Sogancioglu, Ecem
Nodule detection and generation on chest X-rays: NODE21 Challenge
Sogancioglu, Ecem, van Ginneken, Bram, Behrendt, Finn, Bengs, Marcel, Schlaefer, Alexander, Radu, Miron, Xu, Di, Sheng, Ke, Scalzo, Fabien, Marcus, Eric, Papa, Samuele, Teuwen, Jonas, Scholten, Ernst Th., Schalekamp, Steven, Hendrix, Nils, Jacobs, Colin, Hendrix, Ward, Sánchez, Clara I, Murphy, Keelin
Pulmonary nodules may be an early manifestation of lung cancer, the leading cause of cancer-related deaths among both men and women. Numerous studies have established that deep learning methods can yield high-performance levels in the detection of lung nodules in chest X-rays. However, the lack of gold-standard public datasets slows down the progression of the research and prevents benchmarking of methods for this task. To address this, we organized a public research challenge, NODE21, aimed at the detection and generation of lung nodules in chest X-rays. While the detection track assesses state-of-the-art nodule detection systems, the generation track determines the utility of nodule generation algorithms to augment training data and hence improve the performance of the detection systems. This paper summarizes the results of the NODE21 challenge and performs extensive additional experiments to examine the impact of the synthetically generated nodule training images on the detection algorithm performance.
FRODO: Free rejection of out-of-distribution samples: application to chest x-ray analysis
Çallı, Erdi, Murphy, Keelin, Sogancioglu, Ecem, van Ginneken, Bram
In this work, we propose a method to reject out-of-distribution samples which can be adapted to any network architecture and requires no additional training data. Publicly available chest x-ray data (38,353 images) is used to train a standard ResNet-50 model to detect emphysema. Feature activations of intermediate layers are used as descriptors defining the training data distribution. A novel metric, FRODO, is measured by using the Mahalanobis distance of a new test sample to the training data distribution. The method is tested using a held-out test dataset of 21,176 chest x-rays (in-distribution) and a set of 14,821 out-of-distribution x-ray images of incorrect orientation or anatomy. In classifying test samples as in or out-of distribution, our method achieves an AUC score of 0.99.
Chest X-ray Inpainting with Deep Generative Models
Sogancioglu, Ecem, Hu, Shi, Belli, Davide, van Ginneken, Bram
Generative adversarial networks have been successfully applied to inpainting in natural images. However, the current state-of-the-art models have not yet been widely adopted in the medical imaging domain. In this paper, we investigate the performance of three recently published deep learning based inpainting models: context encoders, semantic image inpainting, and the contextual attention model, applied to chest x-rays, as the chest exam is the most commonly performed radiological procedure. We train these generative models on 1.2M 128 $\times$ 128 patches from 60K healthy x-rays, and learn to predict the center 64 $\times$ 64 region in each patch. We test the models on both the healthy and abnormal radiographs. We evaluate the results by visual inspection and comparing the PSNR scores. The outputs of the models are in most cases highly realistic. We show that the methods have potential to enhance and detect abnormalities. In addition, we perform a 2AFC observer study and show that an experienced human observer performs poorly in detecting inpainted regions, particularly those generated by the contextual attention model.