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Real-world data generation often involves complex inter-dependencies among instances, violating the IID-data hypothesis of standard learning paradigms and posing a challenge for uncovering the geometric structures for learning desired…

Machine Learning · Computer Science 2023-05-30 Qitian Wu , Chenxiao Yang , Wentao Zhao , Yixuan He , David Wipf , Junchi Yan

Message passing neural networks (MPNNs) have emerged as go-to models for learning on graph-structured data in the past decade. Despite their effectiveness, most of such models still incur severe issues such as over-smoothing and…

Machine Learning · Computer Science 2025-11-26 Haoran Zheng , Renchi Yang , Yubo Zhou , Jianliang Xu

Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of…

Biomolecules · Quantitative Biology 2024-05-10 Ian Dunn , David Ryan Koes

This paper proposes a unified diffusion framework (dubbed UniDiffuser) to fit all distributions relevant to a set of multi-modal data in one model. Our key insight is -- learning diffusion models for marginal, conditional, and joint…

Machine Learning · Computer Science 2023-05-31 Fan Bao , Shen Nie , Kaiwen Xue , Chongxuan Li , Shi Pu , Yaole Wang , Gang Yue , Yue Cao , Hang Su , Jun Zhu

We present diffusion-convolutional neural networks (DCNNs), a new model for graph-structured data. Through the introduction of a diffusion-convolution operation, we show how diffusion-based representations can be learned from…

Machine Learning · Computer Science 2016-07-11 James Atwood , Don Towsley

Diffusion models have achieved state-of-the-art synthesis quality on both visual and audio tasks, and recent works further adapt them to textual data by diffusing on the embedding space. In this paper, we conduct systematic studies of the…

Computation and Language · Computer Science 2024-04-23 Zhujin Gao , Junliang Guo , Xu Tan , Yongxin Zhu , Fang Zhang , Jiang Bian , Linli Xu

The dominant paradigm for learning on graph-structured data is message passing. Despite being a strong inductive bias, the local message passing mechanism suffers from pathological issues such as over-smoothing, over-squashing, and limited…

Machine Learning · Computer Science 2025-04-15 Jacob Bamberger , Federico Barbero , Xiaowen Dong , Michael M. Bronstein

While many unsupervised learning models focus on one family of tasks, either generative or discriminative, we explore the possibility of a unified representation learner: a model which addresses both families of tasks simultaneously. We…

Computer Vision and Pattern Recognition · Computer Science 2024-09-25 Soumik Mukhopadhyay , Matthew Gwilliam , Yosuke Yamaguchi , Vatsal Agarwal , Namitha Padmanabhan , Archana Swaminathan , Tianyi Zhou , Jun Ohya , Abhinav Shrivastava

End-to-end backpropagation requires storing activations throughout all layers, creating memory bottlenecks that limit model scalability. Existing block-wise training methods offer means to alleviate this problem, but they rely on ad-hoc…

Machine Learning · Computer Science 2026-02-19 Makoto Shing , Masanori Koyama , Takuya Akiba

Graph neural networks (GNNs) have demonstrated significant promise in modelling relational data and have been widely applied in various fields of interest. The key mechanism behind GNNs is the so-called message passing where information is…

Machine Learning · Computer Science 2023-10-31 Andi Han , Dai Shi , Lequan Lin , Junbin Gao

Hypergraph neural networks (HGNNs) have shown remarkable potential in modeling high-order relationships that naturally arise in many real-world data domains. However, existing HGNNs often suffer from shallow propagation, oversmoothing, and…

Machine Learning · Computer Science 2026-04-14 Zhiheng Zhou , Mengyao Zhou , Xixun Lin , Xingqin Qi , Guiying Yan

The capability of generalization is a cornerstone for the success of modern learning systems. For non-Euclidean data, e.g., graphs, that particularly involves topological structures, one important aspect neglected by prior studies is how…

Machine Learning · Computer Science 2025-06-24 Qitian Wu , Chenxiao Yang , Kaipeng Zeng , Michael Bronstein

Diffusion Probabilistic Models (DPMs) have recently demonstrated impressive results on various generative tasks.Despite its promises, the learned representations of pre-trained DPMs, however, have not been fully understood. In this paper,…

Computer Vision and Pattern Recognition · Computer Science 2023-08-23 Xingyi Yang , Xinchao Wang

Integrating the structural inductive biases of Graph Neural Networks (GNNs) with the global contextual modeling capabilities of Transformers represents a pivotal challenge in graph representation learning. While GNNs excel at capturing…

Machine Learning · Computer Science 2025-03-05 Zhihua Duan , Jialin Wang

Deep generative models such as diffusion and flow matching are powerful machine learning tools capable of learning and sampling from high-dimensional distributions. They are particularly useful when the training data appears to be…

High Energy Physics - Phenomenology · Physics 2026-04-30 Zachary Bogorad , Ibrahim Elsharkawy , Yonatan Kahn , Andrew J. Larkoski , Noam Levi

We present Linear Diffusion Networks (LDNs), a novel architecture that reinterprets sequential data processing as a unified diffusion process. Our model integrates adaptive diffusion modules with localized nonlinear updates and a…

Machine Learning · Computer Science 2025-03-27 Jacob Fein-Ashley

Surface wave dispersion curve inversion is crucial for estimating subsurface shear-wave velocity (vs), yet traditional methods often face challenges related to computational cost, non-uniqueness, and sensitivity to initial models. While…

Geophysics · Physics 2025-09-09 Feng Liu , Bao Deng , Rui Su , Lei Bai , Wanli Ouyang

While many unsupervised learning models focus on one family of tasks, either generative or discriminative, we explore the possibility of a unified representation learner: a model which uses a single pre-training stage to address both…

Computer Vision and Pattern Recognition · Computer Science 2023-07-18 Soumik Mukhopadhyay , Matthew Gwilliam , Vatsal Agarwal , Namitha Padmanabhan , Archana Swaminathan , Srinidhi Hegde , Tianyi Zhou , Abhinav Shrivastava

Generative models such as denoising diffusion models are quickly advancing their ability to approximate highly complex data distributions. They are also increasingly leveraged in scientific machine learning, where samples from the implied…

Machine Learning · Computer Science 2025-03-14 Jan-Hendrik Bastek , WaiChing Sun , Dennis M. Kochmann

Supervised learning on molecules has incredible potential to be useful in chemistry, drug discovery, and materials science. Luckily, several promising and closely related neural network models invariant to molecular symmetries have already…

Machine Learning · Computer Science 2017-06-14 Justin Gilmer , Samuel S. Schoenholz , Patrick F. Riley , Oriol Vinyals , George E. Dahl
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