DiCOVA-Net: Diagnosing COVID-19 using Acoustics based on Deep Residual Network for the DiCOVA Challenge 2021

In this paper, we propose a deep residual network-based method, namely the DiCOVA-Net, to identify COVID-19 infected patients based on the acoustic recording of their coughs. Since there are far more healthy people than infected patients, this classification problem faces the challenge of imbalanced data. To improve the model's ability to recognize minority class (the infected patients), we introduce data augmentation and cost-sensitive methods into our model. Besides, considering the particularity of this task, we deploy some fine-tuning techniques to adjust the pre-training ResNet50. Furthermore, to improve the model's generalizability, we use ensemble learning to integrate prediction results from multiple base classifiers generated using different random seeds. To evaluate the proposed DiCOVA-Net's performance, we conducted experiments with the DiCOVA challenge dataset. The results show that our method has achieved 85.43\% in AUC, among the top of all competing teams.Comment: 5 figure

An empirical comparison of several recent epistatic interactions detection methods

ABSTRACT Motivation: Many new methods have recently been proposed for detecting epistatic interactions in GWAS data. There is however no in-depth independent comparison of these methods yet. Results: Five recent methods-TEAM, BOOST, SNPHarvester, SNPRuler, and Screen and Clean (SC)-are evaluated here in terms of power, type-1 error rate, scalability, and completeness. In terms of power, TEAM performs best on data with main effect and BOOST performs best on data without main effect. In terms of type-1 error rate, TEAM and BOOST have higher type-1 error rates than SNPRuler and SNPHarvester. SC does not control type-1 error rate well. In terms of scalability, we tested the five methods using a dataset with 100,000 SNPs on a 64-bit Ubuntu system, with Intel (R) Xeon(R) CPU 2.66GHz, 16G memory. TEAM takes ∼36 days to finish and SNPRuler reports heap allocation problems. BOOST scales up to 100,000 SNPs and the cost is much lower than that of TEAM. SC and SNPHarvester are the most scalable. In terms of completeness, we study how frequently the pruning techniques employed by these methods incorrectly prune away the most significant epistatic interactions. We find that, on average, 20% of datasets without main effect and 60% of datasets with main effect are pruned incorrectly by BOOST, SNPRuler, and SNPHarvester

The search for optimal oxygen saturation targets in critically ill: Patients observational data from large ICU databases

Ministry of Education, Singapore under its Academic Research Funding Tier

A multivariate timeseries modeling approach to severity of illness assessment and forecasting in ICU with sparse, heterogeneous clinical data

The ability to determine patient acuity (or severity of illness) has immediate practical use for clinicians. We evaluate the use of multivariate timeseries modeling with the multi-task Gaussian process (GP) models using noisy, incomplete, sparse, heterogeneous and unevenly-sampled clinical data, including both physiological signals and clinical notes. The learned multi-task GP (MTGP) hyperparameters are then used to assess and forecast patient acuity. Experiments were conducted with two real clinical data sets acquired from ICU patients: firstly, estimating cerebrovascular pressure reactivity, an important indicator of secondary damage for traumatic brain injury patients, by learning the interactions between intracranial pressure and mean arterial blood pressure signals, and secondly, mortality prediction using clinical progress notes. In both cases, MTGPs provided improved results: an MTGP model provided better results than single-task GP models for signal interpolation and forecasting (0.91 vs 0.69 RMSE), and the use of MTGP hyperparameters obtained improved results when used as additional classification features (0.812 vs 0.788 AUC).Intel Science and Technology Center for Big DataNational Institutes of Health. (U.S.). National Library of Medicine (Biomedical Informatics Research Training Grant NIH/NLM 2T15 LM007092-22)National Institute of Biomedical Imaging and Bioengineering (U.S.) (R01 Grant EB001659)Singapore. Agency for Science, Technology and Research (Graduate Scholarship

Towards exploratory hypothesis testing and analysis

10.1109/ICDE.2011.5767907Proceedings - International Conference on Data Engineering745-75

A multivariate timeseries modeling approach to severity of illness assessment and forecasting in ICU with sparse, heterogeneous clinical data

The ability to determine patient acuity (or severity of illness) has immediate practical use for clinicians. We evaluate the use of multivariate timeseries modeling with the multi-task Gaussian process (GP) models using noisy, incomplete, sparse, heterogeneous and unevenly-sampled clinical data, including both physiological signals and clinical notes. The learned multi-task GP (MTGP) hyperparameters are then used to assess and forecast patient acuity. Experiments were conducted with two real clinical data sets acquired from ICU patients: firstly, estimating cerebrovascular pressure reactivity, an important indicator of secondary damage for traumatic brain injury patients, by learning the interactions between intracranial pressure and mean arterial blood pressure signals, and secondly, mortality prediction using clinical progress notes. In both cases, MTGPs provided improved results: an MTGP model provided better results than single-task GP models for signal interpolation and forecasting (0.91 vs 0.69 RMSE), and the use of MTGP hyperparameters obtained improved results when used as additional classification features (0.812 vs 0.788 AUC).Intel Science and Technology Center for Big DataNational Institutes of Health. (U.S.). National Library of Medicine (Biomedical Informatics Research Training Grant NIH/NLM 2T15 LM007092-22)National Institute of Biomedical Imaging and Bioengineering (U.S.) (R01 Grant EB001659)Singapore. Agency for Science, Technology and Research (Graduate Scholarship

Obesity, Acute Kidney Injury, and Mortality in Critical Illness

Objectives: Although obesity is associated with risk for chronic kidney disease and improved survival, less is known about the associations of obesity with risk of acute kidney injury and post acute kidney injury mortality. Design: In a single-center inception cohort of almost 15,000 critically ill patients, we evaluated the association of obesity with acute kidney injury and acute kidney injury severity, as well as in-hospital and 1-year survival. Acute kidney injury was defined using the Kidney Disease Outcome Quality Initiative criteria. Measurements and Main Results: The acute kidney injury prevalence rates for normal, overweight, class I, II, and III obesity were 18.6%, 20.6%, 22.5%, 24.3%, and 24.0%, respectively, and the adjusted odds ratios of acute kidney injury were 1.18 (95% CI, 1.06-1.31), 1.35 (1.19-1.53), 1.47 (1.25-1.73), and 1.59 (1.31-1.87) when compared with normal weight, respectively. Each 5-kg/m 2 increase in body mass index was associated with a 10% risk (95% CI, 1.06-1.24; p < 0.001) of more severe acute kidney injury. Within-hospital and 1-year survival rates associated with the acute kidney injury episodes were similar across body mass index categories. Conclusion: Obesity is a risk factor for acute kidney injury, which is associated with increased short-and long-term mortality.National Institute of Biomedical Imaging and Bioengineering (U.S.) (Grant 2R01 EB001659)National Institutes of Health (U.S.) (Grant R01-EB001659