arXiv subjects

Nassir Navab

Publications and source records attributed to Nassir Navab.

At least 415 records · Page 23Linked to original sources

arXiv2020

Polyp-artifact relationship analysis using graph inductive learned representations

The diagnosis process of colorectal cancer mainly focuses on the localization and characterization of abnormal growths in the colon tissue known as polyps. Despite recent advances in deep object localization, the localization of polyps remains challenging due to the similarities between tissues, and the high level of artifacts. Recent studies have shown the negative impact of the presence of artifacts in the polyp detection task, and have started to take them into account within the training process. However, the use of prior knowledge related to the spatial interaction of polyps and artifacts has not yet been considered. In this work, we incorporate artifact knowledge in a post-processing step. Our method models this task as an inductive graph representation learning problem, and is composed of training and inference steps. Detected bounding boxes around polyps and artifacts are considered as nodes connected by a defined criterion. The training step generates a node classifier with ground truth bounding boxes. In inference, we use this classifier to analyze a second graph, generated from artifact and polyp predictions given by region proposal networks. We evaluate how the choices in the connectivity and artifacts affect the performance of our method and show that it has the potential to reduce the false positives in the results of a region proposal network.

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arXiv2020

CPS++: Improving Class-level 6D Pose and Shape Estimation From Monocular Images With Self-Supervised Learning

Contemporary monocular 6D pose estimation methods can only cope with a handful of object instances. This naturally hampers possible applications as, for instance, robots seamlessly integrated in everyday processes necessarily require the ability to work with hundreds of different objects. To tackle this problem of immanent practical relevance, we propose a novel method for class-level monocular 6D pose estimation, coupled with metric shape retrieval. Unfortunately, acquiring adequate annotations is very time-consuming and labor intensive. This is especially true for class-level 6D pose estimation, as one is required to create a highly detailed reconstruction for all objects and then annotate each object and scene using these models. To overcome this shortcoming, we additionally propose the idea of synthetic-to-real domain transfer for class-level 6D poses by means of self-supervised learning, which removes the burden of collecting numerous manual annotations. In essence, after training our proposed method fully supervised with synthetic data, we leverage recent advances in differentiable rendering to self-supervise the model with unannotated real RGB-D data to improve latter inference. We experimentally demonstrate that we can retrieve precise 6D poses and metric shapes from a single RGB image.

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arXiv2020

Uncertainty-based graph convolutional networks for organ segmentation refinement

Organ segmentation in CT volumes is an important pre-processing step in many computer assisted intervention and diagnosis methods. In recent years, convolutional neural networks have dominated the state of the art in this task. However, since this problem presents a challenging environment due to high variability in the organ's shape and similarity between tissues, the generation of false negative and false positive regions in the output segmentation is a common issue. Recent works have shown that the uncertainty analysis of the model can provide us with useful information about potential errors in the segmentation. In this context, we proposed a segmentation refinement method based on uncertainty analysis and graph convolutional networks. We employ the uncertainty levels of the convolutional network in a particular input volume to formulate a semi-supervised graph learning problem that is solved by training a graph convolutional network. To test our method we refine the initial output of a 2D U-Net. We validate our framework with the NIH pancreas dataset and the spleen dataset of the medical segmentation decathlon. We show that our method outperforms the state-of-the art CRF refinement method by improving the dice score by 1% for the pancreas and 2% for spleen, with respect to the original U-Net's prediction. Finally, we discuss the results and current limitations of the model for future work in this research direction. For reproducibility purposes, we make our code publicly available.

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arXiv2020

Understanding the effects of artifacts on automated polyp detection and incorporating that knowledge via learning without forgetting

Survival rates for colorectal cancer are higher when polyps are detected at an early stage and can be removed before they develop into malignant tumors. Automated polyp detection, which is dominated by deep learning based methods, seeks to improve early detection of polyps. However, current efforts rely heavily on the size and quality of the training datasets. The quality of these datasets often suffers from various image artifacts that affect the visibility and hence, the detection rate. In this work, we conducted a systematic analysis to gain a better understanding of how artifacts affect automated polyp detection. We look at how six different artifact classes, and their location in an image, affect the performance of a RetinaNet based polyp detection model. We found that, depending on the artifact class, they can either benefit or harm the polyp detector. For instance, bubbles are often misclassified as polyps, while specular reflections inside of a polyp region can improve detection capabilities. We then investigated different strategies, such as a learning without forgetting framework, to leverage artifact knowledge to improve automated polyp detection. Our results show that such models can mitigate some of the harmful effects of artifacts, but require more work to significantly improve polyp detection capabilities.

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arXiv2020

SoftPoolNet: Shape Descriptor for Point Cloud Completion and Classification

Point clouds are often the default choice for many applications as they exhibit more flexibility and efficiency than volumetric data. Nevertheless, their unorganized nature -- points are stored in an unordered way -- makes them less suited to be processed by deep learning pipelines. In this paper, we propose a method for 3D object completion and classification based on point clouds. We introduce a new way of organizing the extracted features based on their activations, which we name soft pooling. For the decoder stage, we propose regional convolutions, a novel operator aimed at maximizing the global activation entropy. Furthermore, inspired by the local refining procedure in Point Completion Network (PCN), we also propose a patch-deforming operation to simulate deconvolutional operations for point clouds. This paper proves that our regional activation can be incorporated in many point cloud architectures like AtlasNet and PCN, leading to better performance for geometric completion. We evaluate our approach on different 3D tasks such as object completion and classification, achieving state-of-the-art accuracy.

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arXiv2020

Inverse Distance Aggregation for Federated Learning with Non-IID Data

Federated learning (FL) has been a promising approach in the field of medical imaging in recent years. A critical problem in FL, specifically in medical scenarios is to have a more accurate shared model which is robust to noisy and out-of distribution clients. In this work, we tackle the problem of statistical heterogeneity in data for FL which is highly plausible in medical data where for example the data comes from different sites with different scanner settings. We propose IDA (Inverse Distance Aggregation), a novel adaptive weighting approach for clients based on meta-information which handles unbalanced and non-iid data. We extensively analyze and evaluate our method against the well-known FL approach, Federated Averaging as a baseline.

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arXiv2020

A Learning-based Method for Online Adjustment of C-arm Cone-Beam CT Source Trajectories for Artifact Avoidance

During spinal fusion surgery, screws are placed close to critical nerves suggesting the need for highly accurate screw placement. Verifying screw placement on high-quality tomographic imaging is essential. C-arm Cone-beam CT (CBCT) provides intraoperative 3D tomographic imaging which would allow for immediate verification and, if needed, revision. However, the reconstruction quality attainable with commercial CBCT devices is insufficient, predominantly due to severe metal artifacts in the presence of pedicle screws. These artifacts arise from a mismatch between the true physics of image formation and an idealized model thereof assumed during reconstruction. Prospectively acquiring views onto anatomy that are least affected by this mismatch can, therefore, improve reconstruction quality. We propose to adjust the C-arm CBCT source trajectory during the scan to optimize reconstruction quality with respect to a certain task, i.e. verification of screw placement. Adjustments are performed on-the-fly using a convolutional neural network that regresses a quality index for possible next views given the current x-ray image. Adjusting the CBCT trajectory to acquire the recommended views results in non-circular source orbits that avoid poor images, and thus, data inconsistencies. We demonstrate that convolutional neural networks trained on realistically simulated data are capable of predicting quality metrics that enable scene-specific adjustments of the CBCT source trajectory. Using both realistically simulated data and real CBCT acquisitions of a semi-anthropomorphic phantom, we show that tomographic reconstructions of the resulting scene-specific CBCT acquisitions exhibit improved image quality particularly in terms of metal artifacts. Since the optimization objective is implicitly encoded in a neural network, the proposed approach overcomes the need for 3D information at run-time.

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arXiv2020

Continual Class Incremental Learning for CT Thoracic Segmentation

Deep learning organ segmentation approaches require large amounts of annotated training data, which is limited in supply due to reasons of confidentiality and the time required for expert manual annotation. Therefore, being able to train models incrementally without having access to previously used data is desirable. A common form of sequential training is fine tuning (FT). In this setting, a model learns a new task effectively, but loses performance on previously learned tasks. The Learning without Forgetting (LwF) approach addresses this issue via replaying its own prediction for past tasks during model training. In this work, we evaluate FT and LwF for class incremental learning in multi-organ segmentation using the publicly available AAPM dataset. We show that LwF can successfully retain knowledge on previous segmentations, however, its ability to learn a new class decreases with the addition of each class. To address this problem we propose an adversarial continual learning segmentation approach (ACLSeg), which disentangles feature space into task-specific and task-invariant features. This enables preservation of performance on past tasks and effective acquisition of new knowledge.

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arXiv2020

Structure-SLAM: Low-Drift Monocular SLAM in Indoor Environments

In this paper a low-drift monocular SLAM method is proposed targeting indoor scenarios, where monocular SLAM often fails due to the lack of textured surfaces. Our approach decouples rotation and translation estimation of the tracking process to reduce the long-term drift in indoor environments. In order to take full advantage of the available geometric information in the scene, surface normals are predicted by a convolutional neural network from each input RGB image in real-time. First, a drift-free rotation is estimated based on lines and surface normals using spherical mean-shift clustering, leveraging the weak Manhattan World assumption. Then translation is computed from point and line features. Finally, the estimated poses are refined with a map-to-frame optimization strategy. The proposed method outperforms the state of the art on common SLAM benchmarks such as ICL-NUIM and TUM RGB-D.

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arXiv2020

Self6D: Self-Supervised Monocular 6D Object Pose Estimation

6D object pose estimation is a fundamental problem in computer vision. Convolutional Neural Networks (CNNs) have recently proven to be capable of predicting reliable 6D pose estimates even from monocular images. Nonetheless, CNNs are identified as being extremely data-driven, and acquiring adequate annotations is oftentimes very time-consuming and labor intensive. To overcome this shortcoming, we propose the idea of monocular 6D pose estimation by means of self-supervised learning, removing the need for real annotations. After training our proposed network fully supervised with synthetic RGB data, we leverage recent advances in neural rendering to further self-supervise the model on unannotated real RGB-D data, seeking for a visually and geometrically optimal alignment. Extensive evaluations demonstrate that our proposed self-supervision is able to significantly enhance the model's original performance, outperforming all other methods relying on synthetic data or employing elaborate techniques from the domain adaptation realm.

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arXiv2020

DynaMiTe: A Dynamic Local Motion Model with Temporal Constraints for Robust Real-Time Feature Matching

Feature based visual odometry and SLAM methods require accurate and fast correspondence matching between consecutive image frames for precise camera pose estimation in real-time. Current feature matching pipelines either rely solely on the descriptive capabilities of the feature extractor or need computationally complex optimization schemes. We present the lightweight pipeline DynaMiTe, which is agnostic to the descriptor input and leverages spatial-temporal cues with efficient statistical measures. The theoretical backbone of the method lies within a probabilistic formulation of feature matching and the respective study of physically motivated constraints. A dynamically adaptable local motion model encapsulates groups of features in an efficient data structure. Temporal constraints transfer information of the local motion model across time, thus additionally reducing the search space complexity for matching. DynaMiTe achieves superior results both in terms of matching accuracy and camera pose estimation with high frame rates, outperforming state-of-the-art matching methods while being computationally more efficient.

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arXiv2020

Peri-Diagnostic Decision Support Through Cost-Efficient Feature Acquisition at Test-Time

Computer-aided diagnosis (CADx) algorithms in medicine provide patient-specific decision support for physicians. These algorithms are usually applied after full acquisition of high-dimensional multimodal examination data, and often assume feature-completeness. This, however, is rarely the case due to examination costs, invasiveness, or a lack of indication. A sub-problem in CADx, which to our knowledge has received very little attention among the CADx community so far, is to guide the physician during the entire peri-diagnostic workflow, including the acquisition stage. We model the following question, asked from a physician's perspective: "Given the evidence collected so far, which examination should I perform next, in order to achieve the most accurate and efficient diagnostic prediction?". In this work, we propose a novel approach which is enticingly simple: use dropout at the input layer, and integrated gradients of the trained network at test-time to attribute feature importance dynamically. We validate and explain the effectiveness of our proposed approach using two public medical and two synthetic datasets. Results show that our proposed approach is more cost- and feature-efficient than prior approaches and achieves a higher overall accuracy. This directly translates to less unnecessary examinations for patients, and a quicker, less costly and more accurate decision support for the physician.

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arXiv2020

Attention based Multiple Instance Learning for Classification of Blood Cell Disorders

Red blood cells are highly deformable and present in various shapes. In blood cell disorders, only a subset of all cells is morphologically altered and relevant for the diagnosis. However, manually labeling of all cells is laborious, complicated and introduces inter-expert variability. We propose an attention based multiple instance learning method to classify blood samples of patients suffering from blood cell disorders. Cells are detected using an R-CNN architecture. With the features extracted for each cell, a multiple instance learning method classifies patient samples into one out of four blood cell disorders. The attention mechanism provides a measure of the contribution of each cell to the overall classification and significantly improves the network's classification accuracy as well as its interpretability for the medical expert.

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arXiv2020

6D Camera Relocalization in Ambiguous Scenes via Continuous Multimodal Inference

We present a multimodal camera relocalization framework that captures ambiguities and uncertainties with continuous mixture models defined on the manifold of camera poses. In highly ambiguous environments, which can easily arise due to symmetries and repetitive structures in the scene, computing one plausible solution (what most state-of-the-art methods currently regress) may not be sufficient. Instead we predict multiple camera pose hypotheses as well as the respective uncertainty for each prediction. Towards this aim, we use Bingham distributions, to model the orientation of the camera pose, and a multivariate Gaussian to model the position, with an end-to-end deep neural network. By incorporating a Winner-Takes-All training scheme, we finally obtain a mixture model that is well suited for explaining ambiguities in the scene, yet does not suffer from mode collapse, a common problem with mixture density networks. We introduce a new dataset specifically designed to foster camera localization research in ambiguous environments and exhaustively evaluate our method on synthetic as well as real data on both ambiguous scenes and on non-ambiguous benchmark datasets. We plan to release our code and dataset under $\href{https://multimodal3dvision.github.io}{multimodal3dvision.github.io}$.

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arXiv2020

Towards Unsupervised Learning for Instrument Segmentation in Robotic Surgery with Cycle-Consistent Adversarial Networks

Surgical tool segmentation in endoscopic images is an important problem: it is a crucial step towards full instrument pose estimation and it is used for integration of pre- and intra-operative images into the endoscopic view. While many recent approaches based on convolutional neural networks have shown great results, a key barrier to progress lies in the acquisition of a large number of manually-annotated images which is necessary for an algorithm to generalize and work well in diverse surgical scenarios. Unlike the surgical image data itself, annotations are difficult to acquire and may be of variable quality. On the other hand, synthetic annotations can be automatically generated by using forward kinematic model of the robot and CAD models of tools by projecting them onto an image plane. Unfortunately, this model is very inaccurate and cannot be used for supervised learning of image segmentation models. Since generated annotations will not directly correspond to endoscopic images due to errors, we formulate the problem as an unpaired image-to-image translation where the goal is to learn the mapping between an input endoscopic image and a corresponding annotation using an adversarial model. Our approach allows to train image segmentation models without the need to acquire expensive annotations and can potentially exploit large unlabeled endoscopic image collection outside the annotated distributions of image/annotation data. We test our proposed method on Endovis 2017 challenge dataset and show that it is competitive with supervised segmentation methods.

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arXiv2020

Searching for Efficient Architecture for Instrument Segmentation in Robotic Surgery

Segmentation of surgical instruments is an important problem in robot-assisted surgery: it is a crucial step towards full instrument pose estimation and is directly used for masking of augmented reality overlays during surgical procedures. Most applications rely on accurate real-time segmentation of high-resolution surgical images. While previous research focused primarily on methods that deliver high accuracy segmentation masks, majority of them can not be used for real-time applications due to their computational cost. In this work, we design a light-weight and highly-efficient deep residual architecture which is tuned to perform real-time inference of high-resolution images. To account for reduced accuracy of the discovered light-weight deep residual network and avoid adding any additional computational burden, we perform a differentiable search over dilation rates for residual units of our network. We test our discovered architecture on the EndoVis 2017 Robotic Instruments dataset and verify that our model is the state-of-the-art in terms of speed and accuracy tradeoff with a speed of up to 125 FPS on high resolution images.

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arXiv2020

Augment Yourself: Mixed Reality Self-Augmentation Using Optical See-through Head-mounted Displays and Physical Mirrors

Optical see-though head-mounted displays (OST HMDs) are one of the key technologies for merging virtual objects and physical scenes to provide an immersive mixed reality (MR) environment to its user. A fundamental limitation of HMDs is, that the user itself cannot be augmented conveniently as, in casual posture, only the distal upper extremities are within the field of view of the HMD. Consequently, most MR applications that are centered around the user, such as virtual dressing rooms or learning of body movements, cannot be realized with HMDs. In this paper, we propose a novel concept and prototype system that combines OST HMDs and physical mirrors to enable self-augmentation and provide an immersive MR environment centered around the user. Our system, to the best of our knowledge the first of its kind, estimates the user's pose in the virtual image generated by the mirror using an RGBD camera attached to the HMD and anchors virtual objects to the reflection rather than the user directly. We evaluate our system quantitatively with respect to calibration accuracy and infrared signal degradation effects due to the mirror, and show its potential in applications where large mirrors are already an integral part of the facility. Particularly, we demonstrate its use for virtual fitting rooms, gaming applications, anatomy learning, and personal fitness. In contrast to competing devices such as LCD-equipped smart mirrors, the proposed system consists of only an HMD with RGBD camera and, thus, does not require a prepared environment making it very flexible and generic. In future work, we will aim to investigate how the system can be optimally used for physical rehabilitation and personal training as a promising application.

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arXiv2020

Adversarial Signal Denoising with Encoder-Decoder Networks

The presence of noise is common in signal processing regardless the signal type. Deep neural networks have shown good performance in noise removal, especially on the image domain. In this work, we consider deep neural networks as a denoising tool where our focus is on one dimensional signals. We introduce an encoder-decoder architecture to denoise signals, represented by a sequence of measurements. Instead of relying only on the standard reconstruction error to train the encoder-decoder network, we treat the task of denoising as distribution alignment between the clean and noisy signals. Then, we propose an adversarial learning formulation where the goal is to align the clean and noisy signal latent representation given that both signals pass through the encoder. In our approach, the discriminator has the role of detecting whether the latent representation comes from clean or noisy signals. We evaluate on electrocardiogram and motion signal denoising; and show better performance than learning-based and non-learning approaches.

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