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Neural methods of molecule property prediction require efficient encoding of structure and property relationship to be accurate. Recent work using graph algorithms shows limited generalization in the latent molecule encoding space. We build…

Procuring expressive molecular representations underpins AI-driven molecule design and scientific discovery. The research mainly focuses on atom-level homogeneous molecular graphs, ignoring the rich information in subgraphs or motifs.…

In the real world, a molecule is a 3D geometric structure. Compared to 1D SMILES sequences and 2D molecular graphs, 3D molecules represent the most informative molecular modality. Despite the rapid progress of autoregressive-based language…

Multimodal learning aims to build models that can process and relate information from multiple modalities. Despite years of development in this field, it still remains challenging to design a unified network for processing various…

For several decades, chemical knowledge has been published in written text, and there have been many attempts to make it accessible, for example, by transforming such natural language text to a structured format. Although the discovered…

Molecular property prediction, crucial for early drug candidate screening and optimization, has seen advancements with deep learning-based methods. While deep learning-based methods have advanced considerably, they often fall short in fully…

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…

Astounding results from Transformer models on natural language tasks have intrigued the vision community to study their application to computer vision problems. Among their salient benefits, Transformers enable modeling long dependencies…

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.…

Transformers have demonstrated remarkable performance in natural language processing and computer vision. However, existing vision Transformers struggle to learn from limited medical data and are unable to generalize on diverse medical…

Establishing the relationship between 3D structures and the energy states of molecular systems has proven to be a promising approach for learning 3D molecular representations. However, existing methods are limited to modeling the molecular…

Machine learning in atomistic materials science has grown to become a powerful tool, with most approaches focusing on atomic arrangements, typically decomposed into local atomic environments. This approach, while well-suited for…

Graph neural networks (GNNs), which are capable of learning representations from graphical data, are naturally suitable for modeling molecular systems. This review introduces GNNs and their various applications for small organic molecules.…

Constructing appropriate representations of molecules lies at the core of numerous tasks such as material science, chemistry and drug designs. Recent researches abstract molecules as attributed graphs and employ graph neural networks (GNN)…

In recent years, molecular representation learning has emerged as a key area of focus in various chemical tasks. However, many existing models fail to fully consider the geometric information of molecular structures, resulting in less…

Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

Molecular representations fundamentally shape how machine learning systems reason about molecular structure and physical properties. Most existing approaches adopt a discrete pipeline: molecules are encoded as sequences, graphs, or point…

Molecule representation learning is crucial for understanding and predicting molecular properties. However, conventional atom-centric models, which treat chemical bonds merely as pairwise interactions, often overlook complex bond-level…

Supervised learning on molecules has incredible potential to be useful in chemistry, drug discovery, and materials science. Luckily, several promising and closely related neural network models invariant to molecular symmetries have already…

To learn accurate representations of molecules, it is essential to consider both chemical and geometric features. To encode geometric information, many descriptors have been proposed in constrained circumstances for specific types of…