Consistent segmentation of COVID-19 patient's CT scans across multiple time points is essential to assess disease progression and response to therapy accurately. Existing automatic and interactive segmentation models for medical images only use data from a single time point (static). However, valuable segmentation information from previous time points is often not used to aid the segmentation of a patient's follow-up scans. Also, fully automatic segmentation techniques frequently produce results that would need further editing for clinical use. In this work, we propose a new single network model for interactive segmentation that fully utilizes all available past information to refine the segmentation of follow-up scans. In the first segmentation round, our model takes 3D volumes of medical images from two-time points (target and reference) as concatenated slices with the additional reference time point segmentation as a guide to segment the target scan. In subsequent segmentation refinement rounds, user feedback in the form of scribbles that correct the segmentation and the target's previous segmentation results are additionally fed into the model. This ensures that the segmentation information from previous refinement rounds is retained. Experimental results on our in-house multiclass longitudinal COVID-19 dataset show that the proposed model outperforms its static version and can assist in localizing COVID-19 infections in patient's follow-up scans.
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We study timed systems in which some timing features are unknown parameters. Parametric timed automata (PTAs) are a classical formalism for such systems but for which most interesting problems are undecidable. Notably, the parametric reachability emptiness problem, i.e., the emptiness of the parameter valuations set allowing to reach some given discrete state, is undecidable. Lower-bound/upper-bound parametric timed automata (L/U-PTAs) achieve decidability for reachability properties by enforcing a separation of parameters used as upper bounds in the automaton constraints, and those used as lower bounds. In this paper, we first study reachability. We exhibit a subclass of PTAs (namely integer-points PTAs) with bounded rational-valued parameters for which the parametric reachability emptiness problem is decidable. Using this class, we present further results improving the boundary between decidability and undecidability for PTAs and their subclasses such as L/U-PTAs. We then study liveness. We prove that: (1) the existence of at least one parameter valuation for which there exists an infinite run in an L/U-PTA is PSPACE-complete; (2) the existence of a parameter valuation such that the system has a deadlock is however undecidable; (3) the problem of the existence of a valuation for which a run remains in a given set of locations exhibits a very thin border between decidability and undecidability.
Clinical Utility of the Automatic Phenotype Annotation in Unstructured Clinical Notes: ICU Use Cases
Objective: Clinical notes contain information not present elsewhere, including drug response and symptoms, all of which are highly important when predicting key outcomes in acute care patients. We propose the automatic annotation of phenotypes from clinical notes as a method to capture essential information, which is complementary to typically used vital signs and laboratory test results, to predict outcomes in the Intensive Care Unit (ICU). Methods: We develop a novel phenotype annotation model to annotate phenotypic features of patients which are then used as input features of predictive models to predict ICU patient outcomes. We demonstrate and validate our approach conducting experiments on three ICU prediction tasks including in-hospital mortality, physiological decompensation and length of stay for over 24,000 patients by using MIMIC-III dataset. Results: The predictive models incorporating phenotypic information achieve 0.845 (AUC-ROC) to predict in-hospital mortality, 0.839 (AUC-ROC) for physiological decompensation and 0.430 (Kappa) for length of stay, all of which consistently outperform the baseline models leveraging only vital signs and laboratory test results. Moreover, we conduct a thorough interpretability study, showing that phenotypes provide valuable insights at the patient and cohort levels. Conclusion: The proposed approach demonstrates phenotypic information complements traditionally used vital signs and laboratory test results, improving significantly forecast of outcomes in the ICU.
Bird's-Eye-View (BEV) maps have emerged as one of the most powerful representations for scene understanding due to their ability to provide rich spatial context while being easy to interpret and process. Such maps have found use in many real-world tasks that extensively rely on accurate scene segmentation as well as object instance identification in the BEV space for their operation. However, existing segmentation algorithms only predict the semantics in the BEV space, which limits their use in applications where the notion of object instances is also critical. In this work, we present the first BEV panoptic segmentation approach for directly predicting dense panoptic segmentation maps in the BEV, given a single monocular image in the frontal view (FV). Our architecture follows the top-down paradigm and incorporates a novel dense transformer module consisting of two distinct transformers that learn to independently map vertical and flat regions in the input image from the FV to the BEV. Additionally, we derive a mathematical formulation for the sensitivity of the FV-BEV transformation which allows us to intelligently weight pixels in the BEV space to account for the varying descriptiveness across the FV image. Extensive evaluations on the KITTI-360 and nuScenes datasets demonstrate that our approach exceeds the state-of-the-art in the PQ metric by 3.61 pp and 4.93 pp respectively.
We present MultiBodySync, a novel, end-to-end trainable multi-body motion segmentation and rigid registration framework for multiple input 3D point clouds. The two non-trivial challenges posed by this multi-scan multibody setting that we investigate are: (i) guaranteeing correspondence and segmentation consistency across multiple input point clouds capturing different spatial arrangements of bodies or body parts; and (ii) obtaining robust motion-based rigid body segmentation applicable to novel object categories. We propose an approach to address these issues that incorporates spectral synchronization into an iterative deep declarative network, so as to simultaneously recover consistent correspondences as well as motion segmentation. At the same time, by explicitly disentangling the correspondence and motion segmentation estimation modules, we achieve strong generalizability across different object categories. Our extensive evaluations demonstrate that our method is effective on various datasets ranging from rigid parts in articulated objects to individually moving objects in a 3D scene, be it single-view or full point clouds.
This paper presents a novel Subject-dependent Deep Aging Path (SDAP), which inherits the merits of both Generative Probabilistic Modeling and Inverse Reinforcement Learning to model the facial structures and the longitudinal face aging process of a given subject. The proposed SDAP is optimized using tractable log-likelihood objective functions with Convolutional Neural Networks (CNNs) based deep feature extraction. Instead of applying a fixed aging development path for all input faces and subjects, SDAP is able to provide the most appropriate aging development path for individual subject that optimizes the reward aging formulation. Unlike previous methods that can take only one image as the input, SDAP further allows multiple images as inputs, i.e. all information of a subject at either the same or different ages, to produce the optimal aging path for the given subject. Finally, SDAP allows efficiently synthesizing in-the-wild aging faces. The proposed model is experimented in both tasks of face aging synthesis and cross-age face verification. The experimental results consistently show SDAP achieves the state-of-the-art performance on numerous face aging databases, i.e. FG-NET, MORPH, AginG Faces in the Wild (AGFW), and Cross-Age Celebrity Dataset (CACD). Furthermore, we also evaluate the performance of SDAP on large-scale Megaface challenge to demonstrate the advantages of the proposed solution.
Despite the state-of-the-art performance for medical image segmentation, deep convolutional neural networks (CNNs) have rarely provided uncertainty estimations regarding their segmentation outputs, e.g., model (epistemic) and image-based (aleatoric) uncertainties. In this work, we analyze these different types of uncertainties for CNN-based 2D and 3D medical image segmentation tasks. We additionally propose a test-time augmentation-based aleatoric uncertainty to analyze the effect of different transformations of the input image on the segmentation output. Test-time augmentation has been previously used to improve segmentation accuracy, yet not been formulated in a consistent mathematical framework. Hence, we also propose a theoretical formulation of test-time augmentation, where a distribution of the prediction is estimated by Monte Carlo simulation with prior distributions of parameters in an image acquisition model that involves image transformations and noise. We compare and combine our proposed aleatoric uncertainty with model uncertainty. Experiments with segmentation of fetal brains and brain tumors from 2D and 3D Magnetic Resonance Images (MRI) showed that 1) the test-time augmentation-based aleatoric uncertainty provides a better uncertainty estimation than calculating the test-time dropout-based model uncertainty alone and helps to reduce overconfident incorrect predictions, and 2) our test-time augmentation outperforms a single-prediction baseline and dropout-based multiple predictions.
In this paper, we propose a novel fully convolutional two-stream fusion network (FCTSFN) for interactive image segmentation. The proposed network includes two sub-networks: a two-stream late fusion network (TSLFN) that predicts the foreground at a reduced resolution, and a multi-scale refining network (MSRN) that refines the foreground at full resolution. The TSLFN includes two distinct deep streams followed by a fusion network. The intuition is that, since user interactions are more direction information on foreground/background than the image itself, the two-stream structure of the TSLFN reduces the number of layers between the pure user interaction features and the network output, allowing the user interactions to have a more direct impact on the segmentation result. The MSRN fuses the features from different layers of TSLFN with different scales, in order to seek the local to global information on the foreground to refine the segmentation result at full resolution. We conduct comprehensive experiments on four benchmark datasets. The results show that the proposed network achieves competitive performance compared to current state-of-the-art interactive image segmentation methods.
Medical image segmentation requires consensus ground truth segmentations to be derived from multiple expert annotations. A novel approach is proposed that obtains consensus segmentations from experts using graph cuts (GC) and semi supervised learning (SSL). Popular approaches use iterative Expectation Maximization (EM) to estimate the final annotation and quantify annotator's performance. Such techniques pose the risk of getting trapped in local minima. We propose a self consistency (SC) score to quantify annotator consistency using low level image features. SSL is used to predict missing annotations by considering global features and local image consistency. The SC score also serves as the penalty cost in a second order Markov random field (MRF) cost function optimized using graph cuts to derive the final consensus label. Graph cut obtains a global maximum without an iterative procedure. Experimental results on synthetic images, real data of Crohn's disease patients and retinal images show our final segmentation to be accurate and more consistent than competing methods.
Superpixel segmentation has become an important research problem in image processing. In this paper, we propose an Iterative Spanning Forest (ISF) framework, based on sequences of Image Foresting Transforms, where one can choose i) a seed sampling strategy, ii) a connectivity function, iii) an adjacency relation, and iv) a seed pixel recomputation procedure to generate improved sets of connected superpixels (supervoxels in 3D) per iteration. The superpixels in ISF structurally correspond to spanning trees rooted at those seeds. We present five ISF methods to illustrate different choices of its components. These methods are compared with approaches from the state-of-the-art in effectiveness and efficiency. The experiments involve 2D and 3D datasets with distinct characteristics, and a high level application, named sky image segmentation. The theoretical properties of ISF are demonstrated in the supplementary material and the results show that some of its methods are competitive with or superior to the best baselines in effectiveness and efficiency.
This paper reports Deep LOGISMOS approach to 3D tumor segmentation by incorporating boundary information derived from deep contextual learning to LOGISMOS - layered optimal graph image segmentation of multiple objects and surfaces. Accurate and reliable tumor segmentation is essential to tumor growth analysis and treatment selection. A fully convolutional network (FCN), UNet, is first trained using three adjacent 2D patches centered at the tumor, providing contextual UNet segmentation and probability map for each 2D patch. The UNet segmentation is then refined by Gaussian Mixture Model (GMM) and morphological operations. The refined UNet segmentation is used to provide the initial shape boundary to build a segmentation graph. The cost for each node of the graph is determined by the UNet probability maps. Finally, a max-flow algorithm is employed to find the globally optimal solution thus obtaining the final segmentation. For evaluation, we applied the method to pancreatic tumor segmentation on a dataset of 51 CT scans, among which 30 scans were used for training and 21 for testing. With Deep LOGISMOS, DICE Similarity Coefficient (DSC) and Relative Volume Difference (RVD) reached 83.2+-7.8% and 18.6+-17.4% respectively, both are significantly improved (p<0.05) compared with contextual UNet and/or LOGISMOS alone.
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