Fine-Grained Neural Network Explanation by Identifying Input Features with Predictive Information

One principal approach for illuminating a black-box neural network is feature attribution, i.e. identifying the importance of input features for the network's prediction. The predictive information of features is recently proposed as a proxy for the measure of their importance. So far, the predictive information is only identified for latent features by placing an information bottleneck within the network. We propose a method to identify features with predictive information in the input domain. The method results in fine-grained identification of input features' information and is agnostic to network architecture. The core idea of our method is leveraging a bottleneck on the input that only lets input features associated with predictive latent features pass through. We compare our method with several feature attribution methods using mainstream feature attribution evaluation experiments. The code is publicly available.

Interactive Segmentation for COVID-19 Infection Quantification on Longitudinal CT scans

Consistent segmentation of COVID-19 patient's CT scans across multiple time points is essential to assess disease progression and response to therapy accurately. Existing automatic and interactive segmentation models for medical images only use data from a single time point (static). However, valuable segmentation information from previous time points is often not used to aid the segmentation of a patient's follow-up scans. Also, fully automatic segmentation techniques frequently produce results that would need further editing for clinical use. In this work, we propose a new single network model for interactive segmentation that fully utilizes all available past information to refine the segmentation of follow-up scans. In the first segmentation round, our model takes 3D volumes of medical images from two-time points (target and reference) as concatenated slices with the additional reference time point segmentation as a guide to segment the target scan. In subsequent segmentation refinement rounds, user feedback in the form of scribbles that correct the segmentation and the target's previous segmentation results are additionally fed into the model. This ensures that the segmentation information from previous refinement rounds is retained. Experimental results on our in-house multiclass longitudinal COVID-19 dataset show that the proposed model outperforms its static version and can assist in localizing COVID-19 infections in patient's follow-up scans.

Adversarial Domain Feature Adaptation for Bronchoscopic Depth Estimation

Depth estimation from monocular images is an important task in localization and 3D reconstruction pipelines for bronchoscopic navigation. Various supervised and self-supervised deep learning-based approaches have proven themselves on this task for natural images. However, the lack of labeled data and the bronchial tissue's feature-scarce texture make the utilization of these methods ineffective on bronchoscopic scenes. In this work, we propose an alternative domain-adaptive approach. Our novel two-step structure first trains a depth estimation network with labeled synthetic images in a supervised manner; then adopts an unsupervised adversarial domain feature adaptation scheme to improve the performance on real images. The results of our experiments show that the proposed method improves the network's performance on real images by a considerable margin and can be employed in 3D reconstruction pipelines.

MetaMedSeg: Volumetric Meta-learning for Few-Shot Organ Segmentation

The lack of sufficient annotated image data is a common issue in medical image segmentation. For some organs and densities, the annotation may be scarce, leading to poor model training convergence, while other organs have plenty of annotated data. In this work, we present MetaMedSeg, a gradient-based meta-learning algorithm that redefines the meta-learning task for the volumetric medical data with the goal to capture the variety between the slices. We also explore different weighting schemes for gradients aggregation, arguing that different tasks might have different complexity, and hence, contribute differently to the initialization. We propose an importance-aware weighting scheme to train our model. In the experiments, we present an evaluation of the medical decathlon dataset by extracting 2D slices from CT and MRI volumes of different organs and performing semantic segmentation. The results show that our proposed volumetric task definition leads to up to 30% improvement in terms of IoU compared to related baselines. The proposed update rule is also shown to improve the performance for complex scenarios where the data distribution of the target organ is very different from the source organs.

Sickle Cell Disease Severity Prediction from Percoll Gradient Images using Graph Convolutional Networks

Sickle cell disease (SCD) is a severe genetic hemoglobin disorder that results in premature destruction of red blood cells. Assessment of the severity of the disease is a challenging task in clinical routine since the causes of broad variance in SCD manifestation despite the common genetic cause remain unclear. Identification of the biomarkers that would predict the severity grade is of importance for prognosis and assessment of responsiveness of patients to therapy. Detection of the changes in red blood cell (RBC) density through separation of Percoll density gradient could be such marker as it allows to resolve intercellular differences and follow the most damaged dense cells prone to destruction and vaso-occlusion. Quantification of the images obtained from the distribution of RBCs in Percoll gradient and interpretation of the obtained is an important prerequisite for establishment of this approach. Here, we propose a novel approach combining a graph convolutional network, a convolutional neural network, fast Fourier transform, and recursive feature elimination to predict the severity of SCD directly from a Percoll image. Two important but expensive laboratory blood test parameters measurements are used for training the graph convolutional network. To make the model independent from such tests during prediction, the two parameters are estimated by a neural network from the Percoll image directly. On a cohort of 216 subjects, we achieve a prediction performance that is only slightly below an approach where the groundtruth laboratory measurements are used. Our proposed method is the first computational approach for the difficult task of SCD severity prediction. The two-step approach relies solely on inexpensive and simple blood analysis tools and can have a significant impact on the patients' survival in underdeveloped countries where access to medical instruments and doctors is limited

Graph-to-3D: End-to-End Generation and Manipulation of 3D Scenes Using Scene Graphs

Controllable scene synthesis consists of generating 3D information that satisfy underlying specifications. Thereby, these specifications should be abstract, i.e. allowing easy user interaction, whilst providing enough interface for detailed control. Scene graphs are representations of a scene, composed of objects (nodes) and inter-object relationships (edges), proven to be particularly suited for this task, as they allow for semantic control on the generated content. Previous works tackling this task often rely on synthetic data, and retrieve object meshes, which naturally limits the generation capabilities. To circumvent this issue, we instead propose the first work that directly generates shapes from a scene graph in an end-to-end manner. In addition, we show that the same model supports scene modification, using the respective scene graph as interface. Leveraging Graph Convolutional Networks (GCN) we train a variational Auto-Encoder on top of the object and edge categories, as well as 3D shapes and scene layouts, allowing latter sampling of new scenes and shapes.

SO-Pose: Exploiting Self-Occlusion for Direct 6D Pose Estimation

Directly regressing all 6 degrees-of-freedom (6DoF) for the object pose (e.g. the 3D rotation and translation) in a cluttered environment from a single RGB image is a challenging problem. While end-to-end methods have recently demonstrated promising results at high efficiency, they are still inferior when compared with elaborate P$n$P/RANSAC-based approaches in terms of pose accuracy. In this work, we address this shortcoming by means of a novel reasoning about self-occlusion, in order to establish a two-layer representation for 3D objects which considerably enhances the accuracy of end-to-end 6D pose estimation. Our framework, named SO-Pose, takes a single RGB image as input and respectively generates 2D-3D correspondences as well as self-occlusion information harnessing a shared encoder and two separate decoders. Both outputs are then fused to directly regress the 6DoF pose parameters. Incorporating cross-layer consistencies that align correspondences, self-occlusion and 6D pose, we can further improve accuracy and robustness, surpassing or rivaling all other state-of-the-art approaches on various challenging datasets.

Unconditional Scene Graph Generation

Despite recent advancements in single-domain or single-object image generation, it is still challenging to generate complex scenes containing diverse, multiple objects and their interactions. Scene graphs, composed of nodes as objects and directed-edges as relationships among objects, offer an alternative representation of a scene that is more semantically grounded than images. We hypothesize that a generative model for scene graphs might be able to learn the underlying semantic structure of real-world scenes more effectively than images, and hence, generate realistic novel scenes in the form of scene graphs. In this work, we explore a new task for the unconditional generation of semantic scene graphs. We develop a deep auto-regressive model called SceneGraphGen which can directly learn the probability distribution over labelled and directed graphs using a hierarchical recurrent architecture. The model takes a seed object as input and generates a scene graph in a sequence of steps, each step generating an object node, followed by a sequence of relationship edges connecting to the previous nodes. We show that the scene graphs generated by SceneGraphGen are diverse and follow the semantic patterns of real-world scenes. Additionally, we demonstrate the application of the generated graphs in image synthesis, anomaly detection and scene graph completion.

Tracked 3D Ultrasound and Deep Neural Network-based Thyroid Segmentation reduce Interobserver Variability in Thyroid Volumetry

Background: Thyroid volumetry is crucial in diagnosis, treatment and monitoring of thyroid diseases. However, conventional thyroid volumetry with 2D ultrasound is highly operator-dependent. This study compares 2D ultrasound and tracked 3D ultrasound with an automatic thyroid segmentation based on a deep neural network regarding inter- and intraobserver variability, time and accuracy. Volume reference was MRI. Methods: 28 healthy volunteers were scanned with 2D and 3D ultrasound as well as by MRI. Three physicians (MD 1, 2, 3) with different levels of experience (6, 4 and 1 a) performed three 2D ultrasound and three tracked 3D ultrasound scans on each volunteer. In the 2D scans the thyroid lobe volumes were calculated with the ellipsoid formula. A convolutional deep neural network (CNN) segmented the 3D thyroid lobes automatically. On MRI (T1 VIBE sequence) the thyroid was manually segmented by an experienced medical doctor. Results: The CNN was trained to obtain a dice score of 0.94. The interobserver variability comparing two MDs showed mean differences for 2D and 3D respectively of 0.58 ml to 0.52 ml (MD1 vs. 2), -1.33 ml to -0.17 ml (MD1 vs. 3) and -1.89 ml to -0.70 ml (MD2 vs. 3). Paired samples t-tests showed significant differences in two comparisons for 2D and none for 3D. Intraobsever variability was similar for 2D and 3D ultrasound. Comparison of ultrasound volumes and MRI volumes by paired samples t-tests showed a significant difference for the 2D volumetry of all MDs, and no significant difference for 3D ultrasound. Acquisition time was significantly shorter for 3D ultrasound. Conclusion: Tracked 3D ultrasound combined with a CNN segmentation significantly reduces interobserver variability in thyroid volumetry and increases the accuracy of the measurements with shorter acquisition times.

R4Dyn: Exploring Radar for Self-Supervised Monocular Depth Estimation of Dynamic Scenes

While self-supervised monocular depth estimation in driving scenarios has achieved comparable performance to supervised approaches, violations of the static world assumption can still lead to erroneous depth predictions of traffic participants, posing a potential safety issue. In this paper, we present R4Dyn, a novel set of techniques to use cost-efficient radar data on top of a self-supervised depth estimation framework. In particular, we show how radar can be used during training as weak supervision signal, as well as an extra input to enhance the estimation robustness at inference time. Since automotive radars are readily available, this allows to collect training data from a variety of existing vehicles. Moreover, by filtering and expanding the signal to make it compatible with learning-based approaches, we address radar inherent issues, such as noise and sparsity. With R4Dyn we are able to overcome a major limitation of self-supervised depth estimation, i.e. the prediction of traffic participants. We substantially improve the estimation on dynamic objects, such as cars by 37% on the challenging nuScenes dataset, hence demonstrating that radar is a valuable additional sensor for monocular depth estimation in autonomous vehicles. Additionally, we plan on making the code publicly available.