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The quest for efficient and robust deep learning models for molecular systems representation is increasingly critical in scientific exploration. The advent of message passing neural networks has marked a transformative era in graph-based…

计算物理 · 物理学 2026-01-05 Jian Chang , Shuze Zhu

GNN-to-MLP (G2M) methods have emerged as a promising approach to accelerate Graph Neural Networks (GNNs) by distilling their knowledge into simpler Multi-Layer Perceptrons (MLPs). These methods bridge the gap between the expressive power of…

机器学习 · 计算机科学 2025-07-28 Weigang Lu , Ziyu Guan , Wei Zhao , Yaming Yang , Yujie Sun , Zheng Liang , Yibing Zhan , Dapeng Tao

Molecular Property Prediction (MPP) task involves predicting biochemical properties based on molecular features, such as molecular graph structures, contributing to the discovery of lead compounds in drug development. To address data…

机器学习 · 计算机科学 2023-12-07 Xu Yao , Shuang Liang , Songqiao Han , Hailiang Huang

Multimodal molecular representation learning, which jointly models molecular graphs and their textual descriptions, enhances predictive accuracy and interpretability by enabling more robust and reliable predictions of drug toxicity,…

机器学习 · 计算机科学 2025-10-21 Yingxu Wang , Kunyu Zhang , Jiaxin Huang , Nan Yin , Siwei Liu , Eran Segal

Due to limitations in data quality, some essential visual tasks are difficult to perform independently. Introducing previously unavailable information to transfer informative dark knowledge has been a common way to solve such hard tasks.…

计算机视觉与模式识别 · 计算机科学 2023-06-29 Lingyu Si , Hongwei Dong , Wenwen Qiang , Junzhi Yu , Wenlong Zhai , Changwen Zheng , Fanjiang Xu , Fuchun Sun

Distribution Matching Distillation (DMD) facilitates efficient inference by distilling multi-step diffusion models into few-step variants. Concurrently, Reinforcement Learning (RL) has emerged as a vital tool for aligning generative models…

Predicting molecular properties with data-driven methods has drawn much attention in recent years. Particularly, Graph Neural Networks (GNNs) have demonstrated remarkable success in various molecular generation and prediction tasks. In…

定量方法 · 定量生物学 2021-10-19 Zaixi Zhang , Qi Liu , Hao Wang , Chengqiang Lu , Chee-Kong Lee

Designing accurate deep learning models for molecular property prediction plays an increasingly essential role in drug and material discovery. Recently, due to the scarcity of labeled molecules, self-supervised learning methods for learning…

生物大分子 · 定量生物学 2022-06-08 Han Li , Dan Zhao , Jianyang Zeng

Recent advances in event-based research prioritize sparsity and temporal precision. Approaches using dense frame-based representations processed via well-pretrained CNNs are being replaced by the use of sparse point-based representations…

计算机视觉与模式识别 · 计算机科学 2023-04-18 Yongjian Deng , Hao Chen , Bochen Xie , Hai Liu , Youfu Li

Digraph Representation Learning (DRL) aims to learn representations for directed homogeneous graphs (digraphs). Prior work in DRL is largely constrained (e.g., limited to directed acyclic graphs), or has poor generalizability across tasks…

机器学习 · 计算机科学 2022-09-30 Honglu Zhou , Advith Chegu , Samuel S. Sohn , Zuohui Fu , Gerard de Melo , Mubbasir Kapadia

We introduce a new graph diffusion model for small molecule generation, DMol, which outperforms the state-of-the-art DiGress model in terms of validity by roughly 1.5% across all benchmarking datasets while reducing the number of diffusion…

机器学习 · 计算机科学 2025-11-04 Peizhi Niu , Yu-Hsiang Wang , Vishal Rana , Chetan Rupakheti , Abhishek Pandey , Olgica Milenkovic

Property prediction on molecular graphs is an important application of Graph Neural Networks. Recently, unlabeled molecular data has become abundant, which facilitates the rapid development of self-supervised learning for GNNs in the…

机器学习 · 计算机科学 2023-10-31 Kha-Dinh Luong , Ambuj Singh

Graph deep learning has recently emerged as a powerful ML concept allowing to generalize successful deep neural architectures to non-Euclidean structured data. Such methods have shown promising results on a broad spectrum of applications…

机器学习 · 计算机科学 2022-05-16 Anees Kazi , Luca Cosmo , Seyed-Ahmad Ahmadi , Nassir Navab , Michael Bronstein

This technical report presents GPS++, the first-place solution to the Open Graph Benchmark Large-Scale Challenge (OGB-LSC 2022) for the PCQM4Mv2 molecular property prediction task. Our approach implements several key principles from the…

Recent progresses on self-supervised 3D human action representation learning are largely attributed to contrastive learning. However, in conventional contrastive frameworks, the rich complementarity between different skeleton modalities…

计算机视觉与模式识别 · 计算机科学 2023-10-25 Yunyao Mao , Jiajun Deng , Wengang Zhou , Zhenbo Lu , Wanli Ouyang , Houqiang Li

Molecular Property Prediction (MPP) plays a pivotal role across diverse domains, spanning drug discovery, material science, and environmental chemistry. Fueled by the exponential growth of chemical data and the evolution of artificial…

机器学习 · 计算机科学 2024-08-23 Tanya Liyaqat , Tanvir Ahmad , Chandni Saxena

GNN-to-MLP distillation aims to utilize knowledge distillation (KD) to learn computationally-efficient multi-layer perceptron (student MLP) on graph data by mimicking the output representations of teacher GNN. Existing methods mainly make…

机器学习 · 计算机科学 2024-03-07 Ling Yang , Ye Tian , Minkai Xu , Zhongyi Liu , Shenda Hong , Wei Qu , Wentao Zhang , Bin Cui , Muhan Zhang , Jure Leskovec

With the development of deep convolutional neural networks, medical image segmentation has achieved a series of breakthroughs in recent years. However, the high-performance convolutional neural networks always mean numerous parameters and…

计算机视觉与模式识别 · 计算机科学 2022-08-30 Wenxuan Zou , Muyi Sun

A significant portion of the data today, e.g, social networks, web connections, etc., can be modeled by graphs. A proper analysis of graphs with Machine Learning (ML) algorithms has the potential to yield far-reaching insights into many…

社会与信息网络 · 计算机科学 2020-09-11 Taha Atahan Akyildiz , Amro Alabsi Aljundi , Kamer Kaya

Molecular representation pretraining is critical in various applications for drug and material discovery due to the limited number of labeled molecules, and most existing work focuses on pretraining on 2D molecular graphs. However, the…

机器学习 · 计算机科学 2023-03-02 Shengchao Liu , Hongyu Guo , Jian Tang