn much more attention in molecular property prediction (MPP) problems. The existing graph methods have demonstrated that 3D geometric information is significant for…

Molecular property prediction is one of the fastest-growing applications of deep learning with critical real-world impacts. Including 3D molecular structure as input to learned models improves their performance for many molecular tasks.…

Three-dimensional molecular structure generation is typically performed at the level of individual atoms, yet molecular graph generation techniques often consider fragments as their structural units. Building on the advances in frame-based…

The geometry of three-dimensional (3D) graphs, consisting of nodes and edges, plays a crucial role in many important applications. An excellent example is molecular graphs, whose geometry influences important properties of a molecule…

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…

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…

The three-dimensional shape and conformation of small-molecule ligands are critical for biomolecular recognition, yet encoding 3D geometry has not improved ligand-based virtual screening approaches. We describe an end-to-end deep learning…

In this work we introduce an Autoencoder for molecular conformations. Our proposed model converts the discrete spatial arrangements of atoms in a given molecular graph (conformation) into and from a continuous fixed-sized latent…

We consider the conditional generation of 3D drug-like molecules with \textit{explicit control} over molecular properties such as drug-like properties (e.g., Quantitative Estimate of Druglikeness or Synthetic Accessibility score) and…

We introduce MolMiner, a fragment-based, geometry-aware, and order-agnostic autoregressive model for molecular design. MolMiner supports conditional generation of molecules over twelve properties, enabling flexible control across…

Deep learning has achieved tremendous success in designing novel chemical compounds with desirable pharmaceutical properties. In this work, we focus on a new type of drug design problem -- generating a small "linker" to physically attach…

Molecular property prediction with deep learning has gained much attention over the past years. Owing to the scarcity of labeled molecules, there has been growing interest in self-supervised learning methods that learn generalizable…