Graph neural networks and their current applications in bioinformatics

XM Zhang, L Liang, L Liu, MJ Tang - Frontiers in genetics, 2021 - frontiersin.org
Graph neural networks (GNNs), as a branch of deep learning in non-Euclidean space,
perform particularly well in various tasks that process graph structure data. With the rapid …

[HTML][HTML] Graph neural networks: A review of methods and applications

J Zhou, G Cui, S Hu, Z Zhang, C Yang, Z Liu, L Wang… - AI open, 2020 - Elsevier
Lots of learning tasks require dealing with graph data which contains rich relation
information among elements. Modeling physics systems, learning molecular fingerprints …

Deepgcns: Can gcns go as deep as cnns?

G Li, M Muller, A Thabet… - Proceedings of the IEEE …, 2019 - openaccess.thecvf.com
Abstract Convolutional Neural Networks (CNNs) achieve impressive performance in a wide
variety of fields. Their success benefited from a massive boost when very deep CNN models …

Entity, relation, and event extraction with contextualized span representations

D Wadden, U Wennberg, Y Luan… - arxiv preprint arxiv …, 2019 - arxiv.org
We examine the capabilities of a unified, multi-task framework for three information
extraction tasks: named entity recognition, relation extraction, and event extraction. Our …

A survey of graph neural networks for social recommender systems

K Sharma, YC Lee, S Nambi, A Salian, S Shah… - ACM Computing …, 2024 - dl.acm.org
Social recommender systems (SocialRS) simultaneously leverage the user-to-item
interactions as well as the user-to-user social relations for the task of generating item …

A deep-learning system bridging molecule structure and biomedical text with comprehension comparable to human professionals

Z Zeng, Y Yao, Z Liu, M Sun - Nature communications, 2022 - nature.com
To accelerate biomedical research process, deep-learning systems are developed to
automatically acquire knowledge about molecule entities by reading large-scale biomedical …

Attention guided graph convolutional networks for relation extraction

Z Guo, Y Zhang, W Lu - arxiv preprint arxiv:1906.07510, 2019 - arxiv.org
Dependency trees convey rich structural information that is proven useful for extracting
relations among entities in text. However, how to effectively make use of relevant information …

DocRED: A large-scale document-level relation extraction dataset

Y Yao, D Ye, P Li, X Han, Y Lin, Z Liu, Z Liu… - arxiv preprint arxiv …, 2019 - arxiv.org
Multiple entities in a document generally exhibit complex inter-sentence relations, and
cannot be well handled by existing relation extraction (RE) methods that typically focus on …

Two are better than one: Joint entity and relation extraction with table-sequence encoders

J Wang, W Lu - arxiv preprint arxiv:2010.03851, 2020 - arxiv.org
Named entity recognition and relation extraction are two important fundamental problems.
Joint learning algorithms have been proposed to solve both tasks simultaneously, and many …

Multi-task identification of entities, relations, and coreference for scientific knowledge graph construction

Y Luan, L He, M Ostendorf, H Hajishirzi - arxiv preprint arxiv:1808.09602, 2018 - arxiv.org
We introduce a multi-task setup of identifying and classifying entities, relations, and
coreference clusters in scientific articles. We create SciERC, a dataset that includes …