Graphs are data structures that effectively represent relational data in the real world. Graph representation learning is a significant task since it could facilitate various downstream tasks, such as node classification, link prediction, etc. Graph representation learning aims to map graph entities to low-dimensional vectors while preserving graph structure and entity relationships. Over the decades, many models have been proposed for graph representation learning. This paper aims to show a comprehensive picture of graph representation learning models, including traditional and state-of-the-art models on various graphs in different geometric spaces. First, we begin with five types of graph embedding models: graph kernels, matrix factorization models, shallow models, deep-learning models, and non-Euclidean models. In addition, we also discuss graph transformer models and Gaussian embedding models. Second, we present practical applications of graph embedding models, from constructing graphs for specific domains to applying models to solve tasks. Finally, we discuss challenges for existing models and future research directions in detail. As a result, this paper provides a structured overview of the diversity of graph embedding models.

Background: Ultrasound imaging is the most frequently performed for the patients with chronic hepatitis or liver cirrhosis. However, ultrasound imaging is highly operator dependent and interpretation of ultrasound images is subjective, thus well-trained radiologist is required for evaluation. Automated classification of liver fibrosis could alleviate the shortage of skilled radiologist especially in low-to-middle income countries. The purposed of this study is to evaluate deep convolutional neural networks (DCNNs) for classifying the degree of liver fibrosis according to the METAVIR score using US images. Methods: We used ultrasound (US) images from two tertiary university hospitals. A total of 7920 US images from 933 patients were used for training/validation of DCNNs. All patient were underwent liver biopsy or hepatectomy, and liver fibrosis was categorized based on pathology results using the METAVIR score. Five well-established DCNNs (VGGNet, ResNet, DenseNet, EfficientNet and ViT) was implemented to predict the METAVIR score. The performance of DCNNs for five-level (F0/F1/F2/F3/F4) classification was evaluated through area under the receiver operating characteristic curve (AUC) with 95% confidential interval, accuracy, sensitivity, specificity, positive and negative likelihood ratio. Results: Similar mean AUC values were achieved for five models; VGGNet (0.96), ResNet (0.96), DenseNet (0.95), EfficientNet (0.96), and ViT (0.95). The same mean accuracy (0.94) and specificity values (0.96) were yielded for all models. In terms of sensitivity, EffcientNet achieved highest mean value (0.85) while the other models produced slightly lower values range from 0.82 to 0.84. Conclusion: In this study, we demonstrated that DCNNs can classify the staging of liver fibrosis according to METAVIR score with high performance using conventional B-mode images. Among them, EfficientNET that have fewer parameters and computation cost produced highest performance. From the results, we believe that DCNNs based classification of liver fibrosis may allow fast and accurate diagnosis of liver fibrosis without needs of additional equipment for add-on test and may be powerful tool for supporting radiologists in clinical practice.

With the advances in deep learning, including Convolutional Neural Networks (CNN), automated diagnosis technology using medical images has received considerable attention in medical science. In particular, in the field of ultrasound imaging, CNN trains the features of organs through an amount of image data, so that an expert-level automatic diagnosis is possible only with images of actual patients. However, CNN models are also trained on the features that reflect the inherent bias of the imaging machine used for image acquisition. In other words, when the domain of data used for training is different from that of data applied for an actual diagnosis, it is unclear whether consistent performance can be provided by the domain bias. Therefore, we investigate the effect of domain bias on the model with liver ultrasound imaging data obtained from multiple domains. We have constructed a dataset considering the manufacturer and the year of manufacturing of 8 ultrasound imaging machines. First, training and testing were performed by dividing the entire data, in a commonly used method. Second, we have utilized the training data constructed according to the number of domains for the machine learning process. Then we have measured and compared the performance on internal and external domain data. Through the above experiment, we have analyzed the effect of domains of data on model performance. We show that the performance scores evaluated with the internal domain data and the external domain data do not match. We especially show that the performance measured in the evaluation data including the internal domain was much higher than the performance measured in the evaluation data consisting of the external domain. We also show that 3-level classification performance is slightly improved over 5-level classification by mitigating class imbalance by integrating similar classes. The results highlight the need to develop a new methodology for mitigating the machine bias problem so that the model can work correctly even on external domain data, as opposed to the usual approach of constructing evaluation data in the same domain as the training data.