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Know when you don't know
(2018)
Deep convolutional neural networks show outstanding performance in image-based phenotype classification given that all existing phenotypes are presented during the training of the network. However, in real-world high-content screening (HCS) experiments, it is often impossible to know all phenotypes in advance. Moreover, novel phenotype discovery itself can be an HCS outcome of interest. This aspect of HCS is not yet covered by classical deep learning approaches. When presenting an image with a novel phenotype to a trained network, it fails to indicate a novelty discovery but assigns the image to a wrong phenotype. To tackle this problem and address the need for novelty detection, we use a recently developed Bayesian approach for deep neural networks called Monte Carlo (MC) dropout to define different uncertainty measures for each phenotype prediction. With real HCS data, we show that these uncertainty measures allow us to identify novel or unclear phenotypes. In addition, we also found that the MC dropout method results in a significant improvement of classification accuracy. The proposed procedure used in our HCS case study can be easily transferred to any existing network architecture and will be beneficial in terms of accuracy and novelty detection.
Rheumatoid arthritis is an autoimmune disease that causes chronic inflammation of synovial joints, often resulting in irreversible structural damage. The activity of the disease is evaluated by clinical examinations, laboratory tests, and patient self-assessment. The long-term course of the disease is assessed with radiographs of hands and feet. The evaluation of the X-ray images performed by trained medical staff requires several minutes per patient. We demonstrate that deep convolutional neural networks can be leveraged for a fully automated, fast, and reproducible scoring of X-ray images of patients with rheumatoid arthritis. A comparison of the predictions of different human experts and our deep learning system shows that there is no significant difference in the performance of human experts and our deep learning model.
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.
Outcomes with a natural order commonly occur in prediction problems and often the available input data are a mixture of complex data like images and tabular predictors. Deep Learning (DL) models are state-of-the-art for image classification tasks but frequently treat ordinal outcomes as unordered and lack interpretability. In contrast, classical ordinal regression models consider the outcome’s order and yield interpretable predictor effects but are limited to tabular data. We present ordinal neural network transformation models (ontrams), which unite DL with classical ordinal regression approaches. ontrams are a special case of transformation models and trade off flexibility and interpretability by additively decomposing the transformation function into terms for image and tabular data using jointly trained neural networks. The performance of the most flexible ontram is by definition equivalent to a standard multi-class DL model trained with cross-entropy while being faster in training when facing ordinal outcomes. Lastly, we discuss how to interpret model components for both tabular and image data on two publicly available datasets.
This study aims to investigate the utilization of Bayesian techniques for the calibration of micro-electro-mechanical system (MEMS) accelerometers. These devices have garnered substantial interest in various practical applications and typically require calibration through error-correcting functions. The parameters of these error-correcting functions are determined during a calibration process. However, due to various sources of noise, these parameters cannot be determined with precision, making it desirable to incorporate uncertainty in the calibration models. Bayesian modeling offers a natural and complete way of reflecting uncertainty by treating the model parameters as variables rather than fixed values. In addition, Bayesian modeling enables the incorporation of prior knowledge, making it an ideal choice for calibration. Nevertheless, it is infrequently used in sensor calibration. This study introduces Bayesian methods for the calibration of MEMS accelerometer data in a straightforward manner using recent advances in probabilistic programming.
Study design:
Retrospective, mono-centric cohort research study.
Objectives:
The purpose of this study is to validate a novel artificial intelligence (AI)-based algorithm against human-generated ground truth for radiographic parameters of adolescent idiopathic scoliosis (AIS).
Methods:
An AI-algorithm was developed that is capable of detecting anatomical structures of interest (clavicles, cervical, thoracic, lumbar spine and sacrum) and calculate essential radiographic parameters in AP spine X-rays fully automatically. The evaluated parameters included T1-tilt, clavicle angle (CA), coronal balance (CB), lumbar modifier, and Cobb angles in the proximal thoracic (C-PT), thoracic, and thoracolumbar regions. Measurements from 2 experienced physicians on 100 preoperative AP full spine X-rays of AIS patients were used as ground truth and to evaluate inter-rater and intra-rater reliability. The agreement between human raters and AI was compared by means of single measure Intra-class Correlation Coefficients (ICC; absolute agreement; .75 rated as excellent), mean error and additional statistical metrics.
Results:
The comparison between human raters resulted in excellent ICC values for intra- (range: .97-1) and inter-rater (.85-.99) reliability. The algorithm was able to determine all parameters in 100% of images with excellent ICC values (.78-.98). Consistently with the human raters, ICC values were typically smallest for C-PT (eg, rater 1A vs AI: .78, mean error: 4.7°) and largest for CB (.96, -.5 mm) as well as CA (.98, .2°).
Conclusions:
The AI-algorithm shows excellent reliability and agreement with human raters for coronal parameters in preoperative full spine images. The reliability and speed offered by the AI-algorithm could contribute to the efficient analysis of large datasets (eg, registry studies) and measurements in clinical practice.
Short-Term Density Forecasting of Low-Voltage Load using Bernstein-Polynomial Normalizing Flows
(2023)
The transition to a fully renewable energy grid requires better forecasting of demand at the low-voltage level to increase efficiency and ensure reliable control. However, high fluctuations and increasing electrification cause huge forecast variability, not reflected in traditional point estimates. Probabilistic load forecasts take uncertainties into account and thus allow more informed decision-making for the planning and operation of low-carbon energy systems. We propose an approach for flexible conditional density forecasting of short-term load based on Bernstein polynomial normalizing flows, where a neural network controls the parameters of the flow. In an empirical study with 3639 smart meter customers, our density predictions for 24h-ahead load forecasting compare favorably against Gaussian and Gaussian mixture densities. Furthermore, they outperform a non-parametric approach based on the pinball loss, especially in low-data scenarios.