One of the most common forms of dementia is Alzheimer’s disease (AD), which leads to progressive mental deterioration. Unfortunately, there is no definitive diagnosis and cure that can stop the condition progressing. The diagnosis is often performed based on the clinical history and neuropsychological data, including magnetic resonance imaging (MRI). Deep neural networks (DNN) algorithms are gaining popularity for medical diagnosis, and have been used widely for the analysis of MRI data. DNNs can extract hidden features from thousands of training images automatically. However, they cannot judge how confident they are about their predictions. To use DNNs in safety-critical applications such as medical diagnosis, uncertainty quantification of DNNs predictions is crucial. For this purpose, Monte Carlo dropout (MCD) has been widely used, however, it may lead to overconfident and miss calibrated results. This paper proposes a framework in which the MCD algorithm’s hyper-parameters are optimized during training using Bayesian optimization for the first time. The conducted optimization leads to assigning high predictive entropy to erroneous predictions and making it possible to recognize risky predictions. The proposed framework is used for AD diagnosis, which has not been done before. We compare our method with some existing methods in the literature based on different uncertainty quantification criteria. The results of comprehensive experiments on the Kaggle dataset using a deep model pre-trained on the ImageNet dataset show that the proposed algorithm can quantify uncertainty much better than the existing methods.

Prostate cancer (PC) is the most frequently diagnosed non-skin cancer in the world. Previous studies showed that genomic alterations represent the most common mechanism for molecular alterations that cause the development and progression of PC. Great efforts have been done to identify common protein-coding genetic variations; however, the impact of non-coding variations including regulatory genetic variants is not still well understood. To gain an understanding of the functional impact of genetic variants, particularly, regulatory variants in PC, we developed an integrative pipeline (AGV) that used whole genome/exome sequences, GWAS SNPs, chromosome conformation capture data, and ChIP-Seq signals to investigate the potential impact of genomic variants on the underlying target genes in PC. We identified 646 putative regulatory variants, of which 30 of them significantly altered the expression of at least one protein-coding gene. Our analysis of chromatin interactions data (Hi-C) revealed that the 30 putative regulatory variants may affect 131 coding and non-coding genes. Interestingly, our study showed the 131 protein-coding genes are involved in disease-related pathways including Reactome and MSigDB in which for most of them targeted treatment options are currently available. Together, our results provide a comprehensive map of genomic variants in PC and revealed their potential contribution to prostate cancer progression and development.