arXiv subjects

Nassir Navab

Publications and source records attributed to Nassir Navab.

At least 397 records · Page 22Linked to original sources

arXiv2021

IA-GCN: Interpretable Attention based Graph Convolutional Network for Disease prediction

Interpretability in Graph Convolutional Networks (GCNs) has been explored to some extent in computer vision in general, yet, in the medical domain, it requires further examination. Moreover, most of the interpretability approaches for GCNs, especially in the medical domain, focus on interpreting the model in a post hoc fashion. In this paper, we propose an interpretable graph learning-based model which 1) interprets the clinical relevance of the input features towards the task, 2) uses the explanation to improve the model performance and, 3) learns a population level latent graph that may be used to interpret the cohort's behavior. In a clinical scenario, such a model can assist the clinical experts in better decision-making for diagnosis and treatment planning. The main novelty lies in the interpretable attention module (IAM), which directly operates on multi-modal features. Our IAM learns the attention for each feature based on the unique interpretability-specific losses. We show the application on two publicly available datasets, Tadpole and UKBB, for three tasks of disease, age, and gender prediction. Our proposed model shows superior performance with respect to compared methods with an increase in an average accuracy of 3.2% for Tadpole, 1.6% for UKBB Gender, and 2% for the UKBB Age prediction task. Further, we show exhaustive validation and clinical interpretation of our results.

cs.CV↗

arXiv2021

RGB-D SLAM with Structural Regularities

This work proposes a RGB-D SLAM system specifically designed for structured environments and aimed at improved tracking and mapping accuracy by relying on geometric features that are extracted from the surrounding. Structured environments offer, in addition to points, also an abundance of geometrical features such as lines and planes, which we exploit to design both the tracking and mapping components of our SLAM system. For the tracking part, we explore geometric relationships between these features based on the assumption of a Manhattan World (MW). We propose a decoupling-refinement method based on points, lines, and planes, as well as the use of Manhattan relationships in an additional pose refinement module. For the mapping part, different levels of maps from sparse to dense are reconstructed at a low computational cost. We propose an instance-wise meshing strategy to build a dense map by meshing plane instances independently. The overall performance in terms of pose estimation and reconstruction is evaluated on public benchmarks and shows improved performance compared to state-of-the-art methods. The code is released at \url{https://github.com/yanyan-li/PlanarSLAM}

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arXiv2021

Patient-specific virtual spine straightening and vertebra inpainting: An automatic framework for osteoplasty planning

Symptomatic spinal vertebral compression fractures (VCFs) often require osteoplasty treatment. A cement-like material is injected into the bone to stabilize the fracture, restore the vertebral body height and alleviate pain. Leakage is a common complication and may occur due to too much cement being injected. In this work, we propose an automated patient-specific framework that can allow physicians to calculate an upper bound of cement for the injection and estimate the optimal outcome of osteoplasty. The framework uses the patient CT scan and the fractured vertebra label to build a virtual healthy spine using a high-level approach. Firstly, the fractured spine is segmented with a three-step Convolution Neural Network (CNN) architecture. Next, a per-vertebra rigid registration to a healthy spine atlas restores its curvature. Finally, a GAN-based inpainting approach replaces the fractured vertebra with an estimation of its original shape. Based on this outcome, we then estimate the maximum amount of bone cement for injection. We evaluate our framework by comparing the virtual vertebrae volumes of ten patients to their healthy equivalent and report an average error of 3.88$\pm$7.63\%. The presented pipeline offers a first approach to a personalized automatic high-level framework for planning osteoplasty procedures.

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arXiv2021

GLOWin: A Flow-based Invertible Generative Framework for Learning Disentangled Feature Representations in Medical Images

Disentangled representations can be useful in many downstream tasks, help to make deep learning models more interpretable, and allow for control over features of synthetically generated images that can be useful in training other models that require a large number of labelled or unlabelled data. Recently, flow-based generative models have been proposed to generate realistic images by directly modeling the data distribution with invertible functions. In this work, we propose a new flow-based generative model framework, named GLOWin, that is end-to-end invertible and able to learn disentangled representations. Feature disentanglement is achieved by factorizing the latent space into components such that each component learns the representation for one generative factor. Comprehensive experiments have been conducted to evaluate the proposed method on a public brain tumor MR dataset. Quantitative and qualitative results suggest that the proposed method is effective in disentangling the features from complex medical images.

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arXiv2021

Fourier Transform of Percoll Gradients Boosts CNN Classification of Hereditary Hemolytic Anemias

Hereditary hemolytic anemias are genetic disorders that affect the shape and density of red blood cells. Genetic tests currently used to diagnose such anemias are expensive and unavailable in the majority of clinical labs. Here, we propose a method for identifying hereditary hemolytic anemias based on a standard biochemistry method, called Percoll gradient, obtained by centrifuging a patient's blood. Our hybrid approach consists on using spatial data-driven features, extracted with a convolutional neural network and spectral handcrafted features obtained from fast Fourier transform. We compare late and early feature fusion with AlexNet and VGG16 architectures. AlexNet with late fusion of spectral features performs better compared to other approaches. We achieved an average F1-score of 88% on different classes suggesting the possibility of diagnosing of hereditary hemolytic anemias from Percoll gradients. Finally, we utilize Grad-CAM to explore the spatial features used for classification.

cs.CV↗

arXiv2021

Co-Generation and Segmentation for Generalized Surgical Instrument Segmentation on Unlabelled Data

Surgical instrument segmentation for robot-assisted surgery is needed for accurate instrument tracking and augmented reality overlays. Therefore, the topic has been the subject of a number of recent papers in the CAI community. Deep learning-based methods have shown state-of-the-art performance for surgical instrument segmentation, but their results depend on labelled data. However, labelled surgical data is of limited availability and is a bottleneck in surgical translation of these methods. In this paper, we demonstrate the limited generalizability of these methods on different datasets, including human robot-assisted surgeries. We then propose a novel joint generation and segmentation strategy to learn a segmentation model with better generalization capability to domains that have no labelled data. The method leverages the availability of labelled data in a different domain. The generator does the domain translation from the labelled domain to the unlabelled domain and simultaneously, the segmentation model learns using the generated data while regularizing the generative model. We compared our method with state-of-the-art methods and showed its generalizability on publicly available datasets and on our own recorded video frames from robot-assisted prostatectomies. Our method shows consistently high mean Dice scores on both labelled and unlabelled domains when data is available only for one of the domains. *M. Kalia and T. Aleef contributed equally to the manuscript

cs.CV↗

arXiv2021

OperA: Attention-Regularized Transformers for Surgical Phase Recognition

In this paper we introduce OperA, a transformer-based model that accurately predicts surgical phases from long video sequences. A novel attention regularization loss encourages the model to focus on high-quality frames during training. Moreover, the attention weights are utilized to identify characteristic high attention frames for each surgical phase, which could further be used for surgery summarization. OperA is thoroughly evaluated on two datasets of laparoscopic cholecystectomy videos, outperforming various state-of-the-art temporal refinement approaches.

cs.CV↗

arXiv2021

Panoster: End-to-end Panoptic Segmentation of LiDAR Point Clouds

Panoptic segmentation has recently unified semantic and instance segmentation, previously addressed separately, thus taking a step further towards creating more comprehensive and efficient perception systems. In this paper, we present Panoster, a novel proposal-free panoptic segmentation method for LiDAR point clouds. Unlike previous approaches relying on several steps to group pixels or points into objects, Panoster proposes a simplified framework incorporating a learning-based clustering solution to identify instances. At inference time, this acts as a class-agnostic segmentation, allowing Panoster to be fast, while outperforming prior methods in terms of accuracy. Without any post-processing, Panoster reached state-of-the-art results among published approaches on the challenging SemanticKITTI benchmark, and further increased its lead by exploiting heuristic techniques. Additionally, we showcase how our method can be flexibly and effectively applied on diverse existing semantic architectures to deliver panoptic predictions.

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arXiv2021

Semi-Supervised Few-Shot Learning with Prototypical Random Walks

Recent progress has shown that few-shot learning can be improved with access to unlabelled data, known as semi-supervised few-shot learning(SS-FSL). We introduce an SS-FSL approach, dubbed as Prototypical Random Walk Networks(PRWN), built on top of Prototypical Networks (PN). We develop a random walk semi-supervised loss that enables the network to learn representations that are compact and well-separated. Our work is related to the very recent development of graph-based approaches for few-shot learning. However, we show that compact and well-separated class representations can be achieved by modeling our prototypical random walk notion without needing additional graph-NN parameters or requiring a transductive setting where a collective test set is provided. Our model outperforms baselines in most benchmarks with significant improvements in some cases. Our model, trained with 40$\%$ of the data as labeled, compares competitively against fully supervised prototypical networks, trained on 100$\%$ of the labels, even outperforming it in the 1-shot mini-Imagenet case with 50.89$\%$ to 49.4$\%$ accuracy. We also show that our loss is resistant to distractors, unlabeled data that does not belong to any of the training classes, and hence reflecting robustness to labeled/unlabeled class distribution mismatch. Associated GitHub page can be found at https://prototypical-random-walk.github.io.

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arXiv2020

Deep Bingham Networks: Dealing with Uncertainty and Ambiguity in Pose Estimation

In this work, we introduce Deep Bingham Networks (DBN), a generic framework that can naturally handle pose-related uncertainties and ambiguities arising in almost all real life applications concerning 3D data. While existing works strive to find a single solution to the pose estimation problem, we make peace with the ambiguities causing high uncertainty around which solutions to identify as the best. Instead, we report a family of poses which capture the nature of the solution space. DBN extends the state of the art direct pose regression networks by (i) a multi-hypotheses prediction head which can yield different distribution modes; and (ii) novel loss functions that benefit from Bingham distributions on rotations. This way, DBN can work both in unambiguous cases providing uncertainty information, and in ambiguous scenes where an uncertainty per mode is desired. On a technical front, our network regresses continuous Bingham mixture models and is applicable to both 2D data such as images and to 3D data such as point clouds. We proposed new training strategies so as to avoid mode or posterior collapse during training and to improve numerical stability. Our methods are thoroughly tested on two different applications exploiting two different modalities: (i) 6D camera relocalization from images; and (ii) object pose estimation from 3D point clouds, demonstrating decent advantages over the state of the art. For the former we contributed our own dataset composed of five indoor scenes where it is unavoidable to capture images corresponding to views that are hard to uniquely identify. For the latter we achieve the top results especially for symmetric objects of ModelNet dataset.

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arXiv2020

An Uncertainty-Driven GCN Refinement Strategy for Organ Segmentation

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 perform a sensitivity analysis on the parameters of our proposal and discuss the applicability to other CNN architectures, the results, and current limitations of the model for future work in this research direction. For reproducibility purposes, we make our code publicly available at https://github.com/rodsom22/gcn_refinement.

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arXiv2020

Rethinking Positive Aggregation and Propagation of Gradients in Gradient-based Saliency Methods

Saliency methods interpret the prediction of a neural network by showing the importance of input elements for that prediction. A popular family of saliency methods utilize gradient information. In this work, we empirically show that two approaches for handling the gradient information, namely positive aggregation, and positive propagation, break these methods. Though these methods reflect visually salient information in the input, they do not explain the model prediction anymore as the generated saliency maps are insensitive to the predicted output and are insensitive to model parameter randomization. Specifically for methods that aggregate the gradients of a chosen layer such as GradCAM++ and FullGrad, exclusively aggregating positive gradients is detrimental. We further support this by proposing several variants of aggregation methods with positive handling of gradient information. For methods that backpropagate gradient information such as LRP, RectGrad, and Guided Backpropagation, we show the destructive effect of exclusively propagating positive gradient information.

cs.LG↗

arXiv2020

I Like to Move It: 6D Pose Estimation as an Action Decision Process

Object pose estimation is an integral part of robot vision and AR. Previous 6D pose retrieval pipelines treat the problem either as a regression task or discretize the pose space to classify. We change this paradigm and reformulate the problem as an action decision process where an initial pose is updated in incremental discrete steps that sequentially move a virtual 3D rendering towards the correct solution. A neural network estimates likely moves from a single RGB image iteratively and determines so an acceptable final pose. In comparison to other approaches that train object-specific pose models, we learn a decision process. This allows for a lightweight architecture while it naturally generalizes to unseen objects. A coherent stop action for process termination enables dynamic reduction of the computation cost if there are insignificant changes in a video sequence. Instead of a static inference time, we thereby automatically increase the runtime depending on the object motion. Robustness and accuracy of our action decision network are evaluated on Laval and YCB video scenes where we significantly improve the state-of-the-art.

cs.CV↗

arXiv2020

ROAM: Random Layer Mixup for Semi-Supervised Learning in Medical Imaging

Medical image segmentation is one of the major challenges addressed by machine learning methods. Yet, deep learning methods profoundly depend on a large amount of annotated data, which is time-consuming and costly. Though, semi-supervised learning methods approach this problem by leveraging an abundant amount of unlabeled data along with a small amount of labeled data in the training process. Recently, MixUp regularizer has been successfully introduced to semi-supervised learning methods showing superior performance. MixUp augments the model with new data points through linear interpolation of the data at the input space. We argue that this option is limited. Instead, we propose ROAM, a RandOm lAyer Mixup, which encourages the network to be less confident for interpolated data points at randomly selected space. ROAM generates more data points that have never seen before, and hence it avoids over-fitting and enhances the generalization ability. We conduct extensive experiments to validate our method on three publicly available datasets on whole-brain image segmentation. ROAM achieves state-of-the-art (SOTA) results in fully supervised (89.5%) and semi-supervised (87.0%) settings with a relative improvement of up to 2.40% and 16.50%, respectively for the whole-brain segmentation.

cs.CV↗

arXiv2020

Self-Supervised Out-of-Distribution Detection in Brain CT Scans

Medical imaging data suffers from the limited availability of annotation because annotating 3D medical data is a time-consuming and expensive task. Moreover, even if the annotation is available, supervised learning-based approaches suffer highly imbalanced data. Most of the scans during the screening are from normal subjects, but there are also large variations in abnormal cases. To address these issues, recently, unsupervised deep anomaly detection methods that train the model on large-sized normal scans and detect abnormal scans by calculating reconstruction error have been reported. In this paper, we propose a novel self-supervised learning technique for anomaly detection. Our architecture largely consists of two parts: 1) Reconstruction and 2) predicting geometric transformations. By training the network to predict geometric transformations, the model could learn better image features and distribution of normal scans. In the test time, the geometric transformation predictor can assign the anomaly score by calculating the error between geometric transformation and prediction. Moreover, we further use self-supervised learning with context restoration for pretraining our model. By comparative experiments on clinical brain CT scans, the effectiveness of the proposed method has been verified.

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arXiv2020

Graphite: GRAPH-Induced feaTure Extraction for Point Cloud Registration

3D Point clouds are a rich source of information that enjoy growing popularity in the vision community. However, due to the sparsity of their representation, learning models based on large point clouds is still a challenge. In this work, we introduce Graphite, a GRAPH-Induced feaTure Extraction pipeline, a simple yet powerful feature transform and keypoint detector. Graphite enables intensive down-sampling of point clouds with keypoint detection accompanied by a descriptor. We construct a generic graph-based learning scheme to describe point cloud regions and extract salient points. To this end, we take advantage of 6D pose information and metric learning to learn robust descriptions and keypoints across different scans. We Reformulate the 3D keypoint pipeline with graph neural networks which allow efficient processing of the point set while boosting its descriptive power which ultimately results in more accurate 3D registrations. We demonstrate our lightweight descriptor on common 3D descriptor matching and point cloud registration benchmarks and achieve comparable results with the state of the art. Describing 100 patches of a point cloud and detecting their keypoints takes only ~0.018 seconds with our proposed network.

cs.CV↗

arXiv2020

Exploring Partial Intrinsic and Extrinsic Symmetry in 3D Medical Imaging

We present a novel methodology to detect imperfect bilateral symmetry in CT of human anatomy. In this paper, the structurally symmetric nature of the pelvic bone is explored and is used to provide interventional image augmentation for treatment of unilateral fractures in patients with traumatic injuries. The mathematical basis of our solution is on the incorporation of attributes and characteristics that satisfy the properties of intrinsic and extrinsic symmetry and are robust to outliers. In the first step, feature points that satisfy intrinsic symmetry are automatically detected in the Möbius space defined on the CT data. These features are then pruned via a two-stage RANSAC to attain correspondences that satisfy also the extrinsic symmetry. Then, a disparity function based on Tukey's biweight robust estimator is introduced and minimized to identify a symmetry plane parametrization that yields maximum contralateral similarity. Finally, a novel regularization term is introduced to enhance similarity between bone density histograms across the partial symmetry plane, relying on the important biological observation that, even if injured, the dislocated bone segments remain within the body. Our extensive evaluations on various cases of common fracture types demonstrate the validity of the novel concepts and the robustness and accuracy of the proposed method.

cs.CV↗

arXiv2020

Spatio-temporal Learning from Longitudinal Data for Multiple Sclerosis Lesion Segmentation

Segmentation of Multiple Sclerosis (MS) lesions in longitudinal brain MR scans is performed for monitoring the progression of MS lesions. We hypothesize that the spatio-temporal cues in longitudinal data can aid the segmentation algorithm. Therefore, we propose a multi-task learning approach by defining an auxiliary self-supervised task of deformable registration between two time-points to guide the neural network toward learning from spatio-temporal changes. We show the efficacy of our method on a clinical dataset comprised of 70 patients with one follow-up study for each patient. Our results show that spatio-temporal information in longitudinal data is a beneficial cue for improving segmentation. We improve the result of current state-of-the-art by 2.6% in terms of overall score (p<0.05). Code is publicly available.

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