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Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…

Self-supervised pretraining on molecular graphs has emerged as a promising approach for molecular property prediction, yet most existing methods operate at a single structural granularity and treat bond information as auxiliary edge…

The matching of 3D shapes has been extensively studied for shapes represented as surface meshes, as well as for shapes represented as point clouds. While point clouds are a common representation of raw real-world 3D data (e.g. from laser…

The Vision Transformer (ViT) has demonstrated remarkable performance in Self-Supervised Learning (SSL) for 3D medical image analysis. Masked AutoEncoder (MAE) for feature pre-training can further unleash the potential of ViT on various…

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…

To effectively exploit the potential of large-scale models, various pre-training strategies supported by massive data from different sources are proposed, including supervised pre-training, weakly-supervised pre-training, and…

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…

Industrial design evaluation often relies on high-fidelity simulations of governing partial differential equations (PDEs). While accurate, these simulations are computationally expensive, making dense exploration of design spaces…

Remote sensing image interpretation plays a critical role in environmental monitoring, urban planning, and disaster assessment. However, acquiring high-quality labeled data is often costly and time-consuming. To address this challenge, we…

Generative models in molecular design tend to be richly parameterized, data-hungry neural models, as they must create complex structured objects as outputs. Estimating such models from data may be challenging due to the lack of sufficient…

Recent advances in machine learning have enabled generative models for both optimization and de novo generation of drug candidates with desired properties. Previous generative models have focused on producing SMILES strings or 2D 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…

In recent years, there has been a surge in the development of 3D structure-based pre-trained protein models, representing a significant advancement over pre-trained protein language models in various downstream tasks. However, most existing…

Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their…

Recent advances in 3D perception have shown impressive progress in understanding geometric structures of 3Dshapes and even scenes. Inspired by these advances in geometric understanding, we aim to imbue image-based perception with…

The development of novel pharmaceuticals represents a significant challenge in modern science, with substantial costs and time investments. Deep generative models have emerged as promising tools for accelerating drug discovery by…

Dosing models often use differential equations to model biological dynamics. Neural differential equations in particular can learn to predict the derivative of a process, which permits predictions at irregular points of time. However, this…

When simulating multiscale stochastic differential equations (SDEs) in high-dimensions, separation of timescales, stochastic noise and high-dimensionality can make simulations prohibitively expensive. The computational cost is dictated by…

Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on…

Cross-modal text-molecule retrieval model aims to learn a shared feature space of the text and molecule modalities for accurate similarity calculation, which facilitates the rapid screening of molecules with specific properties and…