Related papers: Coordinating Cross-modal Distillation for Molecula…

The open-world test dataset is often mixed with out-of-distribution (OOD) samples, where the deployed models will struggle to make accurate predictions. Traditional detection methods need to trade off OOD detection and in-distribution (ID)…

Recent years have witnessed the great success of Graph Neural Networks (GNNs) in handling graph-related tasks. However, MLPs remain the primary workhorse for practical industrial applications due to their desirable inference efficiency and…

The selection of coarse-grained (CG) mapping operators is a critical step for CG molecular dynamics (MD) simulation. It is still an open question about what is optimal for this choice and there is a need for theory. The current state-of-the…

Molecule representation learning (MRL) methods aim to embed molecules into a real vector space. However, existing SMILES-based (Simplified Molecular-Input Line-Entry System) or GNN-based (Graph Neural Networks) MRL methods either take…

We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be…

Learning and reasoning about 3D molecular structures with varying size is an emerging and important challenge in machine learning and especially in drug discovery. Equivariant Graph Neural Networks (GNNs) can simultaneously leverage the…

Cross-modality distillation arises as an important topic for data modalities containing limited knowledge such as depth maps and high-quality sketches. Such techniques are of great importance, especially for memory and privacy-restricted…

Graph representation learning has emerged as a powerful tool for preserving graph topology when mapping nodes to vector representations, enabling various downstream tasks such as node classification and community detection. However, most…

Prediction of a molecule's 3D conformer ensemble from the molecular graph holds a key role in areas of cheminformatics and drug discovery. Existing generative models have several drawbacks including lack of modeling important molecular…

Graph Neural Networks (GNNs) have revolutionized graph-based machine learning, but their heavy computational demands pose challenges for latency-sensitive edge devices in practical industrial applications. In response, a new wave of…

To bridge the gaps between powerful Graph Neural Networks (GNNs) and lightweight Multi-Layer Perceptron (MLPs), GNN-to-MLP Knowledge Distillation (KD) proposes to distill knowledge from a well-trained teacher GNN into a student MLP. In this…

Dataset distillation aims to distill the knowledge of a large-scale real dataset into small yet informative synthetic data such that a model trained on it performs as well as a model trained on the full dataset. Despite recent progress,…

Molecular property prediction (MPP) is a fundamental and crucial task in drug discovery. However, prior methods are limited by the requirement for a large number of labeled molecules and their restricted ability to generalize for unseen and…

The recent success of pre-trained 2D vision models is mostly attributable to learning from large-scale datasets. However, compared with 2D image datasets, the current pre-training data of 3D point cloud is limited. To overcome this…

Scaling deep learning models has been at the heart of recent revolutions in language modelling and image generation. Practitioners have observed a strong relationship between model size, dataset size, and performance. However,…

While Large Language Models (LLMs) have shown exceptional generalization capabilities, their ability to process graph data, such as molecular structures, remains limited. To bridge this gap, this paper proposes Graph2Token, an efficient…

Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML…

This work introduces MiDi, a novel diffusion model for jointly generating molecular graphs and their corresponding 3D arrangement of atoms. Unlike existing methods that rely on predefined rules to determine molecular bonds based on the 3D…

Motivation: Despite its great success in various physical modeling, differential geometry (DG) has rarely been devised as a versatile tool for analyzing large, diverse and complex molecular and biomolecular datasets due to the limited…

Graph Representation Learning (GRL) has experienced significant progress as a means to extract structural information in a meaningful way for subsequent learning tasks. Current approaches including shallow embeddings and Graph Neural…