Current progress and open challenges for applying deep learning across the biosciences

N Sapoval, A Aghazadeh, MG Nute… - Nature …, 2022‏ - nature.com
Deep Learning (DL) has recently enabled unprecedented advances in one of the grand
challenges in computational biology: the half-century-old problem of protein structure …

The evolution of distributed systems for graph neural networks and their origin in graph processing and deep learning: A survey

J Vatter, R Mayer, HA Jacobsen - ACM Computing Surveys, 2023‏ - dl.acm.org
Graph neural networks (GNNs) are an emerging research field. This specialized deep
neural network architecture is capable of processing graph structured data and bridges the …

Data augmentation for deep graph learning: A survey

K Ding, Z Xu, H Tong, H Liu - ACM SIGKDD Explorations Newsletter, 2022‏ - dl.acm.org
Graph neural networks, a powerful deep learning tool to model graph-structured data, have
demonstrated remarkable performance on numerous graph learning tasks. To address the …

Graphmae2: A decoding-enhanced masked self-supervised graph learner

Z Hou, Y He, Y Cen, X Liu, Y Dong… - Proceedings of the …, 2023‏ - dl.acm.org
Graph self-supervised learning (SSL), including contrastive and generative approaches,
offers great potential to address the fundamental challenge of label scarcity in real-world …

Graph contrastive learning with augmentations

Y You, T Chen, Y Sui, T Chen… - Advances in neural …, 2020‏ - proceedings.neurips.cc
Generalizable, transferrable, and robust representation learning on graph-structured data
remains a challenge for current graph neural networks (GNNs). Unlike what has been …

NAGphormer: A tokenized graph transformer for node classification in large graphs

J Chen, K Gao, G Li, K He - arxiv preprint arxiv:2206.04910, 2022‏ - arxiv.org
The graph Transformer emerges as a new architecture and has shown superior
performance on various graph mining tasks. In this work, we observe that existing graph …

Gpt-gnn: Generative pre-training of graph neural networks

Z Hu, Y Dong, K Wang, KW Chang, Y Sun - Proceedings of the 26th ACM …, 2020‏ - dl.acm.org
Graph neural networks (GNNs) have been demonstrated to be powerful in modeling graph-
structured data. However, training GNNs requires abundant task-specific labeled data …

Heterogeneous graph transformer

Z Hu, Y Dong, K Wang, Y Sun - Proceedings of the web conference 2020, 2020‏ - dl.acm.org
Recent years have witnessed the emerging success of graph neural networks (GNNs) for
modeling structured data. However, most GNNs are designed for homogeneous graphs, in …

Enhancing graph neural network-based fraud detectors against camouflaged fraudsters

Y Dou, Z Liu, L Sun, Y Deng, H Peng… - Proceedings of the 29th …, 2020‏ - dl.acm.org
Graph Neural Networks (GNNs) have been widely applied to fraud detection problems in
recent years, revealing the suspiciousness of nodes by aggregating their neighborhood …

Decoupling the depth and scope of graph neural networks

H Zeng, M Zhang, Y **a, A Srivastava… - Advances in …, 2021‏ - proceedings.neurips.cc
State-of-the-art Graph Neural Networks (GNNs) have limited scalability with respect to the
graph and model sizes. On large graphs, increasing the model depth often means …