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Keywords
Institute
Contemporary empirical applications frequently require flexible regression models for complex response types and large tabular or non-tabular, including image or text, data. Classical regression models either break down under the computational load of processing such data or require additional manual feature extraction to make these problems tractable. Here, we present deeptrafo, a package for fitting flexible regression models for conditional distributions using a tensorflow backend with numerous additional processors, such as neural networks, penalties, and smoothing splines. Package deeptrafo implements deep conditional transformation models (DCTMs) for binary, ordinal, count, survival, continuous, and time series responses, potentially with uninformative censoring. Unlike other available methods, DCTMs do not assume a parametric family of distributions for the response. Further, the data analyst may trade off interpretability and flexibility by supplying custom neural network architectures and smoothers for each term in an intuitive formula interface. We demonstrate how to set up, fit, and work with DCTMs for several response types. We further showcase how to construct ensembles of these models, evaluate models using inbuilt cross-validation, and use other convenience functions for DCTMs in several applications. Lastly, we discuss DCTMs in light of other approaches to regression with non-tabular data.
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.
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.
We propose a novel end-to-end neural network architecture that, once trained, directly outputs a probabilistic clustering of a batch of input examples in one pass. It estimates a distribution over the number of clusters k, and for each 1≤k≤kmax, a distribution over the individual cluster assignment for each data point. The network is trained in advance in a supervised fashion on separate data to learn grouping by any perceptual similarity criterion based on pairwise labels (same/different group). It can then be applied to different data containing different groups. We demonstrate promising performance on high-dimensional data like images (COIL-100) and speech (TIMIT). We call this “learning to cluster” and show its conceptual difference to deep metric learning, semi-supervise clustering and other related approaches while having the advantage of performing learnable clustering fully end-to-end.
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.
Probabilistic Deep Learning
(2020)
Probabilistic Deep Learning is a hands-on guide to the principles that support neural networks. Learn to improve network performance with the right distribution for different data types, and discover Bayesian variants that can state their own uncertainty to increase accuracy. This book provides easy-to-apply code and uses popular frameworks to keep you focused on practical applications.
Probabilistic Short-Term Low-Voltage Load Forecasting using Bernstein-Polynomial Normalizing Flows
(2021)
The transition to a fully renewable energy grid requires better forecasting of demand at the low-voltage level. However, high fluctuations and increasing electrification cause huge forecast errors with traditional point estimates. Probabilistic load forecasts take future uncertainties into account and thus enables various applications in 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 363 smart meter customers, our density predictions compare favorably against Gaussian and Gaussian mixture densities and also outperform a non-parametric approach based on the pinball loss for 24h-ahead load forecasting for two different neural network architectures.
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.