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Many important problems involving molecular property prediction from 3D structures have limited data, posing a generalization challenge for neural networks. In this paper, we describe a pre-training technique based on denoising that…
Pretraining molecular representation models without labels is fundamental to various applications. Conventional methods mainly process 2D molecular graphs and focus solely on 2D tasks, making their pretrained models incapable of…
Molecular representation learning has attracted much attention recently. A molecule can be viewed as a 2D graph with nodes/atoms connected by edges/bonds, and can also be represented by a 3D conformation with 3-dimensional coordinates of…
Molecular representation learning plays a crucial role in advancing applications such as drug discovery and material design. Existing work leverages 2D and 3D modalities of molecular information for pre-training, aiming to capture…
Machine learning approaches have become popular for molecular modeling tasks, including molecular force fields and properties prediction. Traditional supervised learning methods suffer from scarcity of labeled data for particular tasks,…
Machine learning force fields show great promise in enabling more accurate molecular dynamics simulations compared to manually derived ones. Much of the progress in recent years was driven by exploiting prior knowledge about physical…
Accurate prediction of energy and forces for 3D molecular systems is one of fundamental challenges at the core of AI for Science applications. Many powerful and data-efficient neural networks predict molecular energies and forces from…
Many learning-based approaches have difficulty scaling to unseen data, as the generality of its learned prior is limited to the scale and variations of the training samples. This holds particularly true with 3D learning tasks, given the…
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…
The training set of atomic configurations is key to the performance of any Machine Learning Force Field (MLFF) and, as such, the training set selection determines the applicability of the MLFF model for predictive molecular simulations.…
Molecular 3D conformations play a key role in determining how molecules interact with other molecules or protein surfaces. Recent deep learning advancements have improved conformation prediction, but slow training speeds and difficulties in…
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…
Machine learned chemical potentials have shown great promise as alternatives to conventional computational chemistry methods to represent the potential energy of a given atomic or molecular system as a function of its geometry. However,…
The difficulties in both data acquisition and annotation substantially restrict the sample sizes of training datasets for 3D medical imaging applications. As a result, constructing high-performance 3D convolutional neural networks from…
To address the computational challenges of ab initio molecular dynamics and the accuracy limitations of empirical force fields, the introduction of machine learning force fields has proven effective in various systems including metals and…
Self-supervised learning has proved effective for skeleton-based human action understanding, which is an important yet challenging topic. Previous works mainly rely on contrastive learning or masked motion modeling paradigm to model the…
We present a new pre-training strategy called M$^{3}$3D ($\underline{M}$ulti-$\underline{M}$odal $\underline{M}$asked $\underline{3D}$) built based on Multi-modal masked autoencoders that can leverage 3D priors and learned cross-modal…
Abstract Machine learning models, trained on data from ab initio quantum simulations, are yielding molecular dynamics potentials with unprecedented accuracy. One limiting factor is the quantity of available training data, which can be…
The accuracy of any machine learning potential can only be as good as the data used in the fitting process. The most efficient model therefore selects the training data that will yield the highest accuracy compared to the cost of obtaining…
Recently, a noticeable trend has emerged in developing pre-trained foundation models in the domains of CV and NLP. However, for molecular pre-training, there lacks a universal model capable of effectively applying to various categories of…