arXiv subjects

Nassir Navab

Publications and source records attributed to Nassir Navab.

At least 469 records · Page 26Linked to original sources

arXiv2019

GANs for Medical Image Analysis

Generative Adversarial Networks (GANs) and their extensions have carved open many exciting ways to tackle well known and challenging medical image analysis problems such as medical image de-noising, reconstruction, segmentation, data simulation, detection or classification. Furthermore, their ability to synthesize images at unprecedented levels of realism also gives hope that the chronic scarcity of labeled data in the medical field can be resolved with the help of these generative models. In this review paper, a broad overview of recent literature on GANs for medical applications is given, the shortcomings and opportunities of the proposed methods are thoroughly discussed and potential future work is elaborated. We review the most relevant papers published until the submission date. For quick access, important details such as the underlying method, datasets and performance are tabulated. An interactive visualization which categorizes all papers to keep the review alive, is available at http://livingreview.in.tum.de/GANs_for_Medical_Applications.

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arXiv2019

Learning to Avoid Poor Images: Towards Task-aware C-arm Cone-beam CT Trajectories

Metal artifacts in computed tomography (CT) arise from a mismatch between physics of image formation and idealized assumptions during tomographic reconstruction. These artifacts are particularly strong around metal implants, inhibiting widespread adoption of 3D cone-beam CT (CBCT) despite clear opportunity for intra-operative verification of implant positioning, e.g. in spinal fusion surgery. On synthetic and real data, we demonstrate that much of the artifact can be avoided by acquiring better data for reconstruction in a task-aware and patient-specific manner, and describe the first step towards the envisioned task-aware CBCT protocol. The traditional short-scan CBCT trajectory is planar, with little room for scene-specific adjustment. We extend this trajectory by autonomously adjusting out-of-plane angulation. This enables C-arm source trajectories that are scene-specific in that they avoid acquiring "poor images", characterized by beam hardening, photon starvation, and noise. The recommendation of ideal out-of-plane angulation is performed on-the-fly using a deep convolutional neural network that regresses a detectability-rank derived from imaging physics.

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arXiv2019

Learn to Segment Organs with a Few Bounding Boxes

Semantic segmentation is an import task in the medical field to identify the exact extent and orientation of significant structures like organs and pathology. Deep neural networks can perform this task well by leveraging the information from a large well-labeled data-set. This paper aims to present a method that mitigates the necessity of an extensive well-labeled data-set. This method also addresses semi-supervision by enabling segmentation based on bounding box annotations, avoiding the need for full pixel-level annotations. The network presented consists of a single U-Net based unbranched architecture that generates a few-shot segmentation for an unseen human organ using just 4 example annotations of that specific organ. The network is trained by alternately minimizing the nearest neighbor loss for prototype learning and a weighted cross-entropy loss for segmentation learning to perform a fast 3D segmentation with a median score of 54.64%.

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arXiv2019

Learn to Estimate Labels Uncertainty for Quality Assurance

Deep Learning sets the state-of-the-art in many challenging tasks showing outstanding performance in a broad range of applications. Despite its success, it still lacks robustness hindering its adoption in medical applications. Modeling uncertainty, through Bayesian Inference and Monte-Carlo dropout, has been successfully introduced for better understanding the underlying deep learning models. Yet, another important source of uncertainty, coming from the inter-observer variability, has not been thoroughly addressed in the literature. In this paper, we introduce labels uncertainty which better suits medical applications and show that modeling such uncertainty together with epistemic uncertainty is of high interest for quality control and referral systems.

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arXiv2019

ForkNet: Multi-branch Volumetric Semantic Completion from a Single Depth Image

We propose a novel model for 3D semantic completion from a single depth image, based on a single encoder and three separate generators used to reconstruct different geometric and semantic representations of the original and completed scene, all sharing the same latent space. To transfer information between the geometric and semantic branches of the network, we introduce paths between them concatenating features at corresponding network layers. Motivated by the limited amount of training samples from real scenes, an interesting attribute of our architecture is the capacity to supplement the existing dataset by generating a new training dataset with high quality, realistic scenes that even includes occlusion and real noise. We build the new dataset by sampling the features directly from latent space which generates a pair of partial volumetric surface and completed volumetric semantic surface. Moreover, we utilize multiple discriminators to increase the accuracy and realism of the reconstructions. We demonstrate the benefits of our approach on standard benchmarks for the two most common completion tasks: semantic 3D scene completion and 3D object completion.

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arXiv2019

Object-Driven Multi-Layer Scene Decomposition From a Single Image

We present a method that tackles the challenge of predicting color and depth behind the visible content of an image. Our approach aims at building up a Layered Depth Image (LDI) from a single RGB input, which is an efficient representation that arranges the scene in layers, including originally occluded regions. Unlike previous work, we enable an adaptive scheme for the number of layers and incorporate semantic encoding for better hallucination of partly occluded objects. Additionally, our approach is object-driven, which especially boosts the accuracy for the occluded intermediate objects. The framework consists of two steps. First, we individually complete each object in terms of color and depth, while estimating the scene layout. Second, we rebuild the scene based on the regressed layers and enforce the recomposed image to resemble the structure of the original input. The learned representation enables various applications, such as 3D photography and diminished reality, all from a single RGB image.

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arXiv2019

Towards Unsupervised Image Captioning with Shared Multimodal Embeddings

Understanding images without explicit supervision has become an important problem in computer vision. In this paper, we address image captioning by generating language descriptions of scenes without learning from annotated pairs of images and their captions. The core component of our approach is a shared latent space that is structured by visual concepts. In this space, the two modalities should be indistinguishable. A language model is first trained to encode sentences into semantically structured embeddings. Image features that are translated into this embedding space can be decoded into descriptions through the same language model, similarly to sentence embeddings. This translation is learned from weakly paired images and text using a loss robust to noisy assignments and a conditional adversarial component. Our approach allows to exploit large text corpora outside the annotated distributions of image/caption data. Our experiments show that the proposed domain alignment learns a semantically meaningful representation which outperforms previous work.

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arXiv2019

Explaining the Ambiguity of Object Detection and 6D Pose From Visual Data

3D object detection and pose estimation from a single image are two inherently ambiguous problems. Oftentimes, objects appear similar from different viewpoints due to shape symmetries, occlusion and repetitive textures. This ambiguity in both detection and pose estimation means that an object instance can be perfectly described by several different poses and even classes. In this work we propose to explicitly deal with this uncertainty. For each object instance we predict multiple pose and class outcomes to estimate the specific pose distribution generated by symmetries and repetitive textures. The distribution collapses to a single outcome when the visual appearance uniquely identifies just one valid pose. We show the benefits of our approach which provides not only a better explanation for pose ambiguity, but also a higher accuracy in terms of pose estimation.

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arXiv2019

Learning Interpretable Features via Adversarially Robust Optimization

Neural networks are proven to be remarkably successful for classification and diagnosis in medical applications. However, the ambiguity in the decision-making process and the interpretability of the learned features is a matter of concern. In this work, we propose a method for improving the feature interpretability of neural network classifiers. Initially, we propose a baseline convolutional neural network with state of the art performance in terms of accuracy and weakly supervised localization. Subsequently, the loss is modified to integrate robustness to adversarial examples into the training process. In this work, feature interpretability is quantified via evaluating the weakly supervised localization using the ground truth bounding boxes. Interpretability is also visually assessed using class activation maps and saliency maps. The method is applied to NIH ChestX-ray14, the largest publicly available chest x-rays dataset. We demonstrate that the adversarially robust optimization paradigm improves feature interpretability both quantitatively and visually.

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arXiv2019

Adaptive Image-Feature Learning for Disease Classification Using Inductive Graph Networks

Recently, Geometric Deep Learning (GDL) has been introduced as a novel and versatile framework for computer-aided disease classification. GDL uses patient meta-information such as age and gender to model patient cohort relations in a graph structure. Concepts from graph signal processing are leveraged to learn the optimal mapping of multi-modal features, e.g. from images to disease classes. Related studies so far have considered image features that are extracted in a pre-processing step. We hypothesize that such an approach prevents the network from optimizing feature representations towards achieving the best performance in the graph network. We propose a new network architecture that exploits an inductive end-to-end learning approach for disease classification, where filters from both the CNN and the graph are trained jointly. We validate this architecture against state-of-the-art inductive graph networks and demonstrate significantly improved classification scores on a modified MNIST toy dataset, as well as comparable classification results with higher stability on a chest X-ray image dataset. Additionally, we explain how the structural information of the graph affects both the image filters and the feature learning.

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arXiv2019

LumiPath -- Towards Real-time Physically-based Rendering on Embedded Devices

With the increasing computational power of today's workstations, real-time physically-based rendering is within reach, rapidly gaining attention across a variety of domains. These have expeditiously applied to medicine, where it is a powerful tool for intuitive 3D data visualization. Embedded devices such as optical see-through head-mounted displays (OST HMDs) have been a trend for medical augmented reality. However, leveraging the obvious benefits of physically-based rendering remains challenging on these devices because of limited computational power, memory usage, and power consumption. We navigate the compromise between device limitations and image quality to achieve reasonable rendering results by introducing a novel light field that can be sampled in real-time on embedded devices. We demonstrate its applications in medicine and discuss limitations of the proposed method. An open-source version of this project is available at https://github.com/lorafib/LumiPath which provides full insight on implementation and exemplary demonstrational material.

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arXiv2019

RIO: 3D Object Instance Re-Localization in Changing Indoor Environments

In this work, we introduce the task of 3D object instance re-localization (RIO): given one or multiple objects in an RGB-D scan, we want to estimate their corresponding 6DoF poses in another 3D scan of the same environment taken at a later point in time. We consider RIO a particularly important task in 3D vision since it enables a wide range of practical applications, including AI-assistants or robots that are asked to find a specific object in a 3D scene. To address this problem, we first introduce 3RScan, a novel dataset and benchmark, which features 1482 RGB-D scans of 478 environments across multiple time steps. Each scene includes several objects whose positions change over time, together with ground truth annotations of object instances and their respective 6DoF mappings among re-scans. Automatically finding 6DoF object poses leads to a particular challenging feature matching task due to varying partial observations and changes in the surrounding context. To this end, we introduce a new data-driven approach that efficiently finds matching features using a fully-convolutional 3D correspondence network operating on multiple spatial scales. Combined with a 6DoF pose optimization, our method outperforms state-of-the-art baselines on our newly-established benchmark, achieving an accuracy of 30.58%.

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arXiv2019

Multi-scale Microaneurysms Segmentation Using Embedding Triplet Loss

Deep learning techniques are recently being used in fundus image analysis and diabetic retinopathy detection. Microaneurysms are an important indicator of diabetic retinopathy progression. We introduce a two-stage deep learning approach for microaneurysms segmentation using multiple scales of the input with selective sampling and embedding triplet loss. The model first segments on two scales and then the segmentations are refined with a classification model. To enhance the discriminative power of the classification model, we incorporate triplet embedding loss with a selective sampling routine. The model is evaluated quantitatively to assess the segmentation performance and qualitatively to analyze the model predictions. This approach introduces a 30.29% relative improvement over the fully convolutional neural network.

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arXiv2019

Grasp Type Estimation for Myoelectric Prostheses using Point Cloud Feature Learning

Prosthetic hands can help people with limb difference to return to their life routines. Commercial prostheses, however have several limitations in providing an acceptable dexterity. We approach these limitations by augmenting the prosthetic hands with an off-the-shelf depth sensor to enable the prosthesis to see the object's depth, record a single view (2.5-D) snapshot, and estimate an appropriate grasp type; using a deep network architecture based on 3D point clouds called PointNet. The human can act as the supervisor throughout the procedure by accepting or refusing the suggested grasp type. We achieved the grasp classification accuracy of up to 88%. Contrary to the case of the RGB data, the depth data provides all the necessary object shape information, which is required for grasp recognition. The PointNet not only enables using 3-D data in practice, but it also prevents excessive computations. Augmentation of the prosthetic hands with such a semi-autonomous system can lead to better differentiation of grasp types, less burden on user, and better performance.

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arXiv2019

3DQ: Compact Quantized Neural Networks for Volumetric Whole Brain Segmentation

Model architectures have been dramatically increasing in size, improving performance at the cost of resource requirements. In this paper we propose 3DQ, a ternary quantization method, applied for the first time to 3D Fully Convolutional Neural Networks (F-CNNs), enabling 16x model compression while maintaining performance on par with full precision models. We extensively evaluate 3DQ on two datasets for the challenging task of whole brain segmentation. Additionally, we showcase our method's ability to generalize on two common 3D architectures, namely 3D U-Net and V-Net. Outperforming a variety of baselines, the proposed method is capable of compressing large 3D models to a few MBytes, alleviating the storage needs in space critical applications.

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arXiv2019

`Project & Excite' Modules for Segmentation of Volumetric Medical Scans

Fully Convolutional Neural Networks (F-CNNs) achieve state-of-the-art performance for image segmentation in medical imaging. Recently, squeeze and excitation (SE) modules and variations thereof have been introduced to recalibrate feature maps channel- and spatial-wise, which can boost performance while only minimally increasing model complexity. So far, the development of SE has focused on 2D images. In this paper, we propose `Project & Excite' (PE) modules that base upon the ideas of SE and extend them to operating on 3D volumetric images. `Project & Excite' does not perform global average pooling, but squeezes feature maps along different slices of a tensor separately to retain more spatial information that is subsequently used in the excitation step. We demonstrate that PE modules can be easily integrated in 3D U-Net, boosting performance by 5% Dice points, while only increasing the model complexity by 2%. We evaluate the PE module on two challenging tasks, whole-brain segmentation of MRI scans and whole-body segmentation of CT scans. Code: https://github.com/ai-med/squeeze_and_excitation

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arXiv2019

Perceptual Embedding Consistency for Seamless Reconstruction of Tilewise Style Transfer

Style transfer is a field with growing interest and use cases in deep learning. Recent work has shown Generative Adversarial Networks(GANs) can be used to create realistic images of virtually stained slide images in digital pathology with clinically validated interpretability. Digital pathology images are typically of extremely high resolution, making tilewise analysis necessary for deep learning applications. It has been shown that image generators with instance normalization can cause a tiling artifact when a large image is reconstructed from the tilewise analysis. We introduce a novel perceptual embedding consistency loss significantly reducing the tiling artifact created in the reconstructed whole slide image (WSI). We validate our results by comparing virtually stained slide images with consecutive real stained tissue slide images. We also demonstrate that our model is more robust to contrast, color and brightness perturbations by running comparative sensitivity analysis tests.

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arXiv2019

Webly Supervised Learning for Skin Lesion Classification

Within medical imaging, manual curation of sufficient well-labeled samples is cost, time and scale-prohibitive. To improve the representativeness of the training dataset, for the first time, we present an approach to utilize large amounts of freely available web data through web-crawling. To handle noise and weak nature of web annotations, we propose a two-step transfer learning based training process with a robust loss function, termed as Webly Supervised Learning (WSL) to train deep models for the task. We also leverage search by image to improve the search specificity of our web-crawling and reduce cross-domain noise. Within WSL, we explicitly model the noise structure between classes and incorporate it to selectively distill knowledge from the web data during model training. To demonstrate improved performance due to WSL, we benchmarked on a publicly available 10-class fine-grained skin lesion classification dataset and report a significant improvement of top-1 classification accuracy from 71.25 % to 80.53 % due to the incorporation of web-supervision.

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