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Accurate molecular property predictions require 3D geometries, which are typically obtained using expensive methods such as density functional theory (DFT). Here, we attempt to obtain molecular geometries by relying solely on machine…

Molecular representation is a critical element in our understanding of the physical world and the foundation for modern molecular machine learning. Previous molecular machine learning models have employed strings, fingerprints, global…

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…

The manual annotation for large-scale point clouds costs a lot of time and is usually unavailable in harsh real-world scenarios. Inspired by the great success of the pre-training and fine-tuning paradigm in both vision and language tasks,…

Recent advancements in biology and chemistry have leveraged multi-modal learning, integrating molecules and their natural language descriptions to enhance drug discovery. However, current pre-training frameworks are limited to two…

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…

Self-supervised learning is an efficient pre-training method for medical image analysis. However, current research is mostly confined to specific-modality data pre-training, consuming considerable time and resources without achieving…

Molecular pretraining, which learns molecular representations over massive unlabeled data, has become a prominent paradigm to solve a variety of tasks in computational chemistry and drug discovery. Recently, prosperous progress has been…

Modeling the relationship between chemical structure and molecular activity is a key goal in drug development. Many benchmark tasks have been proposed for molecular property prediction, but these tasks are generally aimed at specific,…

Molecular representation learning lays the foundation for drug discovery. However, existing methods suffer from poor out-of-distribution (OOD) generalization, particularly when data for training and testing originate from different…

This paper proposes a machine learning (ML) method to predict stable molecular geometries from their chemical composition. The method is useful for generating molecular conformations which may serve as initial geometries for saving time…

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 property prediction refers to the task of labeling molecules with some biochemical properties, playing a pivotal role in the drug discovery and design process. Recently, with the advancement of machine learning, deep…

Self-supervised learning has greatly facilitated medical image analysis by suppressing the training data requirement for real-world applications. Current paradigms predominantly rely on self-supervision within uni-modal image data, thereby…

We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning…

Learning meaningful protein representation is important for a variety of biological downstream tasks such as structure-based drug design. Having witnessed the success of protein sequence pretraining, pretraining for structural data which is…

Self-supervised pretraining from static structures of drug-like compounds and proteins enable powerful learned feature representations. Learned features demonstrate state of the art performance on a range of predictive tasks including…

Molecular Representation Learning is essential to solving many drug discovery and computational chemistry problems. It is a challenging problem due to the complex structure of molecules and the vast chemical space. Graph representations of…

Many molecular properties depend on 3D geometry, where non-covalent interactions, stereochemical effects, and medium- to long-range forces are determined by spatial distances and angles that cannot be uniquely captured by a 2D bond graph.…

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations…