12 research outputs found
3D Human Pose Estimation: Using a Top-View Depth Camera
No full textThe onset of delirium, a disturbance in the mental activities of a patient, can be potentially detected by understanding activities within an Intensive Care Unit (ICU) room. Such activities can be extracted by estimating human pose via a visual capture of the scene. This work uses a top-view depth camera in an ICU room to estimate pose of the non-patient stakeholders. The top-view leads to self-occlusions of body joints and thus poses a challenge for estimation of complete human pose. In addition, the presence of multiple persons in the room poses a secondary challenge, as detected body-joints need to be parsed into individual poses. To address these challenges, a 3D point cloud is extracted from the top-view depth image and passed through a 3D Convolutional Neural Network (CNN). This baseline method is capable of estimating both body-joints and body-parts to eventually output human pose for multiple persons. To improve the quality of output poses, the baseline method can benefit from additional spatial context since the problem of human pose estimation has a highly structured output. The proposed techniques either increase the receptive field, perform feature extraction at multiple scales or change the order of data processing. An increase in F1-score for the proposed methods highlights the importance of additional spatial context as a crucial tool to improve the performance of pose estimation models.Computer Scienc
Improving Error Detection in Deep Learning Based Radiotherapy Autocontouring Using Bayesian Uncertainty
No full textBayesian Neural Nets (BNN) are increasingly used for robust organ auto-contouring. Uncertainty heatmaps extracted from BNNs have been shown to correspond to inaccurate regions. To help speed up the mandatory quality assessment (QA) of contours in radiotherapy, these heatmaps could be used as stimuli to direct visual attention of clinicians to potential inaccuracies. In practice, this is non-trivial to achieve since many accurate regions also exhibit uncertainty. To influence the output uncertainty of a BNN, we propose a modified accuracy-versus-uncertainty (AvU) metric as an additional objective during model training that penalizes both accurate regions exhibiting uncertainty as well as inaccurate regions exhibiting certainty. For evaluation, we use an uncertainty-ROC curve that can help differentiate between Bayesian models by comparing the probability of uncertainty in inaccurate versus accurate regions. We train and evaluate a FlipOut BNN model on the MICCAI2015 Head and Neck Segmentation challenge dataset and on the DeepMind-TCIA dataset, and observed an increase in the AUC of uncertainty-ROC curves by 5.6% and 5.9%, respectively, when using the AvU objective. The AvU objective primarily reduced false positives regions (uncertain and accurate), drawing less visual attention to these regions, thereby potentially improving the speed of error detection.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Computer Graphics and VisualisationPattern Recognition and Bioinformatic
Improving Uncertainty-Error Correspondence in Deep Bayesian Medical Image Segmentation
No full textIncreased usage of automated tools like deep learning in medical image segmentation has alleviated the bottleneck of manual contouring. This has shifted manual labour to quality assessment (QA) of automated contours which involves detecting errors and correcting them. A potential solution to semi-automated QA is to use deep Bayesian uncertainty to recommend potentially erroneous regions, thus reducing time spent on error detection. Previous work has investigated the correspondence between uncertainty and error, however, no work has been done on improving the “utility” of Bayesian uncertainty maps such that it is only present in inaccurate regions and not in the accurate ones. Our work trains the FlipOut model with the Accuracy-vsUncertainty (AvU) loss which promotes uncertainty to be present only in inaccurate regions. We apply this method on datasets of two radiotherapy body sites, namely CT scans of head and neck and prostate MRs. Uncertainty heatmaps (i.e. predictive entropy) are evaluated using ROC and Precision-Recall curves. Numerical results show that when compared to the Bayesian baseline the proposed method successfully suppresses uncertainty for accurate voxels, with similar presence of uncertainty for inaccurate voxels.
Code to reproduce experiments is available on https://github.com/prerakmody/ bayesuncertainty-error-correspondence. </p
Analyzing Components of a Transformer under Different Data Scales in 3D Prostate CT Segmentation
No full textLiterature on medical imaging segmentation claims that self-attention-based Transformer blocks perform better than convolution in UNet-based architectures. This recently touted success of Transformers warrants an investigation into which of its components contribute to its performance. Moreover, previous work has a limitation of analysis only at fixed data scales as well as unfair comparisons with others models where parameter counts are not equivalent. This work investigates the performance of the window-Based Transformer for prostate CT Organ-at-Risk (OAR) segmentation at different data scales in context of replacing its various components. To compare with previous literature, the first experiment replaces the window-based Transformer block with convolution. Results show that the convolution prevails as the data scale increases. In the second experiment, to reduce complexity, the self-attention mechanism is replaced with an equivalent albeit simpler spatial mixing operation i.e. max-pooling. We observe improved performance for max-pooling in smaller data scales, indicating that the window-based Transformer may not be the best choice in both small and larger data scales. Finally, since convolution has an inherent local inductive bias of positional information, we conduct a third experiment to imbibe such a property to the Transformer by exploring two kinds of positional encodings. The results show that there are insignificant improvements after adding positional encoding, indicating the Transformers deficiency in capturing positional information given our data scales. We hope that our approach can serve as a framework for others evaluating the utility of Transformers for their tasks.Computer Scienc
Comparing Bayesian models for organ contouring in head and neck radiotherapy
No full textDeep learning models for organ contouring in radiotherapy are poised for clinical usage, but currently, there exist few tools for automated quality assessment (QA) of the predicted contours. Bayesian models and their associated uncertainty, can potentially automate the process of detecting inaccurate predictions. We investigate two Bayesian models for auto-contouring, DropOut and FlipOut, using a quantitative measure – expected calibration error (ECE) and a qualitative measure – region-based accuracy-vs-uncertainty (R-AvU) graphs. It is well understood that a model should have low ECE to be considered trustworthy. However, in a QA context, a model should also have high uncertainty in inaccurate regions and low uncertainty in accurate regions. Such behaviour could direct visual attention of expert users to potentially inaccurate regions, leading to a speed-up in the QA process. Using R-AvU graphs, we qualitatively compare the behaviour of different models in accurate and inaccurate regions. Experiments are conducted on the MICCAI2015 Head and Neck Segmentation Challenge and on the DeepMindTCIA CT dataset using three models: DropOut-DICE, Dropout-CE (Cross Entropy) and FlipOut-CE. Quantitative results show that DropOut-DICE has the highest ECE, while Dropout-CE and FlipOut-CE have the lowest ECE. To better understand the difference between DropOut-CE and FlipOut-CE, we use the R-AvU graph which shows that FlipOut-CE has better uncertainty coverage in inaccurate regions than DropOut-CE. Such a combination of quantitative and qualitative metrics explores a new approach that helps to select which model can be deployed as a QA tool in clinical settings.<br/
Deep Learning for Size-Agnostic Inverse Design of Random-Network 3D Printed Mechanical Metamaterials
No full textPractical applications of mechanical metamaterials often involve solving inverse problems aimed at finding microarchitectures that give rise to certain properties. The limited resolution of additive manufacturing techniques often requires solving such inverse problems for specific specimen sizes. Moreover, the candidate microarchitectures should be resistant to fatigue and fracture. Such a multi-objective inverse design problem is formidably difficult to solve but its solution is the key to real-world applications of mechanical metamaterials. Here, a modular approach titled “Deep-DRAM” that combines four decoupled models is proposed, including two deep learning (DL) models, a deep generative model based on conditional variational autoencoders, and direct finite element (FE) simulations. Deep-DRAM integrates these models into a framework capable of finding many solutions to the posed multi-objective inverse design problem based on random-network unit cells. Using an extensive set of simulations as well as experiments performed on 3D printed specimens, it is demonstrate that: 1) the predictions of the DL models are in agreement with FE simulations and experimental observations, 2) an enlarged envelope of achievable elastic properties (e.g., rare combinations of double auxeticity and high stiffness) is realized using the proposed approach, and 3) Deep-DRAM can provide many solutions to the considered multi-objective inverse design problem.Biomaterials & Tissue Biomechanic
Improving Uncertainty-Error Correspondence in Deep Bayesian Medical Image Segmentation
Get PDFIncreased usage of automated tools like deep learning in medical image segmentation has alleviated the bottleneck of manual contouring. This has shifted manual labour to quality assessment (QA) of automated contours which involves detecting errors and correcting them. A potential solution to semi-automated QA is to use deep Bayesian uncertainty to recommend potentially erroneous regions, thus reducing time spent on error detection. Previous work has investigated the correspondence between uncertainty and error, however, no work has been done on improving the “utility” of Bayesian uncertainty maps such that it is only present in inaccurate regions and not in the accurate ones. Our work trains the FlipOut model with the Accuracy-vs-Uncertainty (AvU) loss which promotes uncertainty to be present only in inaccurate regions. We apply this method on datasets of two radiotherapy body sites, c.f. head-and-neck CT and prostate MR scans. Uncertainty heatmaps (i.e. predictive entropy) are evaluated against voxel inaccuracies using Receiver Operating Characteristic (ROC) and Precision-Recall (PR) curves. Numerical results show that when compared to the Bayesian baseline the proposed method successfully suppresses uncertainty for accurate voxels, with similar presence of uncertainty for inaccurate voxels. Code to reproduce experiments is available at https://github.com/prerakmody/bayesuncertainty-error-correspondenc
Depth for Multi-Modal Contour Ensembles
No full textThe contour depth methodology enables non-parametric summarization of contour ensembles by extracting their representatives, confidence bands, and outliers for visualization (via contour boxplots) and robust downstream procedures. We address two shortcomings of these methods. Firstly, we significantly expedite the computation and recomputation of Inclusion Depth (ID), introducing a linear-time algorithm for epsilon ID, a variant used for handling ensembles with contours with multiple intersections. We also present the inclusion matrix, which contains the pairwise inclusion relationships between contours, and leverage it to accelerate the recomputation of ID. Secondly, extending beyond the single distribution assumption, we present the Relative Depth (ReD), a generalization of contour depth for ensembles with multiple modes. Building upon the linear-time eID, we introduce CDclust, a clustering algorithm that untangles ensemble modes of variation by optimizing ReD. Synthetic and real datasets from medical image segmentation and meteorological forecasting showcase the speed advantages, illustrate the use case of progressive depth computation and enable non-parametric multimodal analysis. To promote research and adoption, we offer the contour-depth Python package.Computer Graphics ForumScalars, Vectors, and Topology43
Inclusion depth for contour ensembles
Get PDF Ensembles of contours arise in various applications like simulation, computer-aided design, and semantic segmentation. Uncovering ensemble patterns and analyzing individual members is a challenging task that suffers from clutter. Ensemble statistical summarization can alleviate this issue by permitting analyzing ensembles’ distributional components like the mean and median, confidence intervals, and outliers. Contour boxplots, powered by Contour Band Depth (CBD), are a popular non-parametric ensemble summarization method that benefits from CBD's generality, robustness, and theoretical properties. In this work, we introduce Inclusion Depth (ID), a new notion of contour depth with three defining characteristics. First, ID is a generalization of functional Half-Region Depth, which offers several theoretical guarantees. Second, ID relies on a simple principle: the inside/outside relationships between contours. This facilitates implementing ID and understanding its results. Third, the computational complexity of ID scales quadratically in the number of members of the ensemble, improving CBD's cubic complexity. This also in practice speeds up the computation enabling the use of ID for exploring large contour ensembles or in contexts requiring multiple depth evaluations like clustering. In a series of experiments on synthetic data and case studies with meteorological and segmentation data, we evaluate ID's performance and demonstrate its capabilities for the visual analysis of contour ensembles. Radiolog
LoGCC: Local-to-Global Correlation Clustering for Scalar Field Ensembles
No full textCorrelation clustering (CC) offers an effective approach to analyze scalar field ensembles by detecting correlated regions and consistent structures, enabling the extraction of meaningful patterns. However, existing CC methods are computationally expensive, making them impractical for both interactive analysis and large-scale scalar fields. We introduce the Local-to-Global Correlation Clustering (LoGCC) framework, which accelerates pivot-based CC by leveraging the spatial structure of scalar fields and the weak transitivity of correlation. LoGCC operates in two stages: a local step that uses the neighborhood graph of the scalar field's spatial domain to build highly correlated local clusters, and a global step that merges them into global clusters. We implement the LoGCC framework for two well-known pivot-based CC methods, Pivot and CN-Pivot, demonstrating its generality. Our evaluation using synthetic and real-world meteorological and medical image segmentation datasets shows that LoGCC achieves speedups—up to 15 × for Pivot and 200 × for CN-Pivot—and improved scalability to larger scalar fields, while maintaining cluster quality. These contributions broaden the applicability of correlation clustering in large-scale and interactive analysis settings
