arXiv subjects

Daniel L. Rubin

Publications and source records attributed to Daniel L. Rubin.

22 records · Page 2Linked to original sources

arXiv2017

A Fully-Automated Pipeline for Detection and Segmentation of Liver Lesions and Pathological Lymph Nodes

We propose a fully-automated method for accurate and robust detection and segmentation of potentially cancerous lesions found in the liver and in lymph nodes. The process is performed in three steps, including organ detection, lesion detection and lesion segmentation. Our method applies machine learning techniques such as marginal space learning and convolutional neural networks, as well as active contour models. The method proves to be robust in its handling of extremely high lesion diversity. We tested our method on volumetric computed tomography (CT) images, including 42 volumes containing liver lesions and 86 volumes containing 595 pathological lymph nodes. Preliminary results under 10-fold cross validation show that for both the liver lesions and the lymph nodes, a total detection sensitivity of 0.53 and average Dice score of $0.71 \pm 0.15$ for segmentation were obtained.

cs.CV↗

arXiv2017

Software for Distributed Computation on Medical Databases: A Demonstration Project

Bringing together the information latent in distributed medical databases promises to personalize medical care by enabling reliable, stable modeling of outcomes with rich feature sets (including patient characteristics and treatments received). However, there are barriers to aggregation of medical data, due to lack of standardization of ontologies, privacy concerns, proprietary attitudes toward data, and a reluctance to give up control over end use. Aggregation of data is not always necessary for model fitting. In models based on maximizing a likelihood, the computations can be distributed, with aggregation limited to the intermediate results of calculations on local data, rather than raw data. Distributed fitting is also possible for singular value decomposition. There has been work on the technical aspects of shared computation for particular applications, but little has been published on the software needed to support the "social networking" aspect of shared computing, to reduce the barriers to collaboration. We describe a set of software tools that allow the rapid assembly of a collaborative computational project, based on the flexible and extensible R statistical software and other open source packages, that can work across a heterogeneous collection of database environments, with full transparency to allow local officials concerned with privacy protections to validate the safety of the method. We describe the principles, architecture, and successful test results for the site-stratified Cox model and rank-k Singular Value Decomposition (SVD).

stat.CO↗

arXiv2016

Computerized Multiparametric MR image Analysis for Prostate Cancer Aggressiveness-Assessment

We propose an automated method for detecting aggressive prostate cancer(CaP) (Gleason score >=7) based on a comprehensive analysis of the lesion and the surrounding normal prostate tissue which has been simultaneously captured in T2-weighted MR images, diffusion-weighted images (DWI) and apparent diffusion coefficient maps (ADC). The proposed methodology was tested on a dataset of 79 patients (40 aggressive, 39 non-aggressive). We evaluated the performance of a wide range of popular quantitative imaging features on the characterization of aggressive versus non-aggressive CaP. We found that a group of 44 discriminative predictors among 1464 quantitative imaging features can be used to produce an area under the ROC curve of 0.73.

cs.CV↗

arXiv2016

Adaptive Local Window for Level Set Segmentation of CT and MRI Liver Lesions

We propose a novel method, the adaptive local window, for improving level set segmentation technique. The window is estimated separately for each contour point, over iterations of the segmentation process, and for each individual object. Our method considers the object scale, the spatial texture, and changes of the energy functional over iterations. Global and local statistics are considered by calculating several gray level co-occurrence matrices. We demonstrate the capabilities of the method in the domain of medical imaging for segmenting 233 images with liver lesions. To illustrate the strength of our method, those images were obtained by either Computed Tomography or Magnetic Resonance Imaging. Moreover, we analyzed images using three different energy models. We compare our method to a global level set segmentation and to local framework that uses predefined fixed-size square windows. The results indicate that our proposed method outperforms the other methods in terms of agreement with the manual marking and dependence on contour initialization or the energy model used. In case of complex lesions, such as low contrast lesions, heterogeneous lesions, or lesions with a noisy background, our method shows significantly better segmentation with an improvement of 0.25+- 0.13 in Dice similarity coefficient, compared with state of the art fixed-size local windows (Wilcoxon, p < 0.001).

cs.CV↗