Automatic segmentation of kidney and kidney tumors using the cascaded dense network combined with cLSTM in CT scan

In this study, we develop the cascaded deep neural network model for automatic segmentation of the kidney and kidney tumors in CT scans. We used the fully dense network (to extract inner-slice image features) combined with bi-cLSTM (to extract inter-slice image features) for segmentation of kidney and kidney tumors. The whole CT scan is preprocessing for resizing (256*256) and intensity normalization (clipping between -600 and 400 and then normalizing between 0 and 1), and then entered into 1 st neural network (growth factor = 8, and the consecutive slices = 3) for segmentation of kidney. And the output of 1 st network is resized into 96*96, and entered into 2 nd neural network, which is the same architecture of 1 st network excepting growth factor = 16, and the consecutive slices = 5. Our cascaded deep neural network showed the dice scores of 0.932 (train), and 0.884 (validation) for segmentation of kidney and the dice scores of 0.845 (train), and 0.696 (validation) for segmentation of kidney tumors

Neuroimaging markers for studying Gulf-War illness: single-subject level analytical method based on machine learning

Gulf War illness (GWI) refers to the multitude of chronic health symptoms, spanning from fatigue, musculoskeletal pain, and neurological complaints to respiratory, gastrointestinal, and dermatologic symptoms experienced by about 250,000 GW veterans who served in the 1991 Gulf War (GW). Longitudinal studies showed that the severity of these symptoms often remain unchanged even years after the GW, and these veterans with GWI continue to have poorer general health and increased chronic medical conditions than their non-deployed counterparts. For better management and treatment of this condition, there is an urgent need for developing objective biomarkers that can help with simple and accurate diagnosis of GWI. In this study, we applied multiple neuroimaging techniques, including T1-weighted magnetic resonance imaging (T1W-MRI), diffusion tensor imaging (DTI), and novel neurite density imaging (NDI) to perform both a group-level statistical comparison and a single-subject level machine learning (ML) analysis to identify diagnostic imaging features of GWI. Our results supported NDI as the most sensitive in defining GWI characteristics. In particular, our classifier trained with white matter NDI features achieved an accuracy of 90% and F-score of 0.941 for classifying GWI cases from controls after the cross-validation. These results are consistent with our previous study which suggests that NDI measures are sensitive to the microstructural and macrostructural changes in the brain of veterans with GWI, which can be valuable for designing better diagnosis method and treatment efficacy studies.W81XWH-17-1-0440 - a department of Defense CDMRP new investigator awardPublished versio

Direct Rating Estimation of Enlarged Perivascular Spaces (EPVS) in Brain MRI Using Deep Neural Network

In this article, we propose a deep-learning-based estimation model for rating enlarged perivascular spaces (EPVS) in the brain’s basal ganglia region using T2-weighted magnetic resonance imaging (MRI) images. The proposed method estimates the EPVS rating directly from the T2-weighted MRI without using either the detection or the segmentation of EVPS. The model uses the cropped basal ganglia region on the T2-weighted MRI. We formulated the rating of EPVS as a multi-class classification problem. Model performance was evaluated using 96 subjects’ T2-weighted MRI data that were collected from two hospitals. The results show that the proposed method can automatically rate EPVS—demonstrating great potential to be used as a risk indicator of dementia to aid early diagnosis

Conditional Random Field (CRF)-Boosting: Constructing a Robust Online Hybrid Boosting Multiple Object Tracker Facilitated by CRF Learning

Due to the reasonably acceptable performance of state-of-the-art object detectors, tracking-by-detection is a standard strategy for visual multi-object tracking (MOT). In particular, online MOT is more demanding due to its diverse applications in time-critical situations. A main issue of realizing online MOT is how to associate noisy object detection results on a new frame with previously being tracked objects. In this work, we propose a multi-object tracker method called CRF-boosting which utilizes a hybrid data association method based on online hybrid boosting facilitated by a conditional random field (CRF) for establishing online MOT. For data association, learned CRF is used to generate reliable low-level tracklets and then these are used as the input of the hybrid boosting. To do so, while existing data association methods based on boosting algorithms have the necessity of training data having ground truth information to improve robustness, CRF-boosting ensures sufficient robustness without such information due to the synergetic cascaded learning procedure. Further, a hierarchical feature association framework is adopted to further improve MOT accuracy. From experimental results on public datasets, we could conclude that the benefit of proposed hybrid approach compared to the other competitive MOT systems is noticeable

Lung Nodule Malignancy Prediction in Sequential CT Scans: Summary of ISBI 2018 Challenge

Lung cancer is by far the leading cause of cancer death in the US. Recent studies have demonstrated the effectiveness of screening using low dose CT (LDCT) in reducing lung cancer related mortality. While lung nodules are detected with a high rate of sensitivity, this exam has a low specificity rate and it is still difficult to separate benign and malignant lesions. The ISBI 2018 Lung Nodule Malignancy Prediction Challenge, developed by a team from the Quantitative Imaging Network of the National Cancer Institute, was focused on the prediction of lung nodule malignancy from two sequential LDCT screening exams using automated (non-manual) algorithms. We curated a cohort of 100 subjects who participated in the National Lung Screening Trial and had established pathological diagnoses. Data from 30 subjects were randomly selected for training and the remaining was used for testing. Participants were evaluated based on the area under the receiver operating characteristic curve (AUC) of nodule-wise malignancy scores generated by their algorithms on the test set. The challenge had 17 participants, with 11 teams submitting reports with method description, mandated by the challenge rules. Participants used quantitative methods, resulting in a reporting test AUC ranging from 0.698 to 0.913. The top five contestants used deep learning approaches, reporting an AUC between 0.87 - 0.91. The team's predictor did not achieve significant differences from each other nor from a volume change estimate (p =.05 with Bonferroni-Holm's correction)