arXiv research

Recent state-of-the-art image segmentation algorithms are mostly based on deep neural networks, thanks to their high performance and fast computation time. However, these methods are usually trained in a supervised manner, which requires large number of high quality ground-truth segmentation masks. On the other hand, c…

The Hausdorff Distance (HD) is widely used in evaluating medical image segmentation methods. However, existing segmentation methods do not attempt to reduce HD directly. In this paper, we present novel loss functions for training convolutional neural network (CNN)-based segmentation methods with the goal of reducing HD…

Differentiable segmented models for non-stationary data.

The paper proposes a mixture model with segmentation for heterogeneous functional data.

The paper extends influence functions to sequence tagging tasks for better model interpretability.

To accurately analyze changes of anatomical structures in longitudinal imaging studies, consistent segmentation across multiple time-points is required. Existing solutions often involve independent registration and segmentation components. Registration between time-points is used either as a prior for segmentation in a…

Many software analysis methods have come to rely on machine learning approaches. Code segmentation - the process of decomposing source code into meaningful blocks - can augment these methods by featurizing code, reducing noise, and limiting the problem space. Traditionally, code segmentation has been done using syntact…

In this paper, we introduce a method for segmenting time series data using tools from Bayesian nonparametrics. We consider the task of temporal segmentation of a set of time series data into representative stationary segments. We use Gaussian process (GP) priors to impose our knowledge about the characteristics of the …

Image normalization is a critical step in medical imaging. This step is often done on a per-dataset basis, preventing current segmentation algorithms from the full potential of exploiting jointly normalized information across multiple datasets. To solve this problem, we propose an adversarial normalization approach for…

We propose UOLO, a novel framework for the simultaneous detection and segmentation of structures of interest in medical images. UOLO consists of an object segmentation module which intermediate abstract representations are processed and used as input for object detection. The resulting system is optimized simultaneousl…

FAST optimizes additive segmentation for faster, more interpretable models.

Image segmentation is widely used in a variety of computer vision tasks, such as object localization and recognition, boundary detection, and medical imaging. This thesis proposes deep learning architectures to improve automatic object localization and boundary delineation for salient object segmentation in natural ima…

We propose and analyze a constrained level-set method for semi-automatic image segmentation. Our level-set model with constraints on the level-set function enables us to specify which parts of the image lie inside respectively outside the segmented objects. Such a-priori information can be expressed in terms of upper a…

We present a fully-supervized method for learning to segment data structured by an adjacency graph. We introduce the graph-structured contrastive loss, a loss function structured by a ground truth segmentation. It promotes learning vertex embeddings which are homogeneous within desired segments, and have high contrast …

Convolutional neural networks (CNN) have achieved state of the art performance on both classification and segmentation tasks. Applying CNNs to microscopy images is challenging due to the lack of datasets labeled at the single cell level. We extend the application of CNNs to microscopy image classification and segmentat…

Kidney function evaluation using dynamic contrast-enhanced MRI (DCE-MRI) images could help in diagnosis and treatment of kidney diseases of children. Automatic segmentation of renal parenchyma is an important step in this process. In this paper, we propose a time and memory efficient fully automated segmentation method…

Background: Cardiac MRI derived biventricular mass and function parameters, such as end-systolic volume (ESV), end-diastolic volume (EDV), ejection fraction (EF), stroke volume (SV), and ventricular mass (VM) are clinically well established. Image segmentation can be challenging and time-consuming, due to the complex a…

This paper explains the method used in the segmentation challenge (Task 1) in the International Skin Imaging Collaboration's (ISIC) Skin Lesion Analysis Towards Melanoma Detection challenge held in 2018. We have trained a U-Net network to perform the segmentation. The key elements for the training were first to adjust …

The simplicity of gradient descent (GD) made it the default method for training ever-deeper and complex neural networks. Both loss functions and architectures are often explicitly tuned to be amenable to this basic local optimization. In the context of weakly-supervised CNN segmentation, we demonstrate a well-motivated…

A new heuristic LM algorithm improves $k$-segmentation accuracy with less computation.

Proposes a unified normalization method for multi-domain medical images.

We present a method for learning options from segmented demonstration trajectories. The trajectories are first segmented into skills using nonparametric Bayesian clustering and a reward function for each segment is then learned using inverse reinforcement learning. From this, a set of inferred trajectories for the demo…

We propose in this paper an exploratory analysis algorithm for functional data. The method partitions a set of functions into $K$ clusters and represents each cluster by a simple prototype (e.g., piecewise constant). The total number of segments in the prototypes, $P$, is chosen by the user and optimally distributed am…

Enhances FM models for numerical features using function basis encoding.

Few-shot cell segmentation from diverse sources to target domain.

Tractograms are mathematical representations of the main paths of axons within the white matter of the brain, from diffusion MRI data. Such representations are in the form of polylines, called streamlines, and one streamline approximates the common path of tens of thousands of axons. The analysis of tractograms is a ta…

The exploitation of large-scale population data has the potential to improve healthcare by discovering and understanding patterns and trends within this data. To enable high throughput analysis of cardiac imaging data automatically, a pipeline should comprise quality monitoring of the input images, segmentation of the …

New method uses contours of segmented images for X-ray classification.

Creating large scale high-quality annotations is a known challenge in medical imaging. In this work, based on the CycleGAN algorithm, we propose leveraging annotations from one modality to be useful in other modalities. More specifically, the proposed algorithm creates highly realistic synthetic CT images (SynCT) from …

Scene understanding and semantic segmentation are at the core of many computer vision tasks, many of which, involve interacting with humans in potentially dangerous ways. It is therefore paramount that techniques for principled design of robust models be developed. In this paper, we provide analytic and empirical evide…

U-Det improves lung nodule segmentation in CT images.

RankSEG-RMA improves semantic segmentation efficiency and applicability.

In this paper we show that on a complete Riemannian manifold of negative curvature and dimension $n>1$ every two points which realize a local maximum for the distance function are connected by at least $2n+1$ geometrically distinct geodesic segments (i.e. length minimizing). Using a similar method, we obtain that in th…

Automatic segmentation of auditory ossicles from CT images using Ricci curvature.

Building a large image dataset with high-quality object masks for semantic segmentation is costly and time consuming. In this paper, we introduce a principled semi-supervised framework that only uses a small set of fully supervised images (having semantic segmentation labels and box labels) and a set of images with onl…

The performance of the state-of-the-art image segmentation methods heavily relies on the high-quality annotations, which are not easily affordable, particularly for medical data. To alleviate this limitation, in this study, we propose a weakly supervised image segmentation method based on a deep geodesic prior. We hypo…

Maps of brain microarchitecture are important for understanding neurological function and behavior, including alterations caused by chronic conditions such as neurodegenerative disease. Techniques such as knife-edge scanning microscopy (KESM) provide the potential for whole organ imaging at sub-cellular resolution. How…

Image partitioning, or segmentation without semantics, is the task of decomposing an image into distinct segments, or equivalently to detect closed contours. Most prior work either requires seeds, one per segment; or a threshold; or formulates the task as multicut / correlation clustering, an NP-hard problem. Here, we …

Anatomical and biophysical modeling of left atrium (LA) and proximal pulmonary veins (PPVs) is important for clinical management of several cardiac diseases. Magnetic resonance imaging (MRI) allows qualitative assessment of LA and PPVs through visualization. However, there is a strong need for an advanced image segment…

Efficiently recovers piecewise linear functions from noisy samples.

Trajectory segmentation is the process of subdividing a trajectory into parts either by grouping points similar with respect to some measure of interest, or by minimizing a global objective function. Here we present a novel online algorithm for segmentation and summary, based on point density along the trajectory, and …

Tract-specific diffusion measures, as derived from brain diffusion MRI, have been linked to white matter tract structural integrity and neurodegeneration. As a consequence, there is a large interest in the automatic segmentation of white matter tract in diffusion tensor MRI data. Methods based on the tractography are p…

This paper introduces a novel mixture model-based approach for simultaneous clustering and optimal segmentation of functional data which are curves presenting regime changes. The proposed model consists in a finite mixture of piecewise polynomial regression models. Each piecewise polynomial regression model is associat…

In many review classification applications, a fine-grained analysis of the reviews is desirable, because different segments (e.g., sentences) of a review may focus on different aspects of the entity in question. However, training supervised models for segment-level classification requires segment labels, which may be m…

We present two graph-based algorithms for multiclass segmentation of high-dimensional data. The algorithms use a diffuse interface model based on the Ginzburg-Landau functional, related to total variation compressed sensing and image processing. A multiclass extension is introduced using the Gibbs simplex, with the fun…

A new snake model improves segmentation of SEM images.

Algorithm selects optimal segment for physiological signal analysis.

Unsupervised segmentation learns features without labels, improving accuracy.