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Structure-informed protein representation learning is essential for effective protein function annotation and \textit{de novo} design. However, the presence of inherent noise in both crystal and AlphaFold-predicted structures poses…

生物大分子 · 定量生物学 2025-03-25 Zhongyue Zhang , Runze Ma , Yanjie Huang , Shuangjia Zheng

The usage of 3D vision algorithms, such as shape reconstruction, remains limited because they require inputs to be at a fixed canonical rotation. Recently, a simple equivariant network, Vector Neuron (VN) has been proposed that can be…

计算机视觉与模式识别 · 计算机科学 2024-05-09 Dongwon Son , Jaehyung Kim , Sanghyeon Son , Beomjoon Kim

Invariance and equivariance to the rotation group have been widely discussed in the 3D deep learning community for pointclouds. Yet most proposed methods either use complex mathematical tools that may limit their accessibility, or are tied…

计算机视觉与模式识别 · 计算机科学 2021-04-27 Congyue Deng , Or Litany , Yueqi Duan , Adrien Poulenard , Andrea Tagliasacchi , Leonidas Guibas

We propose a general architecture that combines the coefficient learning scheme with a residual operator layer for learning mappings between continuous functions in the 3D Euclidean space. Our proposed model is guaranteed to achieve…

机器学习 · 计算机科学 2023-11-21 Chaoran Cheng , Jian Peng

The global attention mechanism is one of the keys to the success of transformer architecture, but it incurs quadratic computational costs in relation to the number of tokens. On the other hand, equivariant models, which leverage the…

Graph learning architectures based on the k-dimensional Weisfeiler-Leman (k-WL) hierarchy offer a theoretically well-understood expressive power. However, such architectures often fail to deliver solid predictive performance on real-world…

机器学习 · 计算机科学 2024-11-11 Luis Müller , Daniel Kusuma , Blai Bonet , Christopher Morris

While (message-passing) graph neural networks have clear limitations in approximating permutation-equivariant functions over graphs or general relational data, more expressive, higher-order graph neural networks do not scale to large…

机器学习 · 计算机科学 2022-08-31 Christopher Morris , Gaurav Rattan , Sandra Kiefer , Siamak Ravanbakhsh

Spiking Neural Networks have attracted significant attention in recent years due to their distinctive low-power characteristics. Meanwhile, Transformer models, known for their powerful self-attention mechanisms and parallel processing…

神经与进化计算 · 计算机科学 2024-12-19 Hangming Zhang , Alexander Sboev , Roman Rybka , Qiang Yu

We present a new class of efficient attention mechanisms applying universal 3D Relative Positional Encoding (RPE) methods given by arbitrary integrable modulation functions $f$. They lead to the new class of 3D-Transformer models, called…

机器学习 · 计算机科学 2026-05-12 Byeongchan Kim , Arijit Sehanobish , Avinava Dubey , Min-hwan Oh , Krzysztof Choromanski

Recent works on multi-modal emotion recognition move towards end-to-end models, which can extract the task-specific features supervised by the target task compared with the two-phase pipeline. However, previous methods only model the…

计算与语言 · 计算机科学 2022-09-21 Yang Wu , Pai Peng , Zhenyu Zhang , Yanyan Zhao , Bing Qin

Transformer architectures can effectively learn language-conditioned, multi-task 3D open-loop manipulation policies from demonstrations by jointly processing natural language instructions and 3D observations. However, although both the…

机器人学 · 计算机科学 2025-05-28 Xupeng Zhu , Yu Qi , Yizhe Zhu , Robin Walters , Robert Platt

Based on the theory of homogeneous spaces we derive geometrically optimal edge attributes to be used within the flexible message-passing framework. We formalize the notion of weight sharing in convolutional networks as the sharing of…

机器学习 · 计算机科学 2024-03-18 Erik J Bekkers , Sharvaree Vadgama , Rob D Hesselink , Putri A van der Linden , David W Romero

Transformers have achieved remarkable performance in a myriad of fields including natural language processing and computer vision. However, when it comes to the graph mining area, where graph neural network (GNN) has been the dominant…

机器学习 · 计算机科学 2021-10-26 Jianan Zhao , Chaozhuo Li , Qianlong Wen , Yiqi Wang , Yuming Liu , Hao Sun , Xing Xie , Yanfang Ye

A symmetry on rigid motion is one of the salient factors in efficient learning of 3D point cloud problems. Group convolution has been a representative method to extract equivariant features, but its realizations have struggled to retain…

计算机视觉与模式识别 · 计算机科学 2026-03-19 Jaein Kim , Hee Bin Yoo , Dong-Sig Han , Byoung-Tak Zhang

Circuit representation learning has shown promising results in advancing the field of Electronic Design Automation (EDA). Existing models, such as DeepGate Family, primarily utilize Graph Neural Networks (GNNs) to encode circuit netlists…

机器学习 · 计算机科学 2024-07-17 Zhengyuan Shi , Ziyang Zheng , Sadaf Khan , Jianyuan Zhong , Min Li , Qiang Xu

The adoption of Vision Transformers (ViTs) based architectures represents a significant advancement in 3D Medical Image (MI) segmentation, surpassing traditional Convolutional Neural Network (CNN) models by enhancing global contextual…

计算机视觉与模式识别 · 计算机科学 2024-04-25 Shehan Perera , Pouyan Navard , Alper Yilmaz

Representing and reasoning about 3D structures of macromolecules is emerging as a distinct challenge in machine learning. Here, we extend recent work on geometric vector perceptrons and apply equivariant graph neural networks to a wide…

机器学习 · 计算机科学 2021-07-14 Bowen Jing , Stephan Eismann , Pratham N. Soni , Ron O. Dror

Equivariant Graph Neural Networks (GNNs) have achieved remarkable success across diverse scientific applications. However, existing approaches face critical efficiency challenges when scaling to large geometric graphs and suffer significant…

机器学习 · 计算机科学 2025-06-25 Yuelin Zhang , Jiacheng Cen , Jiaqi Han , Wenbing Huang

Equivariance of neural networks to transformations helps to improve their performance and reduce generalization error in computer vision tasks, as they apply to datasets presenting symmetries (e.g. scalings, rotations, translations). The…

计算机视觉与模式识别 · 计算机科学 2022-11-08 Mateus Sangalli , Samy Blusseau , Santiago Velasco-Forero , Jesus Angulo

Transformer-based models have recently shown success in representation learning on graph-structured data beyond natural language processing and computer vision. However, the success is limited to small-scale graphs due to the drawbacks of…

机器学习 · 计算机科学 2022-10-05 Jinyoung Park , Seongjun Yun , Hyeonjin Park , Jaewoo Kang , Jisu Jeong , Kyung-Min Kim , Jung-woo Ha , Hyunwoo J. Kim