Confidence intervals for performance estimates in 3D medical image segmentation

Medical segmentation models are evaluated empirically. As such an evaluation is based on a limited set of example images, it is unavoidably noisy. Beyond a mean performance measure, reporting confidence intervals is thus crucial. However, this is rarely done in medical image segmentation. The width of the confidence interval depends on the test set size and on the spread of the performance measure (its standard-deviation across of the test set). For classification, many test images are needed to avoid wide confidence intervals. Segmentation, however, has not been studied, and it differs by the amount of information brought by a given test image. In this paper, we study the typical confidence intervals in medical image segmentation. We carry experiments on 3D image segmentation using the standard nnU-net framework, two datasets from the Medical Decathlon challenge and two performance measures: the Dice accuracy and the Hausdorff distance. We show that the parametric confidence intervals are reasonable approximations of the bootstrap estimates for varying test set sizes and spread of the performance metric. Importantly, we show that the test size needed to achieve a given precision is often much lower than for classification tasks. Typically, a 1% wide confidence interval requires about 100-200 test samples when the spread is low (standard-deviation around 3%). More difficult segmentation tasks may lead to higher spreads and require over 1000 samples.Comment: 10 page

Consanguinity and reproductive health among Arabs

Consanguineous marriages have been practiced since the early existence of modern humans. Until now consanguinity is widely practiced in several global communities with variable rates depending on religion, culture, and geography. Arab populations have a long tradition of consanguinity due to socio-cultural factors. Many Arab countries display some of the highest rates of consanguineous marriages in the world, and specifically first cousin marriages which may reach 25-30% of all marriages. In some countries like Qatar, Yemen, and UAE, consanguinity rates are increasing in the current generation. Research among Arabs and worldwide has indicated that consanguinity could have an effect on some reproductive health parameters such as postnatal mortality and rates of congenital malformations. The association of consanguinity with other reproductive health parameters, such as fertility and fetal wastage, is controversial. The main impact of consanguinity, however, is an increase in the rate of homozygotes for autosomal recessive genetic disorders. Worldwide, known dominant disorders are more numerous than known recessive disorders. However, data on genetic disorders in Arab populations as extracted from the Catalogue of Transmission Genetics in Arabs (CTGA) database indicate a relative abundance of recessive disorders in the region that is clearly associated with the practice of consanguinity

CoordConv-Unet: Investigating CoordConv for Organ Segmentation

International audienceObjectives: Convolutional neural networks (CNNs) have established state-of-the-art performance in computer vision tasks such as object detection and segmentation. One of the major remaining challenges concerns their ability to capture consistent spatial and anatomically plausible attributes in medical image segmentation. To address this issue, many works advocate to integrate prior information at the level of the loss function. However, prior-based losses often suffer from local solutions and training instability. The CoordConv layers are extensions of convolutional neural network wherein convolution is conditioned on spatial coordinates. The objective of this paper is to investigate CoordConv as a proficient substitute to convolutional layers for medical image segmentation tasks when trained under prior-based losses.Methods: This work introduces CoordConv-Unet which is a novel structure that can be used to accommodate training under anatomical prior losses. The proposed architecture demonstrates a dual role relative to prior constrained CNN learning: it either demonstrates a regularizing role that stabilizes learning while maintaining system performance, or improves system performance by allowing the learning to be more stable and to evade local minima.Results: To validate the performance of the proposed model, experiments are conducted on two well-known public datasets from the Decathlon challenge: a mono-modal MRI dataset dedicated to segmentation of the left atrium, and a CT image dataset whose objective is to segment the spleen, an organ characterized with varying size and mild convexity issues.Conclusion: Results show that, despite the inadequacy of CoordConv when trained with the regular dice baseline loss, the proposed CoordConv-Unet structure can improve significantly model performance when trained under anatomically constrained prior losses

Effect of women's perceptions and household practices on children’s waterborne illness in a low income community

An ecosystem approach to human health was adopted in a community-based study carried out in Bebnine, an underserved town in Lebanon. The objective of the study is to examine the association between women’s household practices and diarrhea among children in a setting where contaminated drinking water and intestinal diseases are common. A total of 280 women were randomly selected and interviewed using a structured questionnaire. Data were collected on 712 children between the ages of 6 and 14. The study instrument included determinants of diarrhea such as sociodemographic characteristics, water, sanitation, hygiene practices, gender variables, and behavioral risk factors. Multivariate regression analysis was employed to examine the association between water handling practices and diarrhea. The prevalence of diarrhea is 5%. Female children are more likely to suffer from diarrhea than male children (OR = 2.58; 95% CI: 1.19–5.62). Treatment of drinking water at the household level and the use of drinking water for cooking and the preparation of hot beverages are protective against diarrhea (OR = 0.15; 95% CI: 0.03–0.65). Female caretakers’ behaviors such as daily bathing and seeking medical care at times of illness are protective against diarrhea in children. The findings suggest that diarrhea is a gendered health problem. Female children, who are generally more involved in household activities than male children, are at higher risk of suffering from diarrhea. Female caretakers’ personal hygiene, household practices, and perceptions of diarrhea are additional risk factors. Intervention activities would be more effective if based on a better understanding of gender roles and household power relations

Racial, Ethnic and Socioeconomic Diversity and Outcomes of Patients with Graft-versus-Host Disease: A CIBMTR Analysis

Socioeconomic status (SES) and race/ethnicity have been associated with outcomes of allogeneic hematopoietic cell transplantation (allo-HCT). Certain aspects of GVHD management such as the need for long term care, prolonged immunosuppressive treatment, and need for close follow up for complications may exacerbate disparities. Adults (≥ 18 years) reported to the Center for International Blood and Marrow Transplant Research (CIBMTR) who underwent a first alloHCT for acute leukemia, myelodysplastic syndrome, or myeloproliferative neoplasm between 2008 - 2018 were included. Endpoints for those developing GVHD included overall survival (OS), transplant related mortality (TRM), and disease relapse. Models were adjusted for patient and transplant related variables. A two-sided p-value < 0.01 was considered significant. Among the 14,825 allo-HCT recipients, 6,259 (42.2%) and 6,675 (45.0%) patients developed aGVHD and cGVHD, respectively. In patients with aGVHD, non-Hispanic Blacks had increased TRM (HR 1.50, 95% CI 1.24-1.83, p=0.0001) and overall mortality (HR 1.31, 1.14-1.50, p=0.0002) compared with non-Hispanic Whites, an association that disappeared when severity of aGVHD was included in the model. Lower SES was associated with increased risk of disease relapse (p=0.0016) but not OS or TRM. In patients who developed cGVHD, race and ethnicity were not associated with OS, TRM and disease relapse. However, the highest quartile of annual household income (≥ $80,000) had improved OS (HR 0.77, 0.69-0.85, p<0.0001) and reduced TRM (HR 0.86, 0.67-0.87, p<0.0001) compared with lowest quartile, adjusting for race and ethnicity. Race/ethnicity and SES are associated with outcomes after GVHD. Optimizing health care resources available to low SES patients and strategies to minimize the risk of severe GVHD in non-Hispanic Blacks may improve long-term outcomes