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At present, the majority of the proposed Deep Learning (DL) methods provide point predictions without quantifying the model's uncertainty. However, a quantification of the reliability of automated image analysis is essential, in particular in medicine when physicians rely on the results for making critical treatment decisions. In this work, we provide an entire framework to diagnose ischemic stroke patients incorporating Bayesian uncertainty into the analysis procedure. We present a Bayesian Convolutional Neural Network (CNN) yielding a probability for a stroke lesion on 2D Magnetic Resonance (MR) images with corresponding uncertainty information about the reliability of the prediction. For patient-level diagnoses, different aggregation methods are proposed and evaluated, which combine the individual image-level predictions. Those methods take advantage of the uncertainty in the image predictions and report model uncertainty at the patient-level. In a cohort of 511 patients, our Bayesian CNN achieved an accuracy of 95.33% at the image-level representing a significant improvement of 2% over a non-Bayesian counterpart. The best patient aggregation method yielded 95.89% of accuracy. Integrating uncertainty information about image predictions in aggregation models resulted in higher uncertainty measures to false patient classifications, which enabled to filter critical patient diagnoses that are supposed to be closer examined by a medical doctor. We therefore recommend using Bayesian approaches not only for improved image-level prediction and uncertainty estimation but also for the detection of uncertain aggregations at the patient-level.
Mapping of tree seedlings is useful for tasks ranging from monitoring natural succession and regeneration to effective silvicultural management. Development of methods that are both accurate and cost-effective is especially important considering the dramatic increase in tree planting that is required globally to mitigate the impacts of climate change. The combination of high-resolution imagery from unmanned aerial vehicles and object detection by convolutional neural networks (CNNs) is one promising approach. However, unbiased assessments of these models and methods to integrate them into geospatial workflows are lacking. In this study, we present a method for rapid, large-scale mapping of young conifer seedlings using CNNs applied to RGB orthomosaic imagery. Importantly, we provide an unbiased assessment of model performance by using two well-characterised trial sites together containing over 30,000 seedlings to assemble datasets with a high level of completeness. Our results showed CNN-based models trained on two sites detected seedlings with sensitivities of 99.5% and 98.8%. False positives due to tall weeds at one site and naturally regenerating seedlings of the same species led to slightly lower precision of 98.5% and 96.7%. A model trained on examples from both sites had 99.4% sensitivity and precision of 97%, showing applicability across sites. Additional testing showed that the CNN model was able to detect 68.7% of obscured seedlings missed during the initial annotation of the imagery but present in the field data. Finally, we demonstrate the potential to use a form of weakly supervised training and a tile-based processing chain to enhance the accuracy and efficiency of CNNs applied to large, high-resolution orthomosaics.