3D augmentation for volumetric whole heart segmentation.

Data augmentation is a technique usually deployed to mitigate the possible performance limitation from training a neural network model on a limited dataset, especially in the medical domain. This paper presents a study on effects of applying different rotation settings to augment cardiac volumes from the Multi-modality Whole Heart Segmentation dataset, in order to improve the segmentation performance. This study presents a comparison between conventional 2D (slice-wise) rotation primarily on the axial axis, 3D (volume-wise) rotation, and our proposed rotation setting that takes into account possible cardiac alignment according to its anatomy. The study has suggested two key considerations: 2D slice-wise rotation should be avoided when using 3D data for segmentation, due to intrinsic structural correlation between subsequent slices, and that 3D rotations may help improve segmentation performance on data previously unseen to the model.

COVID-19 detection and heatmap generation in chest x-ray images.

Purpose: The outbreak of COVID-19 or coronavirus was first reported in 2019. It has widely and rapidly spread around the world. The detection of COVID-19 cases is one of the important factors to stop the epidemic, because the infected individuals must be quarantined. One reliable way to detect COVID-19 cases is using chest x-ray images, where signals of the infection are located in lung areas. We propose a solution to automatically classify COVID-19 cases in chest x-ray images. Approach: The ResNet-101 architecture is adopted as the main network with more than 44 millions parameters. The whole net is trained using the large size of 1500 × 1500 x-ray images. The heatmap under the region of interest of segmented lung is constructed to visualize and emphasize signals of COVID-19 in each input x-ray image. Lungs are segmented using the pretrained U-Net. The confidence score of being COVID-19 is also calculated for each classification result. Results: The proposed solution is evaluated based on COVID-19 and normal cases. It is also tested on unseen classes to validate a regularization of the constructed model. They include other normal cases where chest x-ray images are normal without any disease but with some small remarks, and other abnormal cases where chest x-ray images are abnormal with some other diseases containing remarks similar to COVID-19. The proposed method can achieve the sensitivity, specificity, and accuracy of 97%, 98%, and 98%, respectively. Conclusions: It can be concluded that the proposed solution can detect COVID-19 in a chest x-ray image. The heatmap and confidence score of the detection are also demonstrated, such that users or human experts can use them for a final diagnosis in practical usages.

A 'what-if' scenario: Nipah virus attacks pig trade chains in Thailand.

BACKGROUND: Nipah virus (NiV) is a fatal zoonotic agent that was first identified amongst pig farmers in Malaysia in 1998, in an outbreak that resulted in 105 fatal human cases. That epidemic arose from a chain of infection, initiating from bats to pigs, and which then spilled over from pigs to humans. In Thailand, bat-pig-human communities can be observed across the country, particularly in the central plain. The present study therefore aimed to identify high-risk areas for potential NiV outbreaks and to model how the virus is likely to spread. Multi-criteria decision analysis (MCDA) and weighted linear combination (WLC) were employed to produce the NiV risk map. The map was then overlaid with the nationwide pig movement network to identify the index subdistricts in which NiV may emerge. Subsequently, susceptible-exposed-infectious-removed (SEIR) modeling was used to simulate NiV spread within each subdistrict, and network modeling was used to illustrate how the virus disperses across subdistricts. RESULTS: Based on the MCDA and pig movement data, 14 index subdistricts with a high-risk of NiV emergence were identified. We found in our infectious network modeling that the infected subdistricts clustered in, or close to the central plain, within a range of 171 km from the source subdistricts. However, the virus may travel as far as 528.5 km (R0 = 5). CONCLUSIONS: In conclusion, the risk of NiV dissemination through pig movement networks in Thailand is low but not negligible. The risk areas identified in our study can help the veterinary authority to allocate financial and human resources to where preventive strategies, such as pig farm regionalization, are required and to contain outbreaks in a timely fashion once they occur.