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 …

[HTML][HTML] 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 …

Vision Transformers in medical computer vision—A contemplative retrospection

A Parvaiz, MA Khalid, R Zafar, H Ameer, M Ali… - … Applications of Artificial …, 2023 - Elsevier
Abstract Vision Transformers (ViTs), with the magnificent potential to unravel the information
contained within images, have evolved as one of the most contemporary and dominant …

Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens

Z Wu, AE Trevino, E Wu, K Swanson, HJ Kim… - Nature Biomedical …, 2022 - nature.com
Multiplexed immunofluorescence imaging allows the multidimensional molecular profiling of
cellular environments at subcellular resolution. However, identifying and characterizing …

A graph-transformer for whole slide image classification

Y Zheng, RH Gindra, EJ Green, EJ Burks… - IEEE transactions on …, 2022 - ieeexplore.ieee.org
Deep learning is a powerful tool for whole slide image (WSI) analysis. Typically, when
performing supervised deep learning, a WSI is divided into small patches, trained and the …

Pathomic fusion: an integrated framework for fusing histopathology and genomic features for cancer diagnosis and prognosis

RJ Chen, MY Lu, J Wang… - … on Medical Imaging, 2020 - ieeexplore.ieee.org
Cancer diagnosis, prognosis, mymargin and therapeutic response predictions are based on
morphological information from histology slides and molecular profiles from genomic data …

Artificial intelligence for digital and computational pathology

AH Song, G Jaume, DFK Williamson, MY Lu… - Nature Reviews …, 2023 - nature.com
Advances in digitizing tissue slides and the fast-paced progress in artificial intelligence,
including deep learning, have boosted the field of computational pathology. This field holds …

Derivation of prognostic contextual histopathological features from whole-slide images of tumours via graph deep learning

Y Lee, JH Park, S Oh, K Shin, J Sun, M Jung… - Nature Biomedical …, 2022 - nature.com
Methods of computational pathology applied to the analysis of whole-slide images (WSIs) do
not typically consider histopathological features from the tumour microenvironment. Here …

Principles and challenges of modeling temporal and spatial omics data

B Velten, O Stegle - Nature Methods, 2023 - nature.com
Studies with temporal or spatial resolution are crucial to understand the molecular dynamics
and spatial dependencies underlying a biological process or system. With advances in high …

[HTML][HTML] Machine learning methods for cancer classification using gene expression data: A review

F Alharbi, A Vakanski - Bioengineering, 2023 - mdpi.com
Cancer is a term that denotes a group of diseases caused by the abnormal growth of cells
that can spread in different parts of the body. According to the World Health Organization …