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Significant interests have recently risen in leveraging sequence-based large language models (LLMs) for drug design. However, most current applications of LLMs in drug discovery lack the ability to comprehend three-dimensional (3D)…

Current machine learning models for vision are often highly specialized and limited to a single modality and task. In contrast, recent large language models exhibit a wide range of capabilities, hinting at a possibility for similarly…

Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…

n this work, we propose a latent molecular diffusion model that can make the generated 3D molecules rich in diversity and maintain rich geometric features. The model captures the information of the forces and local constraints between atoms…

Many processes in biology and drug discovery involve various 3D interactions between molecules, such as protein and protein, protein and small molecule, etc. Given that different molecules are usually represented in different granularity,…

High-throughput data generation methods and machine learning (ML) algorithms have given rise to a new era of computational materials science by learning relationships among composition, structure, and properties and by exploiting such…

Transformers have been at the heart of the Natural Language Processing (NLP) and Computer Vision (CV) revolutions. The significant success in NLP and CV inspired exploring the use of Transformers in point cloud processing. However, how do…

Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in…

General-purpose 3D modeling in chemistry encompasses molecules and materials, requiring both generative and predictive capabilities. However, most existing AI approaches are optimized for a single domain (molecules or materials) and a…

Although substantial efforts have been made using graph neural networks (GNNs) for AI-driven drug discovery (AIDD), effective molecular representation learning remains an open challenge, especially in the case of insufficient labeled…

Models based on machine learning can enable accurate and fast molecular property predictions, which is of interest in drug discovery and material design. Various supervised machine learning models have demonstrated promising performance,…

Machine learning in drug discovery has been focused on virtual screening of molecular libraries using discriminative models. Generative models are an entirely different approach that learn to represent and optimize molecules in a continuous…

Within the domain of molecular communications, researchers mimic the techniques in nature to come up with alternative communication methods for collaborating nanomachines. This work investigates the channel transfer function for molecular…

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular…

The prediction of physicochemical properties from molecular structures is a crucial task for artificial intelligence aided molecular design. A growing number of Graph Neural Networks (GNNs) have been proposed to address this challenge.…

Generative modeling of three-dimensional (3D) molecules is a fundamental yet challenging problem in drug discovery and materials science. Existing approaches typically represent molecules as 3D graphs and co-generate discrete atom types…

Predicting molecular properties (e.g., atomization energy) is an essential issue in quantum chemistry, which could speed up much research progress, such as drug designing and substance discovery. Traditional studies based on density…

Most current molecular language models transfer the masked language model or image-text generation model from natural language processing to molecular field. However, molecules are not solely characterized by atom/bond symbols; they…

Masked graph modeling excels in the self-supervised representation learning of molecular graphs. Scrutinizing previous studies, we can reveal a common scheme consisting of three key components: (1) graph tokenizer, which breaks a molecular…

Transformer-based models have achieved state-of-the-art results in many natural language processing tasks. The self-attention architecture allows transformer to combine information from all elements of a sequence into context-aware…