arXiv subjects

Nassir Navab

Publications and source records attributed to Nassir Navab.

At least 433 records · Page 24Linked to original sources

arXiv2020

Fairness by Learning Orthogonal Disentangled Representations

Learning discriminative powerful representations is a crucial step for machine learning systems. Introducing invariance against arbitrary nuisance or sensitive attributes while performing well on specific tasks is an important problem in representation learning. This is mostly approached by purging the sensitive information from learned representations. In this paper, we propose a novel disentanglement approach to invariant representation problem. We disentangle the meaningful and sensitive representations by enforcing orthogonality constraints as a proxy for independence. We explicitly enforce the meaningful representation to be agnostic to sensitive information by entropy maximization. The proposed approach is evaluated on five publicly available datasets and compared with state of the art methods for learning fairness and invariance achieving the state of the art performance on three datasets and comparable performance on the rest. Further, we perform an ablative study to evaluate the effect of each component.

cs.CV↗

arXiv2020

Scale-Space Autoencoders for Unsupervised Anomaly Segmentation in Brain MRI

Brain pathologies can vary greatly in size and shape, ranging from few pixels (i.e. MS lesions) to large, space-occupying tumors. Recently proposed Autoencoder-based methods for unsupervised anomaly segmentation in brain MRI have shown promising performance, but face difficulties in modeling distributions with high fidelity, which is crucial for accurate delineation of particularly small lesions. Here, similar to these previous works, we model the distribution of healthy brain MRI to localize pathologies from erroneous reconstructions. However, to achieve improved reconstruction fidelity at higher resolutions, we learn to compress and reconstruct different frequency bands of healthy brain MRI using the laplacian pyramid. In a range of experiments comparing our method to different State-of-the-Art approaches on three different brain MR datasets with MS lesions and tumors, we show improved anomaly segmentation performance and the general capability to obtain much more crisp reconstructions of input data at native resolution. The modeling of the laplacian pyramid further enables the delineation and aggregation of lesions at multiple scales, which allows to effectively cope with different pathologies and lesion sizes using a single model.

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arXiv2020

Model-Based Compensation of Moving Tissue for State Recognition in Robotic-Assisted Pedicle Drilling

Drilling is one of the hardest parts of pedicle screw fixation, and it is one of the most dangerous operations because inaccurate screw placement would injury vital tissues, particularly when the vertebra is not stationary. Here we demonstrate the drilling state recognition method for moving tissue by compensating the displacement based on a simplified motion predication model of a vertebra with respect to the tidal volume. To adapt it to different patients, the prediction model was built based on the physiological data recorded from subjects themselves. In addition, the spindle speed of the drilling tool was investigated to find a suitable speed for the robotic-assisted system. To ensure patient safety, a monitoring system was built based on the thrusting force and tracked position information. Finally, experiments were carried out on a fresh porcine lamellar bone fixed on a 3-PRS parallel robot used to simulate the vertebra displacement. The success rate of the robotic-assisted drilling procedure reached 95% when the moving bone was compensated.

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arXiv2020

Efficient Ensemble Model Generation for Uncertainty Estimation with Bayesian Approximation in Segmentation

Recent studies have shown that ensemble approaches could not only improve accuracy and but also estimate model uncertainty in deep learning. However, it requires a large number of parameters according to the increase of ensemble models for better prediction and uncertainty estimation. To address this issue, a generic and efficient segmentation framework to construct ensemble segmentation models is devised in this paper. In the proposed method, ensemble models can be efficiently generated by using the stochastic layer selection method. The ensemble models are trained to estimate uncertainty through Bayesian approximation. Moreover, to overcome its limitation from uncertain instances, we devise a new pixel-wise uncertainty loss, which improves the predictive performance. To evaluate our method, comprehensive and comparative experiments have been conducted on two datasets. Experimental results show that the proposed method could provide useful uncertainty information by Bayesian approximation with the efficient ensemble model generation and improve the predictive performance.

cs.CV↗

arXiv2020

Simultaneous imputation and disease classification in incomplete medical datasets using Multigraph Geometric Matrix Completion (MGMC)

Large-scale population-based studies in medicine are a key resource towards better diagnosis, monitoring, and treatment of diseases. They also serve as enablers of clinical decision support systems, in particular Computer Aided Diagnosis (CADx) using machine learning (ML). Numerous ML approaches for CADx have been proposed in literature. However, these approaches assume full data availability, which is not always feasible in clinical data. To account for missing data, incomplete data samples are either removed or imputed, which could lead to data bias and may negatively affect classification performance. As a solution, we propose an end-to-end learning of imputation and disease prediction of incomplete medical datasets via Multigraph Geometric Matrix Completion (MGMC). MGMC uses multiple recurrent graph convolutional networks, where each graph represents an independent population model based on a key clinical meta-feature like age, sex, or cognitive function. Graph signal aggregation from local patient neighborhoods, combined with multigraph signal fusion via self-attention, has a regularizing effect on both matrix reconstruction and classification performance. Our proposed approach is able to impute class relevant features as well as perform accurate classification on two publicly available medical datasets. We empirically show the superiority of our proposed approach in terms of classification and imputation performance when compared with state-of-the-art approaches. MGMC enables disease prediction in multimodal and incomplete medical datasets. These findings could serve as baseline for future CADx approaches which utilize incomplete datasets.

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arXiv2020

Domain-specific loss design for unsupervised physical training: A new approach to modeling medical ML solutions

Today, cataract surgery is the most frequently performed ophthalmic surgery in the world. The cataract, a developing opacity of the human eye lens, constitutes the world's most frequent cause for blindness. During surgery, the lens is removed and replaced by an artificial intraocular lens (IOL). To prevent patients from needing strong visual aids after surgery, a precise prediction of the optical properties of the inserted IOL is crucial. There has been lots of activity towards developing methods to predict these properties from biometric eye data obtained by OCT devices, recently also by employing machine learning. They consider either only biometric data or physical models, but rarely both, and often neglect the IOL geometry. In this work, we propose OpticNet, a novel optical refraction network, loss function, and training scheme which is unsupervised, domain-specific, and physically motivated. We derive a precise light propagation eye model using single-ray raytracing and formulate a differentiable loss function that back-propagates physical gradients into the network. Further, we propose a new transfer learning procedure, which allows unsupervised training on the physical model and fine-tuning of the network on a cohort of real IOL patient cases. We show that our network is not only superior to systems trained with standard procedures but also that our method outperforms the current state of the art in IOL calculation when compared on two biometric data sets.

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arXiv2020

Decision Support for Intoxication Prediction Using Graph Convolutional Networks

Every day, poison control centers (PCC) are called for immediate classification and treatment recommendations if an acute intoxication is suspected. Due to the time-sensitive nature of these cases, doctors are required to propose a correct diagnosis and intervention within a minimal time frame. Usually the toxin is known and recommendations can be made accordingly. However, in challenging cases only symptoms are mentioned and doctors have to rely on their clinical experience. Medical experts and our analyses of a regional dataset of intoxication records provide evidence that this is challenging, since occurring symptoms may not always match the textbook description due to regional distinctions, inter-rater variance, and institutional workflow. Computer-aided diagnosis (CADx) can provide decision support, but approaches so far do not consider additional information of the reported cases like age or gender, despite their potential value towards a correct diagnosis. In this work, we propose a new machine learning based CADx method which fuses symptoms and meta information of the patients using graph convolutional networks. We further propose a novel symptom matching method that allows the effective incorporation of prior knowledge into the learning process and evidently stabilizes the poison prediction. We validate our method against 10 medical doctors with different experience diagnosing intoxication cases for 10 different toxins from the PCC in Munich and show our method's superiority in performance for poison prediction.

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arXiv2020

Explicit Domain Adaptation with Loosely Coupled Samples

Transfer learning is an important field of machine learning in general, and particularly in the context of fully autonomous driving, which needs to be solved simultaneously for many different domains, such as changing weather conditions and country-specific driving behaviors. Traditional transfer learning methods often focus on image data and are black-box models. In this work we propose a transfer learning framework, core of which is learning an explicit mapping between domains. Due to its interpretability, this is beneficial for safety-critical applications, like autonomous driving. We show its general applicability by considering image classification problems and then move on to time-series data, particularly predicting lane changes. In our evaluation we adapt a pre-trained model to a dataset exhibiting different driving and sensory characteristics.

cs.LG↗

arXiv2020

Colon Shape Estimation Method for Colonoscope Tracking using Recurrent Neural Networks

We propose an estimation method using a recurrent neural network (RNN) of the colon's shape where deformation was occurred by a colonoscope insertion. Colonoscope tracking or a navigation system that navigates physician to polyp positions is needed to reduce such complications as colon perforation. Previous tracking methods caused large tracking errors at the transverse and sigmoid colons because these areas largely deform during colonoscope insertion. Colon deformation should be taken into account in tracking processes. We propose a colon deformation estimation method using RNN and obtain the colonoscope shape from electromagnetic sensors during its insertion into the colon. This method obtains positional, directional, and an insertion length from the colonoscope shape. From its shape, we also calculate the relative features that represent the positional and directional relationships between two points on a colonoscope. Long short-term memory is used to estimate the current colon shape from the past transition of the features of the colonoscope shape. We performed colon shape estimation in a phantom study and correctly estimated the colon shapes during colonoscope insertion with 12.39 (mm) estimation error.

cs.CV↗

arXiv2020

Colonoscope tracking method based on shape estimation network

This paper presents a colonoscope tracking method utilizing a colon shape estimation method. CT colonography is used as a less-invasive colon diagnosis method. If colonic polyps or early-stage cancers are found, they are removed in a colonoscopic examination. In the colonoscopic examination, understanding where the colonoscope running in the colon is difficult. A colonoscope navigation system is necessary to reduce overlooking of polyps. We propose a colonoscope tracking method for navigation systems. Previous colonoscope tracking methods caused large tracking errors because they do not consider deformations of the colon during colonoscope insertions. We utilize the shape estimation network (SEN), which estimates deformed colon shape during colonoscope insertions. The SEN is a neural network containing long short-term memory (LSTM) layer. To perform colon shape estimation suitable to the real clinical situation, we trained the SEN using data obtained during colonoscope operations of physicians. The proposed tracking method performs mapping of the colonoscope tip position to a position in the colon using estimation results of the SEN. We evaluated the proposed method in a phantom study. We confirmed that tracking errors of the proposed method was enough small to perform navigation in the ascending, transverse, and descending colons.

cs.CV↗

arXiv2020

Autoencoders for Unsupervised Anomaly Segmentation in Brain MR Images: A Comparative Study

Deep unsupervised representation learning has recently led to new approaches in the field of Unsupervised Anomaly Detection (UAD) in brain MRI. The main principle behind these works is to learn a model of normal anatomy by learning to compress and recover healthy data. This allows to spot abnormal structures from erroneous recoveries of compressed, potentially anomalous samples. The concept is of great interest to the medical image analysis community as it i) relieves from the need of vast amounts of manually segmented training data---a necessity for and pitfall of current supervised Deep Learning---and ii) theoretically allows to detect arbitrary, even rare pathologies which supervised approaches might fail to find. To date, the experimental design of most works hinders a valid comparison, because i) they are evaluated against different datasets and different pathologies, ii) use different image resolutions and iii) different model architectures with varying complexity. The intent of this work is to establish comparability among recent methods by utilizing a single architecture, a single resolution and the same dataset(s). Besides providing a ranking of the methods, we also try to answer questions like i) how many healthy training subjects are needed to model normality and ii) if the reviewed approaches are also sensitive to domain shift. Further, we identify open challenges and provide suggestions for future community efforts and research directions.

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arXiv2020

Learning 3D Semantic Scene Graphs from 3D Indoor Reconstructions

Scene understanding has been of high interest in computer vision. It encompasses not only identifying objects in a scene, but also their relationships within the given context. With this goal, a recent line of works tackles 3D semantic segmentation and scene layout prediction. In our work we focus on scene graphs, a data structure that organizes the entities of a scene in a graph, where objects are nodes and their relationships modeled as edges. We leverage inference on scene graphs as a way to carry out 3D scene understanding, mapping objects and their relationships. In particular, we propose a learned method that regresses a scene graph from the point cloud of a scene. Our novel architecture is based on PointNet and Graph Convolutional Networks (GCN). In addition, we introduce 3DSSG, a semi-automatically generated dataset, that contains semantically rich scene graphs of 3D scenes. We show the application of our method in a domain-agnostic retrieval task, where graphs serve as an intermediate representation for 3D-3D and 2D-3D matching.

cs.CV↗

arXiv2020

Ultrasound-Guided Robotic Navigation with Deep Reinforcement Learning

In this paper we introduce the first reinforcement learning (RL) based robotic navigation method which utilizes ultrasound (US) images as an input. Our approach combines state-of-the-art RL techniques, specifically deep Q-networks (DQN) with memory buffers and a binary classifier for deciding when to terminate the task. Our method is trained and evaluated on an in-house collected data-set of 34 volunteers and when compared to pure RL and supervised learning (SL) techniques, it performs substantially better, which highlights the suitability of RL navigation for US-guided procedures. When testing our proposed model, we obtained a 82.91% chance of navigating correctly to the sacrum from 165 different starting positions on 5 different unseen simulated environments.

cs.LG↗

arXiv2020

Semantic Image Manipulation Using Scene Graphs

Image manipulation can be considered a special case of image generation where the image to be produced is a modification of an existing image. Image generation and manipulation have been, for the most part, tasks that operate on raw pixels. However, the remarkable progress in learning rich image and object representations has opened the way for tasks such as text-to-image or layout-to-image generation that are mainly driven by semantics. In our work, we address the novel problem of image manipulation from scene graphs, in which a user can edit images by merely applying changes in the nodes or edges of a semantic graph that is generated from the image. Our goal is to encode image information in a given constellation and from there on generate new constellations, such as replacing objects or even changing relationships between objects, while respecting the semantics and style from the original image. We introduce a spatio-semantic scene graph network that does not require direct supervision for constellation changes or image edits. This makes it possible to train the system from existing real-world datasets with no additional annotation effort.

cs.CV↗

arXiv2020

Confident Coreset for Active Learning in Medical Image Analysis

Recent advances in deep learning have resulted in great successes in various applications. Although semi-supervised or unsupervised learning methods have been widely investigated, the performance of deep neural networks highly depends on the annotated data. The problem is that the budget for annotation is usually limited due to the annotation time and expensive annotation cost in medical data. Active learning is one of the solutions to this problem where an active learner is designed to indicate which samples need to be annotated to effectively train a target model. In this paper, we propose a novel active learning method, confident coreset, which considers both uncertainty and distribution for effectively selecting informative samples. By comparative experiments on two medical image analysis tasks, we show that our method outperforms other active learning methods.

cs.CV↗

arXiv2020

Medical-based Deep Curriculum Learning for Improved Fracture Classification

Current deep-learning based methods do not easily integrate to clinical protocols, neither take full advantage of medical knowledge. In this work, we propose and compare several strategies relying on curriculum learning, to support the classification of proximal femur fracture from X-ray images, a challenging problem as reflected by existing intra- and inter-expert disagreement. Our strategies are derived from knowledge such as medical decision trees and inconsistencies in the annotations of multiple experts, which allows us to assign a degree of difficulty to each training sample. We demonstrate that if we start learning "easy" examples and move towards "hard", the model can reach a better performance, even with fewer data. The evaluation is performed on the classification of a clinical dataset of about 1000 X-ray images. Our results show that, compared to class-uniform and random strategies, the proposed medical knowledge-based curriculum, performs up to 15% better in terms of accuracy, achieving the performance of experienced trauma surgeons.

cs.CV↗

arXiv2020

Precise Proximal Femur Fracture Classification for Interactive Training and Surgical Planning

We demonstrate the feasibility of a fully automatic computer-aided diagnosis (CAD) tool, based on deep learning, that localizes and classifies proximal femur fractures on X-ray images according to the AO classification. The proposed framework aims to improve patient treatment planning and provide support for the training of trauma surgeon residents. A database of 1347 clinical radiographic studies was collected. Radiologists and trauma surgeons annotated all fractures with bounding boxes, and provided a classification according to the AO standard. The proposed CAD tool for the classification of radiographs into types "A", "B" and "not-fractured", reaches a F1-score of 87% and AUC of 0.95, when classifying fractures versus not-fractured cases it improves up to 94% and 0.98. Prior localization of the fracture results in an improvement with respect to full image classification. 100% of the predicted centers of the region of interest are contained in the manually provided bounding boxes. The system retrieves on average 9 relevant images (from the same class) out of 10 cases. Our CAD scheme localizes, detects and further classifies proximal femur fractures achieving results comparable to expert-level and state-of-the-art performance. Our auxiliary localization model was highly accurate predicting the region of interest in the radiograph. We further investigated several strategies of verification for its adoption into the daily clinical routine. A sensitivity analysis of the size of the ROI and image retrieval as a clinical use case were presented.

cs.CV↗

arXiv2020

TeCNO: Surgical Phase Recognition with Multi-Stage Temporal Convolutional Networks

Automatic surgical phase recognition is a challenging and crucial task with the potential to improve patient safety and become an integral part of intra-operative decision-support systems. In this paper, we propose, for the first time in workflow analysis, a Multi-Stage Temporal Convolutional Network (MS-TCN) that performs hierarchical prediction refinement for surgical phase recognition. Causal, dilated convolutions allow for a large receptive field and online inference with smooth predictions even during ambiguous transitions. Our method is thoroughly evaluated on two datasets of laparoscopic cholecystectomy videos with and without the use of additional surgical tool information. Outperforming various state-of-the-art LSTM approaches, we verify the suitability of the proposed causal MS-TCN for surgical phase recognition.

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