Graph representation learning in biomedicine and healthcare

MM Li, K Huang, M Zitnik - Nature Biomedical Engineering, 2022 - nature.com
Networks—or graphs—are universal descriptors of systems of interacting elements. In
biomedicine and healthcare, they can represent, for example, molecular interactions …

Biological network analysis with deep learning

G Muzio, L O'Bray, K Borgwardt - Briefings in bioinformatics, 2021 - academic.oup.com
Recent advancements in experimental high-throughput technologies have expanded the
availability and quantity of molecular data in biology. Given the importance of interactions in …

Simple and deep graph convolutional networks

M Chen, Z Wei, Z Huang, B Ding… - … conference on machine …, 2020 - proceedings.mlr.press
Graph convolutional networks (GCNs) are a powerful deep learning approach for graph-
structured data. Recently, GCNs and subsequent variants have shown superior performance …

Graph neural networks in tensorflow and keras with spektral [application notes]

D Grattarola, C Alippi - IEEE Computational Intelligence …, 2021 - ieeexplore.ieee.org
Graph neural networks have-enabled the application of deep learning to problems that can
be described by graphs, which are found throughout the different fields of sci-ence, from …

Pre-training of graph augmented transformers for medication recommendation

J Shang, T Ma, C **ao, J Sun - arxiv preprint arxiv:1906.00346, 2019 - arxiv.org
Medication recommendation is an important healthcare application. It is commonly
formulated as a temporal prediction task. Hence, most existing works only utilize longitudinal …

Molerec: Combinatorial drug recommendation with substructure-aware molecular representation learning

N Yang, K Zeng, Q Wu, J Yan - Proceedings of the ACM web conference …, 2023 - dl.acm.org
Combinatorial drug recommendation involves recommending a personalized combination of
medication (drugs) to a patient over his/her longitudinal history, which essentially aims at …

Learning the graphical structure of electronic health records with graph convolutional transformer

E Choi, Z Xu, Y Li, M Dusenberry, G Flores… - Proceedings of the …, 2020 - ojs.aaai.org
Effective modeling of electronic health records (EHR) is rapidly becoming an important topic
in both academia and industry. A recent study showed that using the graphical structure …

[BOK][B] Introduction to graph neural networks

Z Liu, J Zhou - 2022 - books.google.com
Graphs are useful data structures in complex real-life applications such as modeling
physical systems, learning molecular fingerprints, controlling traffic networks, and …

Safedrug: Dual molecular graph encoders for recommending effective and safe drug combinations

C Yang, C **ao, F Ma, L Glass, J Sun - arxiv preprint arxiv:2105.02711, 2021 - arxiv.org
Medication recommendation is an essential task of AI for healthcare. Existing works focused
on recommending drug combinations for patients with complex health conditions solely …

Synthesize high-dimensional longitudinal electronic health records via hierarchical autoregressive language model

B Theodorou, C **ao, J Sun - Nature communications, 2023 - nature.com
Synthetic electronic health records (EHRs) that are both realistic and privacy-preserving
offer alternatives to real EHRs for machine learning (ML) and statistical analysis. However …