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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…

Computational Physics · Physics 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…

Machine Learning · Computer Science 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…

Machine Learning · Computer Science 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,…

Machine Learning · Computer Science 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.…

Computer Vision and Pattern Recognition · Computer Science 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…

Computer Vision and Pattern Recognition · Computer Science 2026-03-26 Dengyang Jiang , Dongyang Liu , Zanyi Wang , Qilong Wu , Liuzhuozheng Li , Hengzhuang Li , Xin Jin , David Liu , Changsheng Lu , Zhen Li , Bo Zhang , Mengmeng Wang , Steven Hoi , Peng Gao , Harry Yang

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…

Quantitative Methods · Quantitative Biology 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…

Biomolecules · Quantitative Biology 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…

Computer Vision and Pattern Recognition · Computer Science 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…

Machine Learning · Computer Science 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…

Machine Learning · Computer Science 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…

Machine Learning · Computer Science 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…

Machine Learning · Computer Science 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…

Computer Vision and Pattern Recognition · Computer Science 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…

Machine Learning · Computer Science 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…

Machine Learning · Computer Science 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…

Computer Vision and Pattern Recognition · Computer Science 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…

Social and Information Networks · Computer Science 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…

Machine Learning · Computer Science 2023-03-02 Shengchao Liu , Hongyu Guo , Jian Tang
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