From Modern CNNs to Vision Transformers: Assessing the Performance, Robustness, and Classification Strategies of Deep Learning Models in HistopathologyMaximilian Springenberg, Annika Frommholz, Markus Wenzel et al.
While machine learning is currently transforming the field of histopathology, the domain lacks a comprehensive evaluation of state-of-the-art models based on essential but complementary quality requirements beyond a mere classification accuracy. In order to fill this gap, we developed a new methodology to extensively evaluate a wide range of classification models, including recent vision transformers, and convolutional neural networks such as: ConvNeXt, ResNet (BiT), Inception, ViT and Swin transformer, with and without supervised or self-supervised pretraining. We thoroughly tested the models on five widely used histopathology datasets containing whole slide images of breast, gastric, and colorectal cancer and developed a novel approach using an image-to-image translation model to assess the robustness of a cancer classification model against stain variations. Further, we extended existing interpretability methods to previously unstudied models and systematically reveal insights of the models' classifications strategies that can be transferred to future model architectures.
5.7CVJul 8, 2022
Generative Adversarial Networks and Other Generative ModelsMarkus Wenzel
Generative networks are fundamentally different in their aim and methods compared to CNNs for classification, segmentation, or object detection. They have initially not been meant to be an image analysis tool, but to produce naturally looking images. The adversarial training paradigm has been proposed to stabilize generative methods, and has proven to be highly successful -- though by no means from the first attempt. This chapter gives a basic introduction into the motivation for Generative Adversarial Networks (GANs) and traces the path of their success by abstracting the basic task and working mechanism, and deriving the difficulty of early practical approaches. Methods for a more stable training will be shown, and also typical signs for poor convergence and their reasons. Though this chapter focuses on GANs that are meant for image generation and image analysis, the adversarial training paradigm itself is not specific to images, and also generalizes to tasks in image analysis. Examples of architectures for image semantic segmentation and abnormality detection will be acclaimed, before contrasting GANs with further generative modeling approaches lately entering the scene. This will allow a contextualized view on the limits but also benefits of GANs.
Infant Brain Age Classification: 2D CNN Outperforms 3D CNN in Small DatasetMahdieh Shabanian, Markus Wenzel, John P. DeVincenzo
Determining if the brain is developing normally is a key component of pediatric neuroradiology and neurology. Brain magnetic resonance imaging (MRI) of infants demonstrates a specific pattern of development beyond simply myelination. While radiologists have used myelination patterns, brain morphology and size characteristics to determine age-adequate brain maturity, this requires years of experience in pediatric neuroradiology. With no standardized criteria, visual estimation of the structural maturity of the brain from MRI before three years of age remains dominated by inter-observer and intra-observer variability. A more objective estimation of brain developmental age could help physicians identify many neurodevelopmental conditions and diseases earlier and more reliably. Such data, however, is naturally hard to obtain, and the observer ground truth not much of a gold standard due to subjectivity of assessment. In this light, we explore the general feasibility to tackle this task, and the utility of different approaches, including two- and three-dimensional convolutional neural networks (CNN) that were trained on a fusion of T1-weighted, T2-weighted, and proton density (PD) weighted sequences from 84 individual subjects divided into four age groups from birth to 3 years of age. In the best performing approach, we achieved an accuracy of 0.90 [95% CI:0.86-0.94] using a 2D CNN on a central axial thick slab. We discuss the comparison to 3D networks and show how the performance compares to the use of only one sequence (T1w). In conclusion, despite the theoretical superiority of 3D CNN approaches, in limited-data situations, such approaches are inferior to simpler architectures. The code can be found in https://github.com/shabanian2018/Age_MRI-Classification
5.1QMApr 22, 2020
Risk Estimation of SARS-CoV-2 Transmission from Bluetooth Low Energy MeasurementsFelix Sattler, Jackie Ma, Patrick Wagner et al.
Digital contact tracing approaches based on Bluetooth low energy (BLE) have the potential to efficiently contain and delay outbreaks of infectious diseases such as the ongoing SARS-CoV-2 pandemic. In this work we propose a novel machine learning based approach to reliably detect subjects that have spent enough time in close proximity to be at risk of being infected. Our study is an important proof of concept that will aid the battery of epidemiological policies aiming to slow down the rapid spread of COVID-19.