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Nassir Navab

Nassir Navab appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

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Computer Vision Machine Learning eess.IV Robotics Artificial Intelligence physics.med-ph Computational Geometry Graphics Human-Computer Interaction Neurons and Cognition Computation and Language eess.AS eess.SP eess.SY Neural and Evolutionary Computing Sound Systems and Control

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preprint2026arXiv

COMPOSE: Hypergraph Cover Optimization for Multi-view 3D Human Pose Estimation

3D pose estimation from sparse multi-views is a critical task for numerous applications, including action recognition, sports analysis, and human-robot interaction. Optimization-based methods typically follow a two-stage pipeline, first detecting 2D keypoints in each view and then associating these detections across views to triangulate the 3D pose. Existing methods rely on mere pairwise associations to model this correspondence problem, treating global consistency between views (i.e., cycle consistency) as a soft constraint. Yet, reconciling these constraints for multiple views becomes brittle when spurious associations propagate errors. We thus propose COMPOSE, a novel framework that formulates multi-view pose correspondence matching as a hypergraph partitioning problem rather than through pairwise association. While the complexity of the resulting integer linear program grows exponentially in theory, we introduce an efficient geometric pruning strategy to substantially reduce the search space. COMPOSE achieves improvements of up to 23% in average precision over previous optimization-based methods and up to 11% over self-supervised end-to-end learned methods, offering a promising solution to a widely studied problem.

preprint2026arXiv

Non-intrusive Body Composition Assessment from Full-body mmWave Scans

Body composition assessment (BCA) provides detailed information about the distribution of different tissue types in the body, enabling more precise characterization of individuals than BMI or weight alone. Consistent and frequent BCA would be valuable for personalized medicine, but the gold standard methods for BCA, such as CT and MRI, are only practical for opportunistic monitoring of patients with clinical indications for imaging and are not suitable for routine use in the general population. Here, we consider an imaging modality which is not currently used in medical applications: millimeter wave (mmWave) radar. Commonly used in security settings, mmWave scans enable fast, non-intrusive, and privacy-preserving reconstruction of full body shape without the need to remove clothing. To demonstrate the feasibility of fast and convenient BCA from mmWave scans, we present a method for BCA value regression using a multi-task learning strategy that leverages synthetic mmWave-like point clouds derived from clinical imaging and parametric human models. We evaluate the model on a pilot cohort of real mmWave scans with bioimpedance-derived body fat measurements, supporting the feasibility of estimating VAT and body fat percentage (BFP) from mmWave data acquired through clothing in a standing posture. We find that the model can predict VAT and BFP with a mean absolute error of 1.0 L and 3.2\%, respectively, demonstrating the potential of mmWave scanning for routine BCA in a wide range of settings.

preprint2026arXiv

OpenGaFF: Open-Vocabulary Gaussian Feature Field with Codebook Attention

Understanding open-vocabulary 3D scenes with Gaussian-based representations remains challenging due to fragmented and spatially inconsistent semantic predictions across multi-view observations. In this paper, we present OpenGaFF, a novel framework for open-vocabulary 3D scene understanding built upon 3D Gaussian Splatting. At the core of our method is a Gaussian Feature Field that models semantics as a continuous function of Gaussian geometry and appearance. By explicitly conditioning semantic predictions on geometric structure, this formulation strengthens the coupling between geometry and semantics, leading to improved spatial coherence across similar structures in 3D space. To further enforce object-level semantic consistency, we introduce a structured codebook that serves as a set of shared semantic primitives. Furthermore, a codebook-guided attention mechanism is proposed to retrieve language features via similarity matching between query embeddings and learned codebook entries, enabling robust open-vocabulary reasoning while reducing intra-object feature variance. Extensive experiments on standard 2D and 3D open-vocabulary benchmarks demonstrate that our method consistently outperforms prior approaches, achieving improved segmentation quality, stronger 3D semantic consistency and a semantically interpretable codebook that provides insight into the learned representation.

preprint2026arXiv

SurgGoal: Rethinking Surgical Planning Evaluation via Goal-Satisfiability

Surgical planning integrates visual perception, long-horizon reasoning, and procedural knowledge, yet it remains unclear whether current evaluation protocols reliably assess vision-language models (VLMs) in safety-critical settings. Motivated by a goal-oriented view of surgical planning, we define planning correctness via phase-goal satisfiability, where plan validity is determined by expert-defined surgical rules. Based on this definition, we introduce a multicentric meta-evaluation benchmark with valid procedural variations and invalid plans containing order and content errors. Using this benchmark, we show that sequence similarity metrics systematically misjudge planning quality, penalizing valid plans while failing to identify invalid ones. We therefore adopt a rule-based goal-satisfiability metric as a high-precision meta-evaluation reference to assess Video-LLMs under progressively constrained settings, revealing failures due to perception errors and under-constrained reasoning. Structural knowledge consistently improves performance, whereas semantic guidance alone is unreliable and benefits larger models only when combined with structural constraints.

preprint2024arXiv

Machine Learning in Robotic Ultrasound Imaging: Challenges and Perspectives

This article reviews the recent advances in intelligent robotic ultrasound (US) imaging systems. We commence by presenting the commonly employed robotic mechanisms and control techniques in robotic US imaging, along with their clinical applications. Subsequently, we focus on the deployment of machine learning techniques in the development of robotic sonographers, emphasizing crucial developments aimed at enhancing the intelligence of these systems. The methods for achieving autonomous action reasoning are categorized into two sets of approaches: those relying on implicit environmental data interpretation and those using explicit interpretation. Throughout this exploration, we also discuss practical challenges, including those related to the scarcity of medical data, the need for a deeper understanding of the physical aspects involved, and effective data representation approaches. Moreover, we conclude by highlighting the open problems in the field and analyzing different possible perspectives on how the community could move forward in this research area.

preprint2024arXiv

On Discprecncies between Perturbation Evaluations of Graph Neural Network Attributions

Neural networks are increasingly finding their way into the realm of graphs and modeling relationships between features. Concurrently graph neural network explanation approaches are being invented to uncover relationships between the nodes of the graphs. However, there is a disparity between the existing attribution methods, and it is unclear which attribution to trust. Therefore research has introduced evaluation experiments that assess them from different perspectives. In this work, we assess attribution methods from a perspective not previously explored in the graph domain: retraining. The core idea is to retrain the network on important (or not important) relationships as identified by the attributions and evaluate how networks can generalize based on these relationships. We reformulate the retraining framework to sidestep issues lurking in the previous formulation and propose guidelines for correct analysis. We run our analysis on four state-of-the-art GNN attribution methods and five synthetic and real-world graph classification datasets. The analysis reveals that attributions perform variably depending on the dataset and the network. Most importantly, we observe that the famous GNNExplainer performs similarly to an arbitrary designation of edge importance. The study concludes that the retraining evaluation cannot be used as a generalized benchmark and recommends it as a toolset to evaluate attributions on a specifically addressed network, dataset, and sparsity.

preprint2023arXiv

CommonScenes: Generating Commonsense 3D Indoor Scenes with Scene Graph Diffusion

Controllable scene synthesis aims to create interactive environments for various industrial use cases. Scene graphs provide a highly suitable interface to facilitate these applications by abstracting the scene context in a compact manner. Existing methods, reliant on retrieval from extensive databases or pre-trained shape embeddings, often overlook scene-object and object-object relationships, leading to inconsistent results due to their limited generation capacity. To address this issue, we present CommonScenes, a fully generative model that converts scene graphs into corresponding controllable 3D scenes, which are semantically realistic and conform to commonsense. Our pipeline consists of two branches, one predicting the overall scene layout via a variational auto-encoder and the other generating compatible shapes via latent diffusion, capturing global scene-object and local inter-object relationships in the scene graph while preserving shape diversity. The generated scenes can be manipulated by editing the input scene graph and sampling the noise in the diffusion model. Due to lacking a scene graph dataset offering high-quality object-level meshes with relations, we also construct SG-FRONT, enriching the off-the-shelf indoor dataset 3D-FRONT with additional scene graph labels. Extensive experiments are conducted on SG-FRONT where CommonScenes shows clear advantages over other methods regarding generation consistency, quality, and diversity. Codes and the dataset will be released upon acceptance.

preprint2022arXiv

Adaptive Personlization in Federated Learning for Highly Non-i.i.d. Data

Federated learning (FL) is a distributed learning method that offers medical institutes the prospect of collaboration in a global model while preserving the privacy of their patients. Although most medical centers conduct similar medical imaging tasks, their differences, such as specializations, number of patients, and devices, lead to distinctive data distributions. Data heterogeneity poses a challenge for FL and the personalization of the local models. In this work, we investigate an adaptive hierarchical clustering method for FL to produce intermediate semi-global models, so clients with similar data distribution have the chance of forming a more specialized model. Our method forms several clusters consisting of clients with the most similar data distributions; then, each cluster continues to train separately. Inside the cluster, we use meta-learning to improve the personalization of the participants' models. We compare the clustering approach with classical FedAvg and centralized training by evaluating our proposed methods on the HAM10k dataset for skin lesion classification with extreme heterogeneous data distribution. Our experiments demonstrate significant performance gain in heterogeneous distribution compared to standard FL methods in classification accuracy. Moreover, we show that the models converge faster if applied in clusters and outperform centralized training while using only a small subset of data.

preprint2022arXiv

Affective Medical Estimation and Decision Making via Visualized Learning and Deep Learning

With the advent of sophisticated machine learning (ML) techniques and the promising results they yield, especially in medical applications, where they have been investigated for different tasks to enhance the decision-making process. Since visualization is such an effective tool for human comprehension, memorization, and judgment, we have presented a first-of-its-kind estimation approach we refer to as Visualized Learning for Machine Learning (VL4ML) that not only can serve to assist physicians and clinicians in making reasoned medical decisions, but it also allows to appreciate the uncertainty visualization, which could raise incertitude in making the appropriate classification or prediction. For the proof of concept, and to demonstrate the generalized nature of this visualized estimation approach, five different case studies are examined for different types of tasks including classification, regression, and longitudinal prediction. A survey analysis with more than 100 individuals is also conducted to assess users' feedback on this visualized estimation method. The experiments and the survey demonstrate the practical merits of the VL4ML that include: (1) appreciating visually clinical/medical estimations; (2) getting closer to the patients' preferences; (3) improving doctor-patient communication, and (4) visualizing the uncertainty introduced through the black box effect of the deployed ML algorithm. All the source codes are shared via a GitHub repository.

preprint2022arXiv

Analyzing the Effects of Handling Data Imbalance on Learned Features from Medical Images by Looking Into the Models

One challenging property lurking in medical datasets is the imbalanced data distribution, where the frequency of the samples between the different classes is not balanced. Training a model on an imbalanced dataset can introduce unique challenges to the learning problem where a model is biased towards the highly frequent class. Many methods are proposed to tackle the distributional differences and the imbalanced problem. However, the impact of these approaches on the learned features is not well studied. In this paper, we look deeper into the internal units of neural networks to observe how handling data imbalance affects the learned features. We study several popular cost-sensitive approaches for handling data imbalance and analyze the feature maps of the convolutional neural networks from multiple perspectives: analyzing the alignment of salient features with pathologies and analyzing the pathology-related concepts encoded by the networks. Our study reveals differences and insights regarding the trained models that are not reflected by quantitative metrics such as AUROC and AP and show up only by looking at the models through a lens.

preprint2022arXiv

Bending Graphs: Hierarchical Shape Matching using Gated Optimal Transport

Shape matching has been a long-studied problem for the computer graphics and vision community. The objective is to predict a dense correspondence between meshes that have a certain degree of deformation. Existing methods either consider the local description of sampled points or discover correspondences based on global shape information. In this work, we investigate a hierarchical learning design, to which we incorporate local patch-level information and global shape-level structures. This flexible representation enables correspondence prediction and provides rich features for the matching stage. Finally, we propose a novel optimal transport solver by recurrently updating features on non-confident nodes to learn globally consistent correspondences between the shapes. Our results on publicly available datasets suggest robust performance in presence of severe deformations without the need for extensive training or refinement.

preprint2022arXiv

BFS-Net: Weakly Supervised Cell Instance Segmentation from Bright-Field Microscopy Z-Stacks

Despite its broad availability, volumetric information acquisition from Bright-Field Microscopy (BFM) is inherently difficult due to the projective nature of the acquisition process. We investigate the prediction of 3D cell instances from a set of BFM Z-Stack images. We propose a novel two-stage weakly supervised method for volumetric instance segmentation of cells which only requires approximate cell centroids annotation. Created pseudo-labels are thereby refined with a novel refinement loss with Z-stack guidance. The evaluations show that our approach can generalize not only to BFM Z-Stack data, but to other 3D cell imaging modalities. A comparison of our pipeline against fully supervised methods indicates that the significant gain in reduced data collection and labelling results in minor performance difference.

preprint2022arXiv

Bioelectric Registration of Electromagnetic Tracking and Preoperative Volume Data

For minimally invasive endovascular surgery, the localization of catheters and guidewires inside the human body is essential. Electromagnetic (EM) tracking is one technology that allows localizing such surgical instruments. For localizing intra-operatively EM-tracked instruments with respect to preoperative volume data, it is necessary to bring pre- and intraoperative imaging into the same coordinate frame. In most existing solutions, such registration requires additional interactions, modifying the procedure's original workflow. We propose a new method taking advantage of Bioelectric signals to initialize and register preoperative volumes to the EM tracking system without significantly changing the interventional workflow. We envision the most natural use-case of our concept in cardiac electrophysiology (EP) procedures, in which EP catheters are already equipped with all the necessary sensing, including electric sensing for the measurement of electrophysiological signals and EM tracking for catheter localization. We use EP catheters for Bioelectric sensing to detect local features of the vasculature while advancing the catheter inside the human body. Such features can be automatically labeled before the procedure within the preoperative data. The combination of Bioelectric and EM tracking can localize vascular features such as bifurcations and stenosis within the EM tracking space. Mapping them to preoperative data automatically registers patients' CT space to EM tracking. The proposed registration process is entirely based on Bioelectric sensed features, with no need for external markers or other interventional imaging devices.

preprint2022arXiv

CACTUSS: Common Anatomical CT-US Space for US examinations

Abdominal aortic aneurysm (AAA) is a vascular disease in which a section of the aorta enlarges, weakening its walls and potentially rupturing the vessel. Abdominal ultrasound has been utilized for diagnostics, but due to its limited image quality and operator dependency, CT scans are usually required for monitoring and treatment planning. Recently, abdominal CT datasets have been successfully utilized to train deep neural networks for automatic aorta segmentation. Knowledge gathered from this solved task could therefore be leveraged to improve US segmentation for AAA diagnosis and monitoring. To this end, we propose CACTUSS: a common anatomical CT-US space, which acts as a virtual bridge between CT and US modalities to enable automatic AAA screening sonography. CACTUSS makes use of publicly available labelled data to learn to segment based on an intermediary representation that inherits properties from both US and CT. We train a segmentation network in this new representation and employ an additional image-to-image translation network which enables our model to perform on real B-mode images. Quantitative comparisons against fully supervised methods demonstrate the capabilities of CACTUSS in terms of Dice Score and diagnostic metrics, showing that our method also meets the clinical requirements for AAA scanning and diagnosis.

preprint2022arXiv

CheXplaining in Style: Counterfactual Explanations for Chest X-rays using StyleGAN

Deep learning models used in medical image analysis are prone to raising reliability concerns due to their black-box nature. To shed light on these black-box models, previous works predominantly focus on identifying the contribution of input features to the diagnosis, i.e., feature attribution. In this work, we explore counterfactual explanations to identify what patterns the models rely on for diagnosis. Specifically, we investigate the effect of changing features within chest X-rays on the classifier's output to understand its decision mechanism. We leverage a StyleGAN-based approach (StyleEx) to create counterfactual explanations for chest X-rays by manipulating specific latent directions in their latent space. In addition, we propose EigenFind to significantly reduce the computation time of generated explanations. We clinically evaluate the relevancy of our counterfactual explanations with the help of radiologists. Our code is publicly available.

preprint2022arXiv

CloudAttention: Efficient Multi-Scale Attention Scheme For 3D Point Cloud Learning

Processing 3D data efficiently has always been a challenge. Spatial operations on large-scale point clouds, stored as sparse data, require extra cost. Attracted by the success of transformers, researchers are using multi-head attention for vision tasks. However, attention calculations in transformers come with quadratic complexity in the number of inputs and miss spatial intuition on sets like point clouds. We redesign set transformers in this work and incorporate them into a hierarchical framework for shape classification and part and scene segmentation. We propose our local attention unit, which captures features in a spatial neighborhood. We also compute efficient and dynamic global cross attentions by leveraging sampling and grouping at each iteration. Finally, to mitigate the non-heterogeneity of point clouds, we propose an efficient Multi-Scale Tokenization (MST), which extracts scale-invariant tokens for attention operations. The proposed hierarchical model achieves state-of-the-art shape classification in mean accuracy and yields results on par with the previous segmentation methods while requiring significantly fewer computations. Our proposed architecture predicts segmentation labels with around half the latency and parameter count of the previous most efficient method with comparable performance. The code is available at https://github.com/YigeWang-WHU/CloudAttention.

preprint2022arXiv

DA$^2$ Dataset: Toward Dexterity-Aware Dual-Arm Grasping

In this paper, we introduce DA$^2$, the first large-scale dual-arm dexterity-aware dataset for the generation of optimal bimanual grasping pairs for arbitrary large objects. The dataset contains about 9M pairs of parallel-jaw grasps, generated from more than 6000 objects and each labeled with various grasp dexterity measures. In addition, we propose an end-to-end dual-arm grasp evaluation model trained on the rendered scenes from this dataset. We utilize the evaluation model as our baseline to show the value of this novel and nontrivial dataset by both online analysis and real robot experiments. All data and related code will be open-sourced at https://sites.google.com/view/da2dataset.

preprint2022arXiv

DeStripe: A Self2Self Spatio-Spectral Graph Neural Network with Unfolded Hessian for Stripe Artifact Removal in Light-sheet Microscopy

Light-sheet fluorescence microscopy (LSFM) is a cutting-edge volumetric imaging technique that allows for three-dimensional imaging of mesoscopic samples with decoupled illumination and detection paths. Although the selective excitation scheme of such a microscope provides intrinsic optical sectioning that minimizes out-of-focus fluorescence background and sample photodamage, it is prone to light absorption and scattering effects, which results in uneven illumination and striping artifacts in the images adversely. To tackle this issue, in this paper, we propose a blind stripe artifact removal algorithm in LSFM, called DeStripe, which combines a self-supervised spatio-spectral graph neural network with unfolded Hessian prior. Specifically, inspired by the desirable properties of Fourier transform in condensing striping information into isolated values in the frequency domain, DeStripe firstly localizes the potentially corrupted Fourier coefficients by exploiting the structural difference between unidirectional stripe artifacts and more isotropic foreground images. Affected Fourier coefficients can then be fed into a graph neural network for recovery, with a Hessian regularization unrolled to further ensure structures in the standard image space are well preserved. Since in realistic, stripe-free LSFM barely exists with a standard image acquisition protocol, DeStripe is equipped with a Self2Self denoising loss term, enabling artifact elimination without access to stripe-free ground truth images. Competitive experimental results demonstrate the efficacy of DeStripe in recovering corrupted biomarkers in LSFM with both synthetic and real stripe artifacts.

preprint2022arXiv

Differentiable Graph Module (DGM) for Graph Convolutional Networks

Graph deep learning has recently emerged as a powerful ML concept allowing to generalize successful deep neural architectures to non-Euclidean structured data. Such methods have shown promising results on a broad spectrum of applications ranging from social science, biomedicine, and particle physics to computer vision, graphics, and chemistry. One of the limitations of the majority of current graph neural network architectures is that they are often restricted to the transductive setting and rely on the assumption that the underlying graph is {\em known} and {\em fixed}. Often, this assumption is not true since the graph may be noisy, or partially and even completely unknown. In such cases, it would be helpful to infer the graph directly from the data, especially in inductive settings where some nodes were not present in the graph at training time. Furthermore, learning a graph may become an end in itself, as the inferred structure may provide complementary insights next to the downstream task. In this paper, we introduce Differentiable Graph Module (DGM), a learnable function that predicts edge probabilities in the graph which are optimal for the downstream task. DGM can be combined with convolutional graph neural network layers and trained in an end-to-end fashion. We provide an extensive evaluation of applications from the domains of healthcare (disease prediction), brain imaging (age prediction), computer graphics (3D point cloud segmentation), and computer vision (zero-shot learning). We show that our model provides a significant improvement over baselines both in transductive and inductive settings and achieves state-of-the-art results.

preprint2022arXiv

Do Explanations Explain? Model Knows Best

It is a mystery which input features contribute to a neural network's output. Various explanation (feature attribution) methods are proposed in the literature to shed light on the problem. One peculiar observation is that these explanations (attributions) point to different features as being important. The phenomenon raises the question, which explanation to trust? We propose a framework for evaluating the explanations using the neural network model itself. The framework leverages the network to generate input features that impose a particular behavior on the output. Using the generated features, we devise controlled experimental setups to evaluate whether an explanation method conforms to an axiom. Thus we propose an empirical framework for axiomatic evaluation of explanation methods. We evaluate well-known and promising explanation solutions using the proposed framework. The framework provides a toolset to reveal properties and drawbacks within existing and future explanation solutions.

preprint2022arXiv

Exploiting Diversity of Unlabeled Data for Label-Efficient Semi-Supervised Active Learning

The availability of large labeled datasets is the key component for the success of deep learning. However, annotating labels on large datasets is generally time-consuming and expensive. Active learning is a research area that addresses the issues of expensive labeling by selecting the most important samples for labeling. Diversity-based sampling algorithms are known as integral components of representation-based approaches for active learning. In this paper, we introduce a new diversity-based initial dataset selection algorithm to select the most informative set of samples for initial labeling in the active learning setting. Self-supervised representation learning is used to consider the diversity of samples in the initial dataset selection algorithm. Also, we propose a novel active learning query strategy, which uses diversity-based sampling on consistency-based embeddings. By considering the consistency information with the diversity in the consistency-based embedding scheme, the proposed method could select more informative samples for labeling in the semi-supervised learning setting. Comparative experiments show that the proposed method achieves compelling results on CIFAR-10 and Caltech-101 datasets compared with previous active learning approaches by utilizing the diversity of unlabeled data.

preprint2022arXiv

From 2D to 3D: Re-thinking Benchmarking of Monocular Depth Prediction

There have been numerous recently proposed methods for monocular depth prediction (MDP) coupled with the equally rapid evolution of benchmarking tools. However, we argue that MDP is currently witnessing benchmark over-fitting and relying on metrics that are only partially helpful to gauge the usefulness of the predictions for 3D applications. This limits the design and development of novel methods that are truly aware of - and improving towards estimating - the 3D structure of the scene rather than optimizing 2D-based distances. In this work, we aim to bring structural awareness to MDP, an inherently 3D task, by exhibiting the limits of evaluation metrics towards assessing the quality of the 3D geometry. We propose a set of metrics well suited to evaluate the 3D geometry of MDP approaches and a novel indoor benchmark, RIO-D3D, crucial for the proposed evaluation methodology. Our benchmark is based on a real-world dataset featuring high-quality rendered depth maps obtained from RGB-D reconstructions. We further demonstrate this to help benchmark the closely-tied task of 3D scene completion.

preprint2022arXiv

GPV-Pose: Category-level Object Pose Estimation via Geometry-guided Point-wise Voting

While 6D object pose estimation has recently made a huge leap forward, most methods can still only handle a single or a handful of different objects, which limits their applications. To circumvent this problem, category-level object pose estimation has recently been revamped, which aims at predicting the 6D pose as well as the 3D metric size for previously unseen instances from a given set of object classes. This is, however, a much more challenging task due to severe intra-class shape variations. To address this issue, we propose GPV-Pose, a novel framework for robust category-level pose estimation, harnessing geometric insights to enhance the learning of category-level pose-sensitive features. First, we introduce a decoupled confidence-driven rotation representation, which allows geometry-aware recovery of the associated rotation matrix. Second, we propose a novel geometry-guided point-wise voting paradigm for robust retrieval of the 3D object bounding box. Finally, leveraging these different output streams, we can enforce several geometric consistency terms, further increasing performance, especially for non-symmetric categories. GPV-Pose produces superior results to state-of-the-art competitors on common public benchmarks, whilst almost achieving real-time inference speed at 20 FPS.

preprint2022arXiv

Graph-in-Graph (GiG): Learning interpretable latent graphs in non-Euclidean domain for biological and healthcare applications

Graphs are a powerful tool for representing and analyzing unstructured, non-Euclidean data ubiquitous in the healthcare domain. Two prominent examples are molecule property prediction and brain connectome analysis. Importantly, recent works have shown that considering relationships between input data samples have a positive regularizing effect for the downstream task in healthcare applications. These relationships are naturally modeled by a (possibly unknown) graph structure between input samples. In this work, we propose Graph-in-Graph (GiG), a neural network architecture for protein classification and brain imaging applications that exploits the graph representation of the input data samples and their latent relation. We assume an initially unknown latent-graph structure between graph-valued input data and propose to learn end-to-end a parametric model for message passing within and across input graph samples, along with the latent structure connecting the input graphs. Further, we introduce a degree distribution loss that helps regularize the predicted latent relationships structure. This regularization can significantly improve the downstream task. Moreover, the obtained latent graph can represent patient population models or networks of molecule clusters, providing a level of interpretability and knowledge discovery in the input domain of particular value in healthcare.

preprint2022arXiv

Intelligent Masking: Deep Q-Learning for Context Encoding in Medical Image Analysis

The need for a large amount of labeled data in the supervised setting has led recent studies to utilize self-supervised learning to pre-train deep neural networks using unlabeled data. Many self-supervised training strategies have been investigated especially for medical datasets to leverage the information available in the much fewer unlabeled data. One of the fundamental strategies in image-based self-supervision is context prediction. In this approach, a model is trained to reconstruct the contents of an arbitrary missing region of an image based on its surroundings. However, the existing methods adopt a random and blind masking approach by focusing uniformly on all regions of the images. This approach results in a lot of unnecessary network updates that cause the model to forget the rich extracted features. In this work, we develop a novel self-supervised approach that occludes targeted regions to improve the pre-training procedure. To this end, we propose a reinforcement learning-based agent which learns to intelligently mask input images through deep Q-learning. We show that training the agent against the prediction model can significantly improve the semantic features extracted for downstream classification tasks. We perform our experiments on two public datasets for diagnosing breast cancer in the ultrasound images and detecting lower-grade glioma with MR images. In our experiments, we show that our novel masking strategy advances the learned features according to the performance on the classification task in terms of accuracy, macro F1, and AUROC.

preprint2022arXiv

Interpretable Vertebral Fracture Diagnosis

Do black-box neural network models learn clinically relevant features for fracture diagnosis? The answer not only establishes reliability quenches scientific curiosity but also leads to explainable and verbose findings that can assist the radiologists in the final and increase trust. This work identifies the concepts networks use for vertebral fracture diagnosis in CT images. This is achieved by associating concepts to neurons highly correlated with a specific diagnosis in the dataset. The concepts are either associated with neurons by radiologists pre-hoc or are visualized during a specific prediction and left for the user's interpretation. We evaluate which concepts lead to correct diagnosis and which concepts lead to false positives. The proposed frameworks and analysis pave the way for reliable and explainable vertebral fracture diagnosis.

preprint2022arXiv

Latent-Graph Learning for Disease Prediction

Recently, Graph Convolutional Networks (GCNs) have proven to be a powerful machine learning tool for Computer-Aided Diagnosis (CADx) and disease prediction. A key component in these models is to build a population graph, where the graph adjacency matrix represents pair-wise patient similarities. Until now, the similarity metrics have been defined manually, usually based on meta-features like demographics or clinical scores. The definition of the metric, however, needs careful tuning, as GCNs are very sensitive to the graph structure. In this paper, we demonstrate for the first time in the CADx domain that it is possible to learn a single, optimal graph towards the GCN's downstream task of disease classification. To this end, we propose a novel, end-to-end trainable graph learning architecture for dynamic and localized graph pruning. Unlike commonly employed spectral GCN approaches, our GCN is spatial and inductive, and can thus infer previously unseen patients as well. We demonstrate significant classification improvements with our learned graph on two CADx problems in medicine. We further explain and visualize this result using an artificial dataset, underlining the importance of graph learning for more accurate and robust inference with GCNs in medical applications.

preprint2022arXiv

Learning Local Displacements for Point Cloud Completion

We propose a novel approach aimed at object and semantic scene completion from a partial scan represented as a 3D point cloud. Our architecture relies on three novel layers that are used successively within an encoder-decoder structure and specifically developed for the task at hand. The first one carries out feature extraction by matching the point features to a set of pre-trained local descriptors. Then, to avoid losing individual descriptors as part of standard operations such as max-pooling, we propose an alternative neighbor-pooling operation that relies on adopting the feature vectors with the highest activations. Finally, up-sampling in the decoder modifies our feature extraction in order to increase the output dimension. While this model is already able to achieve competitive results with the state of the art, we further propose a way to increase the versatility of our approach to process point clouds. To this aim, we introduce a second model that assembles our layers within a transformer architecture. We evaluate both architectures on object and indoor scene completion tasks, achieving state-of-the-art performance.

preprint2022arXiv

Longitudinal Self-Supervision for COVID-19 Pathology Quantification

Quantifying COVID-19 infection over time is an important task to manage the hospitalization of patients during a global pandemic. Recently, deep learning-based approaches have been proposed to help radiologists automatically quantify COVID-19 pathologies on longitudinal CT scans. However, the learning process of deep learning methods demands extensive training data to learn the complex characteristics of infected regions over longitudinal scans. It is challenging to collect a large-scale dataset, especially for longitudinal training. In this study, we want to address this problem by proposing a new self-supervised learning method to effectively train longitudinal networks for the quantification of COVID-19 infections. For this purpose, longitudinal self-supervision schemes are explored on clinical longitudinal COVID-19 CT scans. Experimental results show that the proposed method is effective, helping the model better exploit the semantics of longitudinal data and improve two COVID-19 quantification tasks.

preprint2022arXiv

Object-aware Monocular Depth Prediction with Instance Convolutions

With the advent of deep learning, estimating depth from a single RGB image has recently received a lot of attention, being capable of empowering many different applications ranging from path planning for robotics to computational cinematography. Nevertheless, while the depth maps are in their entirety fairly reliable, the estimates around object discontinuities are still far from satisfactory. This can be contributed to the fact that the convolutional operator naturally aggregates features across object discontinuities, resulting in smooth transitions rather than clear boundaries. Therefore, in order to circumvent this issue, we propose a novel convolutional operator which is explicitly tailored to avoid feature aggregation of different object parts. In particular, our method is based on estimating per-part depth values by means of superpixels. The proposed convolutional operator, which we dub "Instance Convolution", then only considers each object part individually on the basis of the estimated superpixels. Our evaluation with respect to the NYUv2 as well as the iBims dataset clearly demonstrates the superiority of Instance Convolutions over the classical convolution at estimating depth around occlusion boundaries, while producing comparable results elsewhere. Code will be made publicly available upon acceptance.

preprint2022arXiv

PhoCaL: A Multi-Modal Dataset for Category-Level Object Pose Estimation with Photometrically Challenging Objects

Object pose estimation is crucial for robotic applications and augmented reality. Beyond instance level 6D object pose estimation methods, estimating category-level pose and shape has become a promising trend. As such, a new research field needs to be supported by well-designed datasets. To provide a benchmark with high-quality ground truth annotations to the community, we introduce a multimodal dataset for category-level object pose estimation with photometrically challenging objects termed PhoCaL. PhoCaL comprises 60 high quality 3D models of household objects over 8 categories including highly reflective, transparent and symmetric objects. We developed a novel robot-supported multi-modal (RGB, depth, polarisation) data acquisition and annotation process. It ensures sub-millimeter accuracy of the pose for opaque textured, shiny and transparent objects, no motion blur and perfect camera synchronisation. To set a benchmark for our dataset, state-of-the-art RGB-D and monocular RGB methods are evaluated on the challenging scenes of PhoCaL.

preprint2022arXiv

Semi-Supervised Federated Peer Learning for Skin Lesion Classification

Globally, Skin carcinoma is among the most lethal diseases. Millions of people are diagnosed with this cancer every year. Sill, early detection can decrease the medication cost and mortality rate substantially. The recent improvement in automated cancer classification using deep learning methods has reached a human-level performance requiring a large amount of annotated data assembled in one location, yet, finding such conditions usually is not feasible. Recently, federated learning (FL) has been proposed to train decentralized models in a privacy-preserved fashion depending on labeled data at the client-side, which is usually not available and costly. To address this, we propose \verb!FedPerl!, a semi-supervised federated learning method. Our method is inspired by peer learning from educational psychology and ensemble averaging from committee machines. FedPerl builds communities based on clients' similarities. Then it encourages communities members to learn from each other to generate more accurate pseudo labels for the unlabeled data. We also proposed the peer anonymization (PA) technique to anonymize clients. As a core component of our method, PA is orthogonal to other methods without additional complexity and reduces the communication cost while enhancing performance. Finally, we propose a dynamic peer-learning policy that controls the learning stream to avoid any degradation in the performance, especially for individual clients. Our experimental setup consists of 71,000 skin lesion images collected from 5 publicly available datasets. We test our method in four different scenarios in SSFL. With few annotated data, FedPerl is on par with a state-of-the-art method in skin lesion classification in the standard setup while outperforming SSFLs and the baselines by 1.8% and 15.8%, respectively. Also, it generalizes better to unseen clients while being less sensitive to noisy ones.

preprint2022arXiv

Shape-Aware Masking for Inpainting in Medical Imaging

Inpainting has recently been proposed as a successful deep learning technique for unsupervised medical image model discovery. The masks used for inpainting are generally independent of the dataset and are not tailored to perform on different given classes of anatomy. In this work, we introduce a method for generating shape-aware masks for inpainting, which aims at learning the statistical shape prior. We hypothesize that although the variation of masks improves the generalizability of inpainting models, the shape of the masks should follow the topology of the organs of interest. Hence, we propose an unsupervised guided masking approach based on an off-the-shelf inpainting model and a superpixel over-segmentation algorithm to generate a wide range of shape-dependent masks. Experimental results on abdominal MR image reconstruction show the superiority of our proposed masking method over standard methods using square-shaped or dataset of irregular shape masks.

preprint2022arXiv

SoftPool++: An Encoder-Decoder Network for Point Cloud Completion

We propose a novel convolutional operator for the task of point cloud completion. One striking characteristic of our approach is that, conversely to related work it does not require any max-pooling or voxelization operation. Instead, the proposed operator used to learn the point cloud embedding in the encoder extracts permutation-invariant features from the point cloud via a soft-pooling of feature activations, which are able to preserve fine-grained geometric details. These features are then passed on to a decoder architecture. Due to the compression in the encoder, a typical limitation of this type of architectures is that they tend to lose parts of the input shape structure. We propose to overcome this limitation by using skip connections specifically devised for point clouds, where links between corresponding layers in the encoder and the decoder are established. As part of these connections, we introduce a transformation matrix that projects the features from the encoder to the decoder and vice-versa. The quantitative and qualitative results on the task of object completion from partial scans on the ShapeNet dataset show that incorporating our approach achieves state-of-the-art performance in shape completion both at low and high resolutions.

preprint2022arXiv

Sonification as a Reliable Alternative to Conventional Visual Surgical Navigation

Despite the undeniable advantages of image-guided surgical assistance systems in terms of accuracy, such systems have not yet fully met surgeons' needs or expectations regarding usability, time efficiency, and their integration into the surgical workflow. On the other hand, perceptual studies have shown that presenting independent but causally correlated information via multimodal feedback involving different sensory modalities can improve task performance. This article investigates an alternative method for computer-assisted surgical navigation, introduces a novel sonification methodology for navigated pedicle screw placement, and discusses advanced solutions based on multisensory feedback. The proposed method comprises a novel sonification solution for alignment tasks in four degrees of freedom based on frequency modulation (FM) synthesis. We compared the resulting accuracy and execution time of the proposed sonification method with visual navigation, which is currently considered the state of the art. We conducted a phantom study in which 17 surgeons executed the pedicle screw placement task in the lumbar spine, guided by either the proposed sonification-based or the traditional visual navigation method. The results demonstrated that the proposed method is as accurate as the state of the art while decreasing the surgeon's need to focus on visual navigation displays instead of the natural focus on surgical tools and targeted anatomy during task execution.

preprint2022arXiv

Speckle2Speckle: Unsupervised Learning of Ultrasound Speckle Filtering Without Clean Data

In ultrasound imaging the appearance of homogeneous regions of tissue is subject to speckle, which for certain applications can make the detection of tissue irregularities difficult. To cope with this, it is common practice to apply speckle reduction filters to the images. Most conventional filtering techniques are fairly hand-crafted and often need to be finely tuned to the present hardware, imaging scheme and application. Learning based techniques on the other hand suffer from the need for a target image for training (in case of fully supervised techniques) or require narrow, complex physics-based models of the speckle appearance that might not apply in all cases. With this work we propose a deep-learning based method for speckle removal without these limitations. To enable this, we make use of realistic ultrasound simulation techniques that allow for instantiation of several independent speckle realizations that represent the exact same tissue, thus allowing for the application of image reconstruction techniques that work with pairs of differently corrupted data. Compared to two other state-of-the-art approaches (non-local means and the Optimized Bayesian non-local means filter) our method performs favorably in qualitative comparisons and quantitative evaluation, despite being trained on simulations alone, and is several orders of magnitude faster.

preprint2022arXiv

Spotlight on nerves: Portable multispectral optoacoustic imaging of peripheral nerve vascularization and morphology

Various morphological and functional parameters of peripheral nerves and their vascular supply are indicative of pathological changes due to injury or disease. Based on recent improvements in optoacoustic image quality, we explore the ability of multispectral optoacoustic tomography, in tandem with ultrasound imaging (OPUS), to investigate the vascular environment and morphology of peripheral nerves in vivo in a pilot study on healthy volunteers. We showcase the unique ability of optoacoustic imaging to visualize the vasa nervorum by observing intraneurial vessels in healthy nerves in vivo for the first time. In addition, we demonstrate that the label-free spectral optoacoustic contrast of the perfused connective tissue of peripheral nerves can be linked to the endogenous contrast of haemoglobin and collagen. We introduce metrics to analyze the composition of tissue based on its optoacoustic contrast and show that the high-resolution spectral contrast reveals specific differences between nervous tissue and reference tissue in the nerve's surrounding. We discuss how this showcased extraction of peripheral nerve characteristics using multispectral optoacoustic and ultrasound imaging can offer new insights into the pathophysiology of nerve damage and neuropathies, for example, in the context of diabetes.

preprint2022arXiv

STTAR: Surgical Tool Tracking using off-the-shelf Augmented Reality Head-Mounted Displays

The use of Augmented Reality (AR) for navigation purposes has shown beneficial in assisting physicians during the performance of surgical procedures. These applications commonly require knowing the pose of surgical tools and patients to provide visual information that surgeons can use during the task performance. Existing medical-grade tracking systems use infrared cameras placed inside the Operating Room (OR) to identify retro-reflective markers attached to objects of interest and compute their pose. Some commercially available AR Head-Mounted Displays (HMDs) use similar cameras for self-localization, hand tracking, and estimating the objects' depth. This work presents a framework that uses the built-in cameras of AR HMDs to enable accurate tracking of retro-reflective markers, such as those used in surgical procedures, without the need to integrate any additional components. This framework is also capable of simultaneously tracking multiple tools. Our results show that the tracking and detection of the markers can be achieved with an accuracy of 0.09 +- 0.06 mm on lateral translation, 0.42 +- 0.32 mm on longitudinal translation, and 0.80 +- 0.39 deg for rotations around the vertical axis. Furthermore, to showcase the relevance of the proposed framework, we evaluate the system's performance in the context of surgical procedures. This use case was designed to replicate the scenarios of k-wire insertions in orthopedic procedures. For evaluation, two surgeons and one biomedical researcher were provided with visual navigation, each performing 21 injections. Results from this use case provide comparable accuracy to those reported in the literature for AR-based navigation procedures.

preprint2022arXiv

Towards Autonomous Atlas-based Ultrasound Acquisitions in Presence of Articulated Motion

Robotic ultrasound (US) imaging aims at overcoming some of the limitations of free-hand US examinations, e.g. difficulty in guaranteeing intra- and inter-operator repeatability. However, due to anatomical and physiological variations between patients and relative movement of anatomical substructures, it is challenging to robustly generate optimal trajectories to examine the anatomies of interest, in particular, when they comprise articulated joints. To address this challenge, this paper proposes a vision-based approach allowing autonomous robotic US limb scanning. To this end, an atlas MRI template of a human arm with annotated vascular structures is used to generate trajectories and register and project them onto patients' skin surfaces for robotic US acquisition. To effectively segment and accurately reconstruct the targeted 3D vessel, we make use of spatial continuity in consecutive US frames by incorporating channel attention modules into a U-Net-type neural network. The automatic trajectory generation method is evaluated on six volunteers with various articulated joint angles. In all cases, the system can successfully acquire the planned vascular structure on volunteers' limbs. For one volunteer the MRI scan was also available, which allows the evaluation of the average radius of the scanned artery from US images, resulting in a radius estimation ($1.2\pm0.05~mm$) comparable to the MRI ground truth ($1.2\pm0.04~mm$).

preprint2022arXiv

Tracking accuracy evaluation of electromagnetic sensor-based colonoscope tracking method

This paper reports a detailed evaluation results of a colonoscope tracking method. A colonoscope tracking method utilizing electromagnetic sensors and a CT volume has been proposed. Tracking accuracy of this method was evaluated by using a colon phantom. In the previously proposed paper, tracking errors were measured only at six points on the colon phantom for the accuracy evaluation. The point number is not enough to evaluate relationships between the tracking errors and positions in the colon. In this paper, we evaluated the colonoscope tracking method based on more detailed measurement results of the tracking errors. We measured tracking errors at 52 points on the colon phantom and visualized magnitudes of the tracking errors. From our experiments, tracking errors in the ascending and descending colons were enough small to perform colonoscope navigations. However, tracking errors in the transverse and descending colons were large due to colon deformations.

preprint2022arXiv

Transformers in Action: Weakly Supervised Action Segmentation

The video action segmentation task is regularly explored under weaker forms of supervision, such as transcript supervision, where a list of actions is easier to obtain than dense frame-wise labels. In this formulation, the task presents various challenges for sequence modeling approaches due to the emphasis on action transition points, long sequence lengths, and frame contextualization, making the task well-posed for transformers. Given developments enabling transformers to scale linearly, we demonstrate through our architecture how they can be applied to improve action alignment accuracy over the equivalent RNN-based models with the attention mechanism focusing around salient action transition regions. Additionally, given the recent focus on inference-time transcript selection, we propose a supplemental transcript embedding approach to select transcripts more quickly at inference-time. Furthermore, we subsequently demonstrate how this approach can also improve the overall segmentation performance. Finally, we evaluate our proposed methods across the benchmark datasets to better understand the applicability of transformers and the importance of transcript selection on this video-driven weakly-supervised task.

preprint2022arXiv

U-PET: MRI-based Dementia Detection with Joint Generation of Synthetic FDG-PET Images

Alzheimer's disease (AD) is the most common cause of dementia. An early detection is crucial for slowing down the disease and mitigating risks related to the progression. While the combination of MRI and FDG-PET is the best image-based tool for diagnosis, FDG-PET is not always available. The reliable detection of Alzheimer's disease with only MRI could be beneficial, especially in regions where FDG-PET might not be affordable for all patients. To this end, we propose a multi-task method based on U-Net that takes T1-weighted MR images as an input to generate synthetic FDG-PET images and classifies the dementia progression of the patient into cognitive normal (CN), cognitive impairment (MCI), and AD. The attention gates used in both task heads can visualize the most relevant parts of the brain, guiding the examiner and adding interpretability. Results show the successful generation of synthetic FDG-PET images and a performance increase in disease classification over the naive single-task baseline.

preprint2022arXiv

Unsupervised Cross-Domain Feature Extraction for Single Blood Cell Image Classification

Diagnosing hematological malignancies requires identification and classification of white blood cells in peripheral blood smears. Domain shifts caused by different lab procedures, staining, illumination, and microscope settings hamper the re-usability of recently developed machine learning methods on data collected from different sites. Here, we propose a cross-domain adapted autoencoder to extract features in an unsupervised manner on three different datasets of single white blood cells scanned from peripheral blood smears. The autoencoder is based on an R-CNN architecture allowing it to focus on the relevant white blood cell and eliminate artifacts in the image. To evaluate the quality of the extracted features we use a simple random forest to classify single cells. We show that thanks to the rich features extracted by the autoencoder trained on only one of the datasets, the random forest classifier performs satisfactorily on the unseen datasets, and outperforms published oracle networks in the cross-domain task. Our results suggest the possibility of employing this unsupervised approach in more complicated diagnosis and prognosis tasks without the need to add expensive expert labels to unseen data.

preprint2022arXiv

Unsupervised Pre-Training on Patient Population Graphs for Patient-Level Predictions

Pre-training has shown success in different areas of machine learning, such as Computer Vision (CV), Natural Language Processing (NLP) and medical imaging. However, it has not been fully explored for clinical data analysis. Even though an immense amount of Electronic Health Record (EHR) data is recorded, data and labels can be scarce if the data is collected in small hospitals or deals with rare diseases. In such scenarios, pre-training on a larger set of EHR data could improve the model performance. In this paper, we apply unsupervised pre-training to heterogeneous, multi-modal EHR data for patient outcome prediction. To model this data, we leverage graph deep learning over population graphs. We first design a network architecture based on graph transformer designed to handle various input feature types occurring in EHR data, like continuous, discrete, and time-series features, allowing better multi-modal data fusion. Further, we design pre-training methods based on masked imputation to pre-train our network before fine-tuning on different end tasks. Pre-training is done in a fully unsupervised fashion, which lays the groundwork for pre-training on large public datasets with different tasks and similar modalities in the future. We test our method on two medical datasets of patient records, TADPOLE and MIMIC-III, including imaging and non-imaging features and different prediction tasks. We find that our proposed graph based pre-training method helps in modeling the data at a population level and further improves performance on the fine tuning tasks in terms of AUC on average by 4.15% for MIMIC and 7.64% for TADPOLE.

preprint2022arXiv

VesNet-RL: Simulation-based Reinforcement Learning for Real-World US Probe Navigation

Ultrasound (US) is one of the most common medical imaging modalities since it is radiation-free, low-cost, and real-time. In freehand US examinations, sonographers often navigate a US probe to visualize standard examination planes with rich diagnostic information. However, reproducibility and stability of the resulting images often suffer from intra- and inter-operator variation. Reinforcement learning (RL), as an interaction-based learning method, has demonstrated its effectiveness in visual navigating tasks; however, RL is limited in terms of generalization. To address this challenge, we propose a simulation-based RL framework for real-world navigation of US probes towards the standard longitudinal views of vessels. A UNet is used to provide binary masks from US images; thereby, the RL agent trained on simulated binary vessel images can be applied in real scenarios without further training. To accurately characterize actual states, a multi-modality state representation structure is introduced to facilitate the understanding of environments. Moreover, considering the characteristics of vessels, a novel standard view recognition approach based on the minimum bounding rectangle is proposed to terminate the searching process. To evaluate the effectiveness of the proposed method, the trained policy is validated virtually on 3D volumes of a volunteer's in-vivo carotid artery, and physically on custom-designed gel phantoms using robotic US. The results demonstrate that proposed approach can effectively and accurately navigate the probe towards the longitudinal view of vessels.

preprint2022arXiv

Virtual embeddings and self-consistency for self-supervised learning

Self-supervised Learning (SSL) has recently gained much attention due to the high cost and data limitation in the training of supervised learning models. The current paradigm in the SSL is to utilize data augmentation at the input space to create different views of the same images and train a model to maximize the representations between similar images and minimize them for different ones. While this approach achieves state-of-the-art (SOTA) results in various downstream tasks, it still lakes the opportunity to investigate the latent space augmentation. This paper proposes TriMix, a novel concept for SSL that generates virtual embeddings through linear interpolation of the data, thus providing the model with novel representations. Our strategy focuses on training the model to extract the original embeddings from virtual ones, hence, better representation learning. Additionally, we propose a self-consistency term that improves the consistency between the virtual and actual embeddings. We validate TriMix on eight benchmark datasets consisting of natural and medical images with an improvement of 2.71% and 0.41% better than the second-best models for both data types. Further, our approach outperformed the current methods in semi-supervised learning, particularly in low data regimes. Besides, our pre-trained models showed better transfer to other datasets.

preprint2022arXiv

Weakly-supervised Biomechanically-constrained CT/MRI Registration of the Spine

CT and MRI are two of the most informative modalities in spinal diagnostics and treatment planning. CT is useful when analysing bony structures, while MRI gives information about the soft tissue. Thus, fusing the information of both modalities can be very beneficial. Registration is the first step for this fusion. While the soft tissues around the vertebra are deformable, each vertebral body is constrained to move rigidly. We propose a weakly-supervised deep learning framework that preserves the rigidity and the volume of each vertebra while maximizing the accuracy of the registration. To achieve this goal, we introduce anatomy-aware losses for training the network. We specifically design these losses to depend only on the CT label maps since automatic vertebra segmentation in CT gives more accurate results contrary to MRI. We evaluate our method on an in-house dataset of 167 patients. Our results show that adding the anatomy-aware losses increases the plausibility of the inferred transformation while keeping the accuracy untouched.

preprint2022arXiv

Wild ToFu: Improving Range and Quality of Indirect Time-of-Flight Depth with RGB Fusion in Challenging Environments

Indirect Time-of-Flight (I-ToF) imaging is a widespread way of depth estimation for mobile devices due to its small size and affordable price. Previous works have mainly focused on quality improvement for I-ToF imaging especially curing the effect of Multi Path Interference (MPI). These investigations are typically done in specifically constrained scenarios at close distance, indoors and under little ambient light. Surprisingly little work has investigated I-ToF quality improvement in real-life scenarios where strong ambient light and far distances pose difficulties due to an extreme amount of induced shot noise and signal sparsity, caused by the attenuation with limited sensor power and light scattering. In this work, we propose a new learning based end-to-end depth prediction network which takes noisy raw I-ToF signals as well as an RGB image and fuses their latent representation based on a multi step approach involving both implicit and explicit alignment to predict a high quality long range depth map aligned to the RGB viewpoint. We test our approach on challenging real-world scenes and show more than 40% RMSE improvement on the final depth map compared to the baseline approach.

preprint2022arXiv

Y-Net: A Spatiospectral Dual-Encoder Networkfor Medical Image Segmentation

Automated segmentation of retinal optical coherence tomography (OCT) images has become an important recent direction in machine learning for medical applications. We hypothesize that the anatomic structure of layers and their high-frequency variation in OCT images make retinal OCT a fitting choice for extracting spectral-domain features and combining them with spatial domain features. In this work, we present $Υ$-Net, an architecture that combines the frequency domain features with the image domain to improve the segmentation performance of OCT images. The results of this work demonstrate that the introduction of two branches, one for spectral and one for spatial domain features, brings a very significant improvement in fluid segmentation performance and allows outperformance as compared to the well-known U-Net model. Our improvement was 13% on the fluid segmentation dice score and 1.9% on the average dice score. Finally, removing selected frequency ranges in the spectral domain demonstrates the impact of these features on the fluid segmentation outperformance.

preprint2022arXiv

ZebraPose: Coarse to Fine Surface Encoding for 6DoF Object Pose Estimation

Establishing correspondences from image to 3D has been a key task of 6DoF object pose estimation for a long time. To predict pose more accurately, deeply learned dense maps replaced sparse templates. Dense methods also improved pose estimation in the presence of occlusion. More recently researchers have shown improvements by learning object fragments as segmentation. In this work, we present a discrete descriptor, which can represent the object surface densely. By incorporating a hierarchical binary grouping, we can encode the object surface very efficiently. Moreover, we propose a coarse to fine training strategy, which enables fine-grained correspondence prediction. Finally, by matching predicted codes with object surface and using a PnP solver, we estimate the 6DoF pose. Results on the public LM-O and YCB-V datasets show major improvement over the state of the art w.r.t. ADD(-S) metric, even surpassing RGB-D based methods in some cases.

preprint2021arXiv

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.

preprint2020arXiv

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 $\href{https://multimodal3dvision.github.io}{multimodal3dvision.github.io}$.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

Animals in Virtual Environments

The core idea in an XR (VR/MR/AR) application is to digitally stimulate one or more sensory systems (e.g. visual, auditory, olfactory) of the human user in an interactive way to achieve an immersive experience. Since the early 2000s biologists have been using Virtual Environments (VE) to investigate the mechanisms of behavior in non-human animals including insect, fish, and mammals. VEs have become reliable tools for studying vision, cognition, and sensory-motor control in animals. In turn, the knowledge gained from studying such behaviors can be harnessed by researchers designing biologically inspired robots, smart sensors, and multi-agent artificial intelligence. VE for animals is becoming a widely used application of XR technology but such applications have not previously been reported in the technical literature related to XR. Biologists and computer scientists can benefit greatly from deepening interdisciplinary research in this emerging field and together we can develop new methods for conducting fundamental research in behavioral sciences and engineering. To support our argument we present this review which provides an overview of animal behavior experiments conducted in virtual environments.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

Force-Ultrasound Fusion: Bringing Spine Robotic-US to the Next "Level"

Spine injections are commonly performed in several clinical procedures. The localization of the target vertebral level (i.e. the position of a vertebra in a spine) is typically done by back palpation or under X-ray guidance, yielding either higher chances of procedure failure or exposure to ionizing radiation. Preliminary studies have been conducted in the literature, suggesting that ultrasound imaging may be a precise and safe alternative to X-ray for spine level detection. However, ultrasound data are noisy and complicated to interpret. In this study, a robotic-ultrasound approach for automatic vertebral level detection is introduced. The method relies on the fusion of ultrasound and force data, thus providing both "tactile" and visual feedback during the procedure, which results in higher performances in presence of data corruption. A robotic arm automatically scans the volunteer's back along the spine by using force-ultrasound data to locate vertebral levels. The occurrences of vertebral levels are visible on the force trace as peaks, which are enhanced by properly controlling the force applied by the robot on the patient back. Ultrasound data are processed with a Deep Learning method to extract a 1D signal modelling the probabilities of having a vertebra at each location along the spine. Processed force and ultrasound data are fused using a 1D Convolutional Network to compute the location of the vertebral levels. The method is compared to pure image and pure force-based methods for vertebral level counting, showing improved performance. In particular, the fusion method is able to correctly classify 100% of the vertebral levels in the test set, while pure image and pure force-based method could only classify 80% and 90% vertebrae, respectively. The potential of the proposed method is evaluated in an exemplary simulated clinical application.

preprint2020arXiv

From Perspective X-ray Imaging to Parallax-Robust Orthographic Stitching

Stitching images acquired under perspective projective geometry is a relevant topic in computer vision with multiple applications ranging from smartphone panoramas to the construction of digital maps. Image stitching is an equally prominent challenge in medical imaging, where the limited field-of-view captured by single images prohibits holistic analysis of patient anatomy. The barrier that prevents straight-forward mosaicing of 2D images is depth mismatch due to parallax. In this work, we leverage the Fourier slice theorem to aggregate information from multiple transmission images in parallax-free domains using fundamental principles of X-ray image formation. The semantics of the stitched image are restored using a novel deep learning strategy that exploits similarity measures designed around frequency, as well as dense and sparse spatial image content. Our pipeline, not only stitches images, but also provides orthographic reconstruction that enables metric measurements of clinically relevant quantities directly on the 2D image plane.

preprint2020arXiv

Improving Feature Attribution through Input-specific Network Pruning

Attributing the output of a neural network to the contribution of given input elements is a way of shedding light on the black-box nature of neural networks. Due to the complexity of current network architectures, current gradient-based attribution methods provide very noisy or coarse results. We propose to prune a neural network for a given single input to keep only neurons that highly contribute to the prediction. We show that by input-specific pruning, network gradients change from reflecting local (noisy) importance information to global importance. Our proposed method is efficient and generates fine-grained attribution maps. We further provide a theoretical justification of the pruning approach relating it to perturbations and validate it through a novel experimental setup. Our method is evaluated by multiple benchmarks: sanity checks, pixel perturbation, and Remove-and-Retrain (ROAR). These benchmarks evaluate the method from different perspectives and our method performs better than other methods across all evaluations.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

On the Effectiveness of Virtual Reality-based Training for Robotic Setup

Virtual Reality (VR) is rapidly increasing in popularity as a teaching tool. It allows for the creation of a highly immersive, three-dimensional virtual environment intended to simulate real-life environments. With more robots saturating the industry - from manufacturing to healthcare, there is a need to train end-users on how to set up, operate, tear down, and troubleshoot the robot. Even though VR has become widely used in training surgeons on the psychomotor skills associated with operating the robot, little research has been done to see how the benefits of VR could translate to teaching the bedside staff, tasked with supporting the robot during the full end-to-end surgical procedure. We trained 30 participants on how to set up a robotic arm in an environment mimicking clinical setup. We divided these participants equally into 3 groups with one group trained with paper-based instructions, one with video-based instructions and one with VR-based instructions. We then compared and contrasted these three different training methods. VR and paper-based were highly favored training mediums over video-based. VR-trained participants achieved slightly higher fidelity of individual robotic joint angles, suggesting better comprehension of the spatial awareness skills necessary to achieve desired arm positioning. In addition, VR resulted in higher reproducibility of setup fidelity and more consistency in user confidence levels as compared to paper and video-based training.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

Reflective-AR Display: An Interaction Methodology for Virtual-Real Alignment in Medical Robotics

Robot-assisted minimally invasive surgery has shown to improve patient outcomes, as well as reduce complications and recovery time for several clinical applications. While increasingly configurable robotic arms can maximize reach and avoid collisions in cluttered environments, positioning them appropriately during surgery is complicated because safety regulations prevent automatic driving. We propose a head-mounted display (HMD) based augmented reality (AR) system designed to guide optimal surgical arm set up. The staff equipped with HMD aligns the robot with its planned virtual counterpart. In this user-centric setting, the main challenge is the perspective ambiguities hindering such collaborative robotic solution. To overcome this challenge, we introduce a novel registration concept for intuitive alignment of AR content to its physical counterpart by providing a multi-view AR experience via reflective-AR displays that simultaneously show the augmentations from multiple viewpoints. Using this system, users can visualize different perspectives while actively adjusting the pose to determine the registration transformation that most closely superimposes the virtual onto the real. The experimental results demonstrate improvement in the interactive alignment of a virtual and real robot when using a reflective-AR display. We also present measurements from configuring a robotic manipulator in a simulated trocar placement surgery using the AR guidance methodology.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

Spatiotemporal-Aware Augmented Reality: Redefining HCI in Image-Guided Therapy

Suboptimal interaction with patient data and challenges in mastering 3D anatomy based on ill-posed 2D interventional images are essential concerns in image-guided therapies. Augmented reality (AR) has been introduced in the operating rooms in the last decade; however, in image-guided interventions, it has often only been considered as a visualization device improving traditional workflows. As a consequence, the technology is gaining minimum maturity that it requires to redefine new procedures, user interfaces, and interactions. The main contribution of this paper is to reveal how exemplary workflows are redefined by taking full advantage of head-mounted displays when entirely co-registered with the imaging system at all times. The proposed AR landscape is enabled by co-localizing the users and the imaging devices via the operating room environment and exploiting all involved frustums to move spatial information between different bodies. The awareness of the system from the geometric and physical characteristics of X-ray imaging allows the redefinition of different human-machine interfaces. We demonstrate that this AR paradigm is generic, and can benefit a wide variety of procedures. Our system achieved an error of $4.76\pm2.91$ mm for placing K-wire in a fracture management procedure, and yielded errors of $1.57\pm1.16^\circ$ and $1.46\pm1.00^\circ$ in the abduction and anteversion angles, respectively, for total hip arthroplasty. We hope that our holistic approach towards improving the interface of surgery not only augments the surgeon's capabilities but also augments the surgical team's experience in carrying out an effective intervention with reduced complications and provide novel approaches of documenting procedures for training purposes.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2020arXiv

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.

preprint2019arXiv

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.

preprint2019arXiv

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.

preprint2019arXiv

Image to Images Translation for Multi-Task Organ Segmentation and Bone Suppression in Chest X-Ray Radiography

Chest X-ray radiography is one of the earliest medical imaging technologies and remains one of the most widely-used for diagnosis, screening, and treatment follow up of diseases related to lungs and heart. The literature in this field of research reports many interesting studies dealing with the challenging tasks of bone suppression and organ segmentation but performed separately, limiting any learning that comes with the consolidation of parameters that could optimize both processes. This study, and for the first time, introduces a multitask deep learning model that generates simultaneously the bone-suppressed image and the organ-segmented image, enhancing the accuracy of tasks, minimizing the number of parameters needed by the model and optimizing the processing time, all by exploiting the interplay between the network parameters to benefit the performance of both tasks. The architectural design of this model, which relies on a conditional generative adversarial network, reveals the process on how the well-established pix2pix network (image-to-image network) is modified to fit the need for multitasking and extending it to the new image-to-images architecture. The developed source code of this multitask model is shared publicly on Github as the first attempt for providing the two-task pix2pix extension, a supervised/paired/aligned/registered image-to-images translation which would be useful in many multitask applications. Dilated convolutions are also used to improve the results through a more effective receptive field assessment. The comparison with state-of-the-art algorithms along with ablation study and a demonstration video are provided to evaluate efficacy and gauge the merits of the proposed approach.

preprint2018arXiv

Adversarial Semantic Scene Completion from a Single Depth Image

We propose a method to reconstruct, complete and semantically label a 3D scene from a single input depth image. We improve the accuracy of the regressed semantic 3D maps by a novel architecture based on adversarial learning. In particular, we suggest using multiple adversarial loss terms that not only enforce realistic outputs with respect to the ground truth, but also an effective embedding of the internal features. This is done by correlating the latent features of the encoder working on partial 2.5D data with the latent features extracted from a variational 3D auto-encoder trained to reconstruct the complete semantic scene. In addition, differently from other approaches that operate entirely through 3D convolutions, at test time we retain the original 2.5D structure of the input during downsampling to improve the effectiveness of the internal representation of our model. We test our approach on the main benchmark datasets for semantic scene completion to qualitatively and quantitatively assess the effectiveness of our proposal.

preprint2016arXiv

A Deep Metric for Multimodal Registration

Multimodal registration is a challenging problem in medical imaging due the high variability of tissue appearance under different imaging modalities. The crucial component here is the choice of the right similarity measure. We make a step towards a general learning-based solution that can be adapted to specific situations and present a metric based on a convolutional neural network. Our network can be trained from scratch even from a few aligned image pairs. The metric is validated on intersubject deformable registration on a dataset different from the one used for training, demonstrating good generalization. In this task, we outperform mutual information by a significant margin.

preprint2016arXiv

An Efficient Training Algorithm for Kernel Survival Support Vector Machines

Survival analysis is a fundamental tool in medical research to identify predictors of adverse events and develop systems for clinical decision support. In order to leverage large amounts of patient data, efficient optimisation routines are paramount. We propose an efficient training algorithm for the kernel survival support vector machine (SSVM). We directly optimise the primal objective function and employ truncated Newton optimisation and order statistic trees to significantly lower computational costs compared to previous training algorithms, which require $O(n^4)$ space and $O(p n^6)$ time for datasets with $n$ samples and $p$ features. Our results demonstrate that our proposed optimisation scheme allows analysing data of a much larger scale with no loss in prediction performance. Experiments on synthetic and 5 real-world datasets show that our technique outperforms existing kernel SSVM formulations if the amount of right censoring is high ($\geq85\%$), and performs comparably otherwise.

preprint2016arXiv

An Octree-Based Approach towards Efficient Variational Range Data Fusion

Volume-based reconstruction is usually expensive both in terms of memory consumption and runtime. Especially for sparse geometric structures, volumetric representations produce a huge computational overhead. We present an efficient way to fuse range data via a variational Octree-based minimization approach by taking the actual range data geometry into account. We transform the data into Octree-based truncated signed distance fields and show how the optimization can be conducted on the newly created structures. The main challenge is to uphold speed and a low memory footprint without sacrificing the solutions' accuracy during optimization. We explain how to dynamically adjust the optimizer's geometric structure via joining/splitting of Octree nodes and how to define the operators. We evaluate on various datasets and outline the suitability in terms of performance and geometric accuracy.

preprint2016arXiv

Cross-Modal Manifold Learning for Cross-modal Retrieval

This paper presents a new scalable algorithm for cross-modal similarity preserving retrieval in a learnt manifold space. Unlike existing approaches that compromise between preserving global and local geometries, the proposed technique respects both simultaneously during manifold alignment. The global topologies are maintained by recovering underlying mapping functions in the joint manifold space by deploying partially corresponding instances. The inter-, and intra-modality affinity matrices are then computed to reinforce original data skeleton using perturbed minimum spanning tree (pMST), and maximizing the affinity among similar cross-modal instances, respectively. The performance of proposed algorithm is evaluated upon two multimodal image datasets (coronary atherosclerosis histology and brain MRI) for two applications: classification, and regression. Our exhaustive validations and results demonstrate the superiority of our technique over comparative methods and its feasibility for improving computer-assisted diagnosis systems, where disease-specific complementary information shall be aggregated and interpreted across modalities to form the final decision.

preprint2016arXiv

Deep Active Contours

We propose a method for interactive boundary extraction which combines a deep, patch-based representation with an active contour framework. We train a class-specific convolutional neural network which predicts a vector pointing from the respective point on the evolving contour towards the closest point on the boundary of the object of interest. These predictions form a vector field which is then used for evolving the contour by the Sobolev active contour framework proposed by Sundaramoorthi et al. The resulting interactive segmentation method is very efficient in terms of required computational resources and can even be trained on comparatively small graphics cards. We evaluate the potential of the proposed method on both medical and non-medical challenge data sets, such as the STACOM data set and the PASCAL VOC 2012 data set.

preprint2016arXiv

Deep Learning of Local RGB-D Patches for 3D Object Detection and 6D Pose Estimation

We present a 3D object detection method that uses regressed descriptors of locally-sampled RGB-D patches for 6D vote casting. For regression, we employ a convolutional auto-encoder that has been trained on a large collection of random local patches. During testing, scene patch descriptors are matched against a database of synthetic model view patches and cast 6D object votes which are subsequently filtered to refined hypotheses. We evaluate on three datasets to show that our method generalizes well to previously unseen input data, delivers robust detection results that compete with and surpass the state-of-the-art while being scalable in the number of objects.

preprint2016arXiv

Deep Residual Hashing

Hashing aims at generating highly compact similarity preserving code words which are well suited for large-scale image retrieval tasks. Most existing hashing methods first encode the images as a vector of hand-crafted features followed by a separate binarization step to generate hash codes. This two-stage process may produce sub-optimal encoding. In this paper, for the first time, we propose a deep architecture for supervised hashing through residual learning, termed Deep Residual Hashing (DRH), for an end-to-end simultaneous representation learning and hash coding. The DRH model constitutes four key elements: (1) a sub-network with multiple stacked residual blocks; (2) hashing layer for binarization; (3) supervised retrieval loss function based on neighbourhood component analysis for similarity preserving embedding; and (4) hashing related losses and regularisation to control the quantization error and improve the quality of hash coding. We present results of extensive experiments on a large public chest x-ray image database with co-morbidities and discuss the outcome showing substantial improvements over the latest state-of-the art methods.

preprint2016arXiv

Deeper Depth Prediction with Fully Convolutional Residual Networks

This paper addresses the problem of estimating the depth map of a scene given a single RGB image. We propose a fully convolutional architecture, encompassing residual learning, to model the ambiguous mapping between monocular images and depth maps. In order to improve the output resolution, we present a novel way to efficiently learn feature map up-sampling within the network. For optimization, we introduce the reverse Huber loss that is particularly suited for the task at hand and driven by the value distributions commonly present in depth maps. Our model is composed of a single architecture that is trained end-to-end and does not rely on post-processing techniques, such as CRFs or other additional refinement steps. As a result, it runs in real-time on images or videos. In the evaluation, we show that the proposed model contains fewer parameters and requires fewer training data than the current state of the art, while outperforming all approaches on depth estimation. Code and models are publicly available.

preprint2016arXiv

Hands-Free Segmentation of Medical Volumes via Binary Inputs

We propose a novel hands-free method to interactively segment 3D medical volumes. In our scenario, a human user progressively segments an organ by answering a series of questions of the form "Is this voxel inside the object to segment?". At each iteration, the chosen question is defined as the one halving a set of candidate segmentations given the answered questions. For a quick and efficient exploration, these segmentations are sampled according to the Metropolis-Hastings algorithm. Our sampling technique relies on a combination of relaxed shape prior, learnt probability map and consistency with previous answers. We demonstrate the potential of our strategy on a prostate segmentation MRI dataset. Through the study of failure cases with synthetic examples, we demonstrate the adaptation potential of our method. We also show that our method outperforms two intuitive baselines: one based on random questions, the other one being the thresholded probability map.

preprint2016arXiv

Hashmod: A Hashing Method for Scalable 3D Object Detection

We present a scalable method for detecting objects and estimating their 3D poses in RGB-D data. To this end, we rely on an efficient representation of object views and employ hashing techniques to match these views against the input frame in a scalable way. While a similar approach already exists for 2D detection, we show how to extend it to estimate the 3D pose of the detected objects. In particular, we explore different hashing strategies and identify the one which is more suitable to our problem. We show empirically that the complexity of our method is sublinear with the number of objects and we enable detection and pose estimation of many 3D objects with high accuracy while outperforming the state-of-the-art in terms of runtime.

preprint2016arXiv

Hough-CNN: Deep Learning for Segmentation of Deep Brain Regions in MRI and Ultrasound

In this work we propose a novel approach to perform segmentation by leveraging the abstraction capabilities of convolutional neural networks (CNNs). Our method is based on Hough voting, a strategy that allows for fully automatic localisation and segmentation of the anatomies of interest. This approach does not only use the CNN classification outcomes, but it also implements voting by exploiting the features produced by the deepest portion of the network. We show that this learning-based segmentation method is robust, multi-region, flexible and can be easily adapted to different modalities. In the attempt to show the capabilities and the behaviour of CNNs when they are applied to medical image analysis, we perform a systematic study of the performances of six different network architectures, conceived according to state-of-the-art criteria, in various situations. We evaluate the impact of both different amount of training data and different data dimensionality (2D, 2.5D and 3D) on the final results. We show results on both MRI and transcranial US volumes depicting respectively 26 regions of the basal ganglia and the midbrain.

preprint2016arXiv

Mitosis Detection in Intestinal Crypt Images with Hough Forest and Conditional Random Fields

Intestinal enteroendocrine cells secrete hormones that are vital for the regulation of glucose metabolism but their differentiation from intestinal stem cells is not fully understood. Asymmetric stem cell divisions have been linked to intestinal stem cell homeostasis and secretory fate commitment. We monitored cell divisions using 4D live cell imaging of cultured intestinal crypts to characterize division modes by means of measurable features such as orientation or shape. A statistical analysis of these measurements requires annotation of mitosis events, which is currently a tedious and time-consuming task that has to be performed manually. To assist data processing, we developed a learning based method to automatically detect mitosis events. The method contains a dual-phase framework for joint detection of dividing cells (mothers) and their progeny (daughters). In the first phase we detect mother and daughters independently using Hough Forest whilst in the second phase we associate mother and daughters by modelling their joint probability as Conditional Random Field (CRF). The method has been evaluated on 32 movies and has achieved an AUC of 72%, which can be used in conjunction with manual correction and dramatically speed up the processing pipeline.

preprint2016arXiv

Towards MRI-Based Autonomous Robotic US Acquisitions: A First Feasibility Study

Robotic ultrasound has the potential to assist and guide physicians during interventions. In this work, we present a set of methods and a workflow to enable autonomous MRI-guided ultrasound acquisitions. Our approach uses a structured-light 3D scanner for patient-to-robot and image-to-patient calibration, which in turn is used to plan 3D ultrasound trajectories. These MRI-based trajectories are followed autonomously by the robot and are further refined online using automatic MRI/US registration. Despite the low spatial resolution of structured light scanners, the initial planned acquisition path can be followed with an accuracy of 2.46 +/- 0.96 mm. This leads to a good initialization of the MRI/US registration: the 3D-scan-based alignment for planning and acquisition shows an accuracy (distance between planned ultrasound and MRI) of 4.47 mm, and 0.97 mm after an online-update of the calibration based on a closed loop registration.

preprint2016arXiv

V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation

Convolutional Neural Networks (CNNs) have been recently employed to solve problems from both the computer vision and medical image analysis fields. Despite their popularity, most approaches are only able to process 2D images while most medical data used in clinical practice consists of 3D volumes. In this work we propose an approach to 3D image segmentation based on a volumetric, fully convolutional, neural network. Our CNN is trained end-to-end on MRI volumes depicting prostate, and learns to predict segmentation for the whole volume at once. We introduce a novel objective function, that we optimise during training, based on Dice coefficient. In this way we can deal with situations where there is a strong imbalance between the number of foreground and background voxels. To cope with the limited number of annotated volumes available for training, we augment the data applying random non-linear transformations and histogram matching. We show in our experimental evaluation that our approach achieves good performances on challenging test data while requiring only a fraction of the processing time needed by other previous methods.

preprint2015arXiv

Robust Optimization for Deep Regression

Convolutional Neural Networks (ConvNets) have successfully contributed to improve the accuracy of regression-based methods for computer vision tasks such as human pose estimation, landmark localization, and object detection. The network optimization has been usually performed with L2 loss and without considering the impact of outliers on the training process, where an outlier in this context is defined by a sample estimation that lies at an abnormal distance from the other training sample estimations in the objective space. In this work, we propose a regression model with ConvNets that achieves robustness to such outliers by minimizing Tukey's biweight function, an M-estimator robust to outliers, as the loss function for the ConvNet. In addition to the robust loss, we introduce a coarse-to-fine model, which processes input images of progressively higher resolutions for improving the accuracy of the regressed values. In our experiments, we demonstrate faster convergence and better generalization of our robust loss function for the tasks of human pose estimation and age estimation from face images. We also show that the combination of the robust loss function with the coarse-to-fine model produces comparable or better results than current state-of-the-art approaches in four publicly available human pose estimation datasets.

preprint2015arXiv

Semi-Automatic Segmentation of Autosomal Dominant Polycystic Kidneys using Random Forests

This paper presents a method for 3D segmentation of kidneys from patients with autosomal dominant polycystic kidney disease (ADPKD) and severe renal insufficiency, using computed tomography (CT) data. ADPKD severely alters the shape of the kidneys due to non-uniform formation of cysts. As a consequence, fully automatic segmentation of such kidneys is very challenging. We present a segmentation method with minimal user interaction based on a random forest classifier. One of the major novelties of the proposed approach is the usage of geodesic distance volumes as additional source of information. These volumes contain the intensity weighted distance to a manual outline of the respective kidney in only one slice (for each kidney) of the CT volume. We evaluate our method qualitatively and quantitatively on 55 CT acquisitions using ground truth annotations from clinical experts.

Nassir Navab

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111 published item(s)

COMPOSE: Hypergraph Cover Optimization for Multi-view 3D Human Pose Estimation

Non-intrusive Body Composition Assessment from Full-body mmWave Scans

OpenGaFF: Open-Vocabulary Gaussian Feature Field with Codebook Attention

SurgGoal: Rethinking Surgical Planning Evaluation via Goal-Satisfiability

Machine Learning in Robotic Ultrasound Imaging: Challenges and Perspectives

On Discprecncies between Perturbation Evaluations of Graph Neural Network Attributions

CommonScenes: Generating Commonsense 3D Indoor Scenes with Scene Graph Diffusion

Adaptive Personlization in Federated Learning for Highly Non-i.i.d. Data

Affective Medical Estimation and Decision Making via Visualized Learning and Deep Learning

Analyzing the Effects of Handling Data Imbalance on Learned Features from Medical Images by Looking Into the Models

Bending Graphs: Hierarchical Shape Matching using Gated Optimal Transport

BFS-Net: Weakly Supervised Cell Instance Segmentation from Bright-Field Microscopy Z-Stacks

Bioelectric Registration of Electromagnetic Tracking and Preoperative Volume Data

CACTUSS: Common Anatomical CT-US Space for US examinations

CheXplaining in Style: Counterfactual Explanations for Chest X-rays using StyleGAN

CloudAttention: Efficient Multi-Scale Attention Scheme For 3D Point Cloud Learning

DA$^2$ Dataset: Toward Dexterity-Aware Dual-Arm Grasping

DeStripe: A Self2Self Spatio-Spectral Graph Neural Network with Unfolded Hessian for Stripe Artifact Removal in Light-sheet Microscopy

Differentiable Graph Module (DGM) for Graph Convolutional Networks

Do Explanations Explain? Model Knows Best

Exploiting Diversity of Unlabeled Data for Label-Efficient Semi-Supervised Active Learning

From 2D to 3D: Re-thinking Benchmarking of Monocular Depth Prediction

GPV-Pose: Category-level Object Pose Estimation via Geometry-guided Point-wise Voting

Graph-in-Graph (GiG): Learning interpretable latent graphs in non-Euclidean domain for biological and healthcare applications

Intelligent Masking: Deep Q-Learning for Context Encoding in Medical Image Analysis

Interpretable Vertebral Fracture Diagnosis

Latent-Graph Learning for Disease Prediction

Learning Local Displacements for Point Cloud Completion

Longitudinal Self-Supervision for COVID-19 Pathology Quantification

Object-aware Monocular Depth Prediction with Instance Convolutions

PhoCaL: A Multi-Modal Dataset for Category-Level Object Pose Estimation with Photometrically Challenging Objects

Semi-Supervised Federated Peer Learning for Skin Lesion Classification

Shape-Aware Masking for Inpainting in Medical Imaging

SoftPool++: An Encoder-Decoder Network for Point Cloud Completion

Sonification as a Reliable Alternative to Conventional Visual Surgical Navigation

Speckle2Speckle: Unsupervised Learning of Ultrasound Speckle Filtering Without Clean Data

Spotlight on nerves: Portable multispectral optoacoustic imaging of peripheral nerve vascularization and morphology

STTAR: Surgical Tool Tracking using off-the-shelf Augmented Reality Head-Mounted Displays

Towards Autonomous Atlas-based Ultrasound Acquisitions in Presence of Articulated Motion

Tracking accuracy evaluation of electromagnetic sensor-based colonoscope tracking method

Transformers in Action: Weakly Supervised Action Segmentation

U-PET: MRI-based Dementia Detection with Joint Generation of Synthetic FDG-PET Images

Unsupervised Cross-Domain Feature Extraction for Single Blood Cell Image Classification

Unsupervised Pre-Training on Patient Population Graphs for Patient-Level Predictions

VesNet-RL: Simulation-based Reinforcement Learning for Real-World US Probe Navigation

Virtual embeddings and self-consistency for self-supervised learning

Weakly-supervised Biomechanically-constrained CT/MRI Registration of the Spine

Wild ToFu: Improving Range and Quality of Indirect Time-of-Flight Depth with RGB Fusion in Challenging Environments

Y-Net: A Spatiospectral Dual-Encoder Networkfor Medical Image Segmentation

ZebraPose: Coarse to Fine Surface Encoding for 6DoF Object Pose Estimation

Semi-Supervised Few-Shot Learning with Prototypical Random Walks

6D Camera Relocalization in Ambiguous Scenes via Continuous Multimodal Inference

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

Adversarial Signal Denoising with Encoder-Decoder Networks

Animals in Virtual Environments

Attention based Multiple Instance Learning for Classification of Blood Cell Disorders

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

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

Colon Shape Estimation Method for Colonoscope Tracking using Recurrent Neural Networks

Colonoscope tracking method based on shape estimation network

Confident Coreset for Active Learning in Medical Image Analysis

Continual Class Incremental Learning for CT Thoracic Segmentation

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

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

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

Explicit Domain Adaptation with Loosely Coupled Samples

Fairness by Learning Orthogonal Disentangled Representations

Force-Ultrasound Fusion: Bringing Spine Robotic-US to the Next "Level"

From Perspective X-ray Imaging to Parallax-Robust Orthographic Stitching

Improving Feature Attribution through Input-specific Network Pruning

Inverse Distance Aggregation for Federated Learning with Non-IID Data

Learning 3D Semantic Scene Graphs from 3D Indoor Reconstructions

Medical-based Deep Curriculum Learning for Improved Fracture Classification

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