arXiv subjects

Nassir Navab

Publications and source records attributed to Nassir Navab.

At least 379 records · Page 21Linked to original sources

arXiv2021

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.

cs.CV↗

arXiv2021

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.

cs.CV↗

arXiv2021

Explaining COVID-19 and Thoracic Pathology Model Predictions by Identifying Informative Input Features

Neural networks have demonstrated remarkable performance in classification and regression tasks on chest X-rays. In order to establish trust in the clinical routine, the networks' prediction mechanism needs to be interpretable. One principal approach to interpretation is feature attribution. Feature attribution methods identify the importance of input features for the output prediction. Building on Information Bottleneck Attribution (IBA) method, for each prediction we identify the chest X-ray regions that have high mutual information with the network's output. Original IBA identifies input regions that have sufficient predictive information. We propose Inverse IBA to identify all informative regions. Thus all predictive cues for pathologies are highlighted on the X-rays, a desirable property for chest X-ray diagnosis. Moreover, we propose Regression IBA for explaining regression models. Using Regression IBA we observe that a model trained on cumulative severity score labels implicitly learns the severity of different X-ray regions. Finally, we propose Multi-layer IBA to generate higher resolution and more detailed attribution/saliency maps. We evaluate our methods using both human-centric (ground-truth-based) interpretability metrics, and human-independent feature importance metrics on NIH Chest X-ray8 and BrixIA datasets. The Code is publicly available.

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arXiv2021

Towards Semantic Interpretation of Thoracic Disease and COVID-19 Diagnosis Models

Convolutional neural networks are showing promise in the automatic diagnosis of thoracic pathologies on chest x-rays. Their black-box nature has sparked many recent works to explain the prediction via input feature attribution methods (aka saliency methods). However, input feature attribution methods merely identify the importance of input regions for the prediction and lack semantic interpretation of model behavior. In this work, we first identify the semantics associated with internal units (feature maps) of the network. We proceed to investigate the following questions; Does a regression model that is only trained with COVID-19 severity scores implicitly learn visual patterns associated with thoracic pathologies? Does a network that is trained on weakly labeled data (e.g. healthy, unhealthy) implicitly learn pathologies? Moreover, we investigate the effect of pretraining and data imbalance on the interpretability of learned features. In addition to the analysis, we propose semantic attribution to semantically explain each prediction. We present our findings using publicly available chest pathologies (CheXpert, NIH ChestX-ray8) and COVID-19 datasets (BrixIA, and COVID-19 chest X-ray segmentation dataset). The Code is publicly available.

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arXiv2021

Surgical Data Science -- from Concepts toward Clinical Translation

Recent developments in data science in general and machine learning in particular have transformed the way experts envision the future of surgery. Surgical Data Science (SDS) is a new research field that aims to improve the quality of interventional healthcare through the capture, organization, analysis and modeling of data. While an increasing number of data-driven approaches and clinical applications have been studied in the fields of radiological and clinical data science, translational success stories are still lacking in surgery. In this publication, we shed light on the underlying reasons and provide a roadmap for future advances in the field. Based on an international workshop involving leading researchers in the field of SDS, we review current practice, key achievements and initiatives as well as available standards and tools for a number of topics relevant to the field, namely (1) infrastructure for data acquisition, storage and access in the presence of regulatory constraints, (2) data annotation and sharing and (3) data analytics. We further complement this technical perspective with (4) a review of currently available SDS products and the translational progress from academia and (5) a roadmap for faster clinical translation and exploitation of the full potential of SDS, based on an international multi-round Delphi process.

cs.CY↗

arXiv2021

U-GAT: Multimodal Graph Attention Network for COVID-19 Outcome Prediction

During the first wave of COVID-19, hospitals were overwhelmed with the high number of admitted patients. An accurate prediction of the most likely individual disease progression can improve the planning of limited resources and finding the optimal treatment for patients. However, when dealing with a newly emerging disease such as COVID-19, the impact of patient- and disease-specific factors (e.g. body weight or known co-morbidities) on the immediate course of disease is by and large unknown. In the case of COVID-19, the need for intensive care unit (ICU) admission of pneumonia patients is often determined only by acute indicators such as vital signs (e.g. breathing rate, blood oxygen levels), whereas statistical analysis and decision support systems that integrate all of the available data could enable an earlier prognosis. To this end, we propose a holistic graph-based approach combining both imaging and non-imaging information. Specifically, we introduce a multimodal similarity metric to build a population graph for clustering patients and an image-based end-to-end Graph Attention Network to process this graph and predict the COVID-19 patient outcomes: admission to ICU, need for ventilation and mortality. Additionally, the network segments chest CT images as an auxiliary task and extracts image features and radiomics for feature fusion with the available metadata. Results on a dataset collected in Klinikum rechts der Isar in Munich, Germany show that our approach outperforms single modality and non-graph baselines. Moreover, our clustering and graph attention allow for increased understanding of the patient relationships within the population graph and provide insight into the network's decision-making process.

cs.CV↗

arXiv2021

Longitudinal Quantitative Assessment of COVID-19 Infection Progression from Chest CTs

Chest computed tomography (CT) has played an essential diagnostic role in assessing patients with COVID-19 by showing disease-specific image features such as ground-glass opacity and consolidation. Image segmentation methods have proven to help quantify the disease burden and even help predict the outcome. The availability of longitudinal CT series may also result in an efficient and effective method to reliably assess the progression of COVID-19, monitor the healing process and the response to different therapeutic strategies. In this paper, we propose a new framework to identify infection at a voxel level (identification of healthy lung, consolidation, and ground-glass opacity) and visualize the progression of COVID-19 using sequential low-dose non-contrast CT scans. In particular, we devise a longitudinal segmentation network that utilizes the reference scan information to improve the performance of disease identification. Experimental results on a clinical longitudinal dataset collected in our institution show the effectiveness of the proposed method compared to the static deep neural networks for disease quantification.

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arXiv2021

Deformation-Aware Robotic 3D Ultrasound

Tissue deformation in ultrasound (US) imaging leads to geometrical errors when measuring tissues due to the pressure exerted by probes. Such deformation has an even larger effect on 3D US volumes as the correct compounding is limited by the inconsistent location and geometry. This work proposes a patient-specified stiffness-based method to correct the tissue deformations in robotic 3D US acquisitions. To obtain the patient-specified model, robotic palpation is performed at sampling positions on the tissue. The contact force, US images and the probe poses of the palpation procedure are recorded. The contact force and the probe poses are used to estimate the nonlinear tissue stiffness. The images are fed to an optical flow algorithm to compute the pixel displacement. Then the pixel-wise tissue deformation under different forces is characterized by a coupled quadratic regression. To correct the deformation at unseen positions on the trajectory for building 3D volumes, an interpolation is performed based on the stiffness values computed at the sampling positions. With the stiffness and recorded force, the tissue displacement could be corrected. The method was validated on two blood vessel phantoms with different stiffness. The results demonstrate that the method can effectively correct the force-induced deformation and finally generate 3D tissue geometries

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arXiv2021

Motion-Aware Robotic 3D Ultrasound

Robotic three-dimensional (3D) ultrasound (US) imaging has been employed to overcome the drawbacks of traditional US examinations, such as high inter-operator variability and lack of repeatability. However, object movement remains a challenge as unexpected motion decreases the quality of the 3D compounding. Furthermore, attempted adjustment of objects, e.g., adjusting limbs to display the entire limb artery tree, is not allowed for conventional robotic US systems. To address this challenge, we propose a vision-based robotic US system that can monitor the object's motion and automatically update the sweep trajectory to provide 3D compounded images of the target anatomy seamlessly. To achieve these functions, a depth camera is employed to extract the manually planned sweep trajectory after which the normal direction of the object is estimated using the extracted 3D trajectory. Subsequently, to monitor the movement and further compensate for this motion to accurately follow the trajectory, the position of firmly attached passive markers is tracked in real-time. Finally, a step-wise compounding was performed. The experiments on a gel phantom demonstrate that the system can resume a sweep when the object is not stationary during scanning.

cs.RO↗

arXiv2021

Autonomous Robotic Screening of Tubular Structures based only on Real-Time Ultrasound Imaging Feedback

Ultrasound (US) imaging is widely employed for diagnosis and staging of peripheral vascular diseases (PVD), mainly due to its high availability and the fact it does not emit radiation. However, high inter-operator variability and a lack of repeatability of US image acquisition hinder the implementation of extensive screening programs. To address this challenge, we propose an end-to-end workflow for automatic robotic US screening of tubular structures using only the real-time US imaging feedback. We first train a U-Net for real-time segmentation of the vascular structure from cross-sectional US images. Then, we represent the detected vascular structure as a 3D point cloud and use it to estimate the longitudinal axis of the target tubular structure and its mean radius by solving a constrained non-linear optimization problem. Iterating the previous processes, the US probe is automatically aligned to the orientation normal to the target tubular tissue and adjusted online to center the tracked tissue based on the spatial calibration. The real-time segmentation result is evaluated both on a phantom and in-vivo on brachial arteries of volunteers. In addition, the whole process is validated both in simulation and physical phantoms. The mean absolute radius error and orientation error ($\pm$ SD) in the simulation are $1.16\pm0.1~mm$ and $2.7\pm3.3^{\circ}$, respectively. On a gel phantom, these errors are $1.95\pm2.02~mm$ and $3.3\pm2.4^{\circ}$. This shows that the method is able to automatically screen tubular tissues with an optimal probe orientation (i.e. normal to the vessel) and at the same to accurately estimate the mean radius, both in real-time.

cs.RO↗

arXiv2021

Deep Direct Volume Rendering: Learning Visual Feature Mappings From Exemplary Images

Volume Rendering is an important technique for visualizing three-dimensional scalar data grids and is commonly employed for scientific and medical image data. Direct Volume Rendering (DVR) is a well established and efficient rendering algorithm for volumetric data. Neural rendering uses deep neural networks to solve inverse rendering tasks and applies techniques similar to DVR. However, it has not been demonstrated successfully for the rendering of scientific volume data. In this work, we introduce Deep Direct Volume Rendering (DeepDVR), a generalization of DVR that allows for the integration of deep neural networks into the DVR algorithm. We conceptualize the rendering in a latent color space, thus enabling the use of deep architectures to learn implicit mappings for feature extraction and classification, replacing explicit feature design and hand-crafted transfer functions. Our generalization serves to derive novel volume rendering architectures that can be trained end-to-end directly from examples in image space, obviating the need to manually define and fine-tune multidimensional transfer functions while providing superior classification strength. We further introduce a novel stepsize annealing scheme to accelerate the training of DeepDVR models and validate its effectiveness in a set of experiments. We validate our architectures on two example use cases: (1) learning an optimized rendering from manually adjusted reference images for a single volume and (2) learning advanced visualization concepts like shading and semantic colorization that generalize to unseen volume data. We find that deep volume rendering architectures with explicit modeling of the DVR pipeline effectively enable end-to-end learning of scientific volume rendering tasks from target images.

cs.GR↗

arXiv2021

Multimodal Semantic Scene Graphs for Holistic Modeling of Surgical Procedures

From a computer science viewpoint, a surgical domain model needs to be a conceptual one incorporating both behavior and data. It should therefore model actors, devices, tools, their complex interactions and data flow. To capture and model these, we take advantage of the latest computer vision methodologies for generating 3D scene graphs from camera views. We then introduce the Multimodal Semantic Scene Graph (MSSG) which aims at providing a unified symbolic, spatiotemporal and semantic representation of surgical procedures. This methodology aims at modeling the relationship between different components in surgical domain including medical staff, imaging systems, and surgical devices, opening the path towards holistic understanding and modeling of surgical procedures. We then use MSSG to introduce a dynamically generated graphical user interface tool for surgical procedure analysis which could be used for many applications including process optimization, OR design and automatic report generation. We finally demonstrate that the proposed MSSGs could also be used for synchronizing different complex surgical procedures. While the system still needs to be integrated into real operating rooms before getting validated, this conference paper aims mainly at providing the community with the basic principles of this novel concept through a first prototypal partial realization based on MVOR dataset.

cs.CV↗

arXiv2021

Rethinking Ultrasound Augmentation: A Physics-Inspired Approach

Medical Ultrasound (US), despite its wide use, is characterized by artifacts and operator dependency. Those attributes hinder the gathering and utilization of US datasets for the training of Deep Neural Networks used for Computer-Assisted Intervention Systems. Data augmentation is commonly used to enhance model generalization and performance. However, common data augmentation techniques, such as affine transformations do not align with the physics of US and, when used carelessly can lead to unrealistic US images. To this end, we propose a set of physics-inspired transformations, including deformation, reverb and Signal-to-Noise Ratio, that we apply on US B-mode images for data augmentation. We evaluate our method on a new spine US dataset for the tasks of bone segmentation and classification.

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arXiv2021

Pose-dependent weights and Domain Randomization for fully automatic X-ray to CT Registration

Fully automatic X-ray to CT registration requires a solid initialization to provide an initial alignment within the capture range of existing intensity-based registrations. This work adresses that need by providing a novel automatic initialization, which enables end to end registration. First, a neural network is trained once to detect a set of anatomical landmarks on simulated X-rays. A domain randomization scheme is proposed to enable the network to overcome the challenge of being trained purely on simulated data and run inference on real Xrays. Then, for each patient CT, a patient-specific landmark extraction scheme is used. It is based on backprojecting and clustering the previously trained networks predictions on a set of simulated X-rays. Next, the network is retrained to detect the new landmarks. Finally the combination of network and 3D landmark locations is used to compute the initialization using a perspective-n-point algorithm. During the computation of the pose, a weighting scheme is introduced to incorporate the confidence of the network in detecting the landmarks. The algorithm is evaluated on the pelvis using both real and simulated x-rays. The mean (+-standard deviation) target registration error in millimetres is 4.1 +- 4.3 for simulated X-rays with a success rate of 92% and 4.2 +- 3.9 for real X-rays with a success rate of 86.8%, where a success is defined as a translation error of less than 30mm.

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arXiv2021

GKD: Semi-supervised Graph Knowledge Distillation for Graph-Independent Inference

The increased amount of multi-modal medical data has opened the opportunities to simultaneously process various modalities such as imaging and non-imaging data to gain a comprehensive insight into the disease prediction domain. Recent studies using Graph Convolutional Networks (GCNs) provide novel semi-supervised approaches for integrating heterogeneous modalities while investigating the patients' associations for disease prediction. However, when the meta-data used for graph construction is not available at inference time (e.g., coming from a distinct population), the conventional methods exhibit poor performance. To address this issue, we propose a novel semi-supervised approach named GKD based on knowledge distillation. We train a teacher component that employs the label-propagation algorithm besides a deep neural network to benefit from the graph and non-graph modalities only in the training phase. The teacher component embeds all the available information into the soft pseudo-labels. The soft pseudo-labels are then used to train a deep student network for disease prediction of unseen test data for which the graph modality is unavailable. We perform our experiments on two public datasets for diagnosing Autism spectrum disorder, and Alzheimer's disease, along with a thorough analysis on synthetic multi-modal datasets. According to these experiments, GKD outperforms the previous graph-based deep learning methods in terms of accuracy, AUC, and Macro F1.

cs.LG↗

arXiv2021

SceneGraphFusion: Incremental 3D Scene Graph Prediction from RGB-D Sequences

Scene graphs are a compact and explicit representation successfully used in a variety of 2D scene understanding tasks. This work proposes a method to incrementally build up semantic scene graphs from a 3D environment given a sequence of RGB-D frames. To this end, we aggregate PointNet features from primitive scene components by means of a graph neural network. We also propose a novel attention mechanism well suited for partial and missing graph data present in such an incremental reconstruction scenario. Although our proposed method is designed to run on submaps of the scene, we show it also transfers to entire 3D scenes. Experiments show that our approach outperforms 3D scene graph prediction methods by a large margin and its accuracy is on par with other 3D semantic and panoptic segmentation methods while running at 35 Hz.

cs.CV↗

arXiv2021

Neural Response Interpretation through the Lens of Critical Pathways

Is critical input information encoded in specific sparse pathways within the neural network? In this work, we discuss the problem of identifying these critical pathways and subsequently leverage them for interpreting the network's response to an input. The pruning objective -- selecting the smallest group of neurons for which the response remains equivalent to the original network -- has been previously proposed for identifying critical pathways. We demonstrate that sparse pathways derived from pruning do not necessarily encode critical input information. To ensure sparse pathways include critical fragments of the encoded input information, we propose pathway selection via neurons' contribution to the response. We proceed to explain how critical pathways can reveal critical input features. We prove that pathways selected via neuron contribution are locally linear (in an L2-ball), a property that we use for proposing a feature attribution method: "pathway gradient". We validate our interpretation method using mainstream evaluation experiments. The validation of pathway gradient interpretation method further confirms that selected pathways using neuron contributions correspond to critical input features. The code is publicly available.

cs.CV↗

arXiv2021

SCFusion: Real-time Incremental Scene Reconstruction with Semantic Completion

Real-time scene reconstruction from depth data inevitably suffers from occlusion, thus leading to incomplete 3D models. Partial reconstructions, in turn, limit the performance of algorithms that leverage them for applications in the context of, e.g., augmented reality, robotic navigation, and 3D mapping. Most methods address this issue by predicting the missing geometry as an offline optimization, thus being incompatible with real-time applications. We propose a framework that ameliorates this issue by performing scene reconstruction and semantic scene completion jointly in an incremental and real-time manner, based on an input sequence of depth maps. Our framework relies on a novel neural architecture designed to process occupancy maps and leverages voxel states to accurately and efficiently fuse semantic completion with the 3D global model. We evaluate the proposed approach quantitatively and qualitatively, demonstrating that our method can obtain accurate 3D semantic scene completion in real-time.

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