Deep Neural Network with l2-norm Unit for Brain Lesions Detection

Automated brain lesions detection is an important and very challenging clinical diagnostic task because the lesions have different sizes, shapes, contrasts, and locations. Deep Learning recently has shown promising progress in many application fields, which motivates us to apply this technology for such important problem. In this paper, we propose a novel and end-to-end trainable approach for brain lesions classification and detection by using deep Convolutional Neural Network (CNN). In order to investigate the applicability, we applied our approach on several brain diseases including high and low-grade glioma tumor, ischemic stroke, Alzheimer diseases, by which the brain Magnetic Resonance Images (MRI) have been applied as an input for the analysis. We proposed a new operating unit which receives features from several projections of a subset units of the bottom layer and computes a normalized l2-norm for next layer. We evaluated the proposed approach on two different CNN architectures and number of popular benchmark datasets. The experimental results demonstrate the superior ability of the proposed approach.Comment: Accepted for presentation in ICONIP-201

Hypothesis Disparity Regularized Mutual Information Maximization

We propose a hypothesis disparity regularized mutual information maximization~(HDMI) approach to tackle unsupervised hypothesis transfer -- as an effort towards unifying hypothesis transfer learning (HTL) and unsupervised domain adaptation (UDA) -- where the knowledge from a source domain is transferred solely through hypotheses and adapted to the target domain in an unsupervised manner. In contrast to the prevalent HTL and UDA approaches that typically use a single hypothesis, HDMI employs multiple hypotheses to leverage the underlying distributions of the source and target hypotheses. To better utilize the crucial relationship among different hypotheses -- as opposed to unconstrained optimization of each hypothesis independently -- while adapting to the unlabeled target domain through mutual information maximization, HDMI incorporates a hypothesis disparity regularization that coordinates the target hypotheses jointly learn better target representations while preserving more transferable source knowledge with better-calibrated prediction uncertainty. HDMI achieves state-of-the-art adaptation performance on benchmark datasets for UDA in the context of HTL, without the need to access the source data during the adaptation.Comment: Accepted to AAAI 202

Adversarial training and dilated convolutions for brain MRI segmentation

Convolutional neural networks (CNNs) have been applied to various automatic image segmentation tasks in medical image analysis, including brain MRI segmentation. Generative adversarial networks have recently gained popularity because of their power in generating images that are difficult to distinguish from real images. In this study we use an adversarial training approach to improve CNN-based brain MRI segmentation. To this end, we include an additional loss function that motivates the network to generate segmentations that are difficult to distinguish from manual segmentations. During training, this loss function is optimised together with the conventional average per-voxel cross entropy loss. The results show improved segmentation performance using this adversarial training procedure for segmentation of two different sets of images and using two different network architectures, both visually and in terms of Dice coefficients.Comment: MICCAI 2017 Workshop on Deep Learning in Medical Image Analysi

Dilated Convolutional Neural Networks for Cardiovascular MR Segmentation in Congenital Heart Disease

We propose an automatic method using dilated convolutional neural networks (CNNs) for segmentation of the myocardium and blood pool in cardiovascular MR (CMR) of patients with congenital heart disease (CHD). Ten training and ten test CMR scans cropped to an ROI around the heart were provided in the MICCAI 2016 HVSMR challenge. A dilated CNN with a receptive field of 131x131 voxels was trained for myocardium and blood pool segmentation in axial, sagittal and coronal image slices. Performance was evaluated within the HVSMR challenge. Automatic segmentation of the test scans resulted in Dice indices of 0.80$\pm$0.06 and 0.93$\pm$0.02, average distances to boundaries of 0.96$\pm$0.31 and 0.89$\pm$0.24 mm, and Hausdorff distances of 6.13$\pm$3.76 and 7.07$\pm$3.01 mm for the myocardium and blood pool, respectively. Segmentation took 41.5$\pm$14.7 s per scan. In conclusion, dilated CNNs trained on a small set of CMR images of CHD patients showing large anatomical variability provide accurate myocardium and blood pool segmentations

Molecular characterization of Panton-Valentine Leukocidin positive Staphylococcus aureus isolates obtained from clinical sample in Isfahan, Iran

Staphylococcus aureus is one of the main significant human pathogens which can produce various toxins such as Panton-Valentine Leukocidin (PVL) which is known as a prominent toxin associated with S. aureus infections. PVL-positive strains can cause a wide variety of skin, soft tissue, necrotizing pneumonia, fasciitis and life-threatening infections. Therefore, the aim of this study was evaluating the molecular characteristics of PVL-positive strains such as the presence of mecA, SCCmec types, agr types and exfoliative toxin genes. In this study, a total of 152 S. aureus strains were collected from clinical samples of patients who referred to Isfahan’s Alzahra hospital (Iran). The isolates were confirmed phenotypically by conventional methods and then PVL-positive isolates were identified by PCR molecular test. Thereafter, antibiotic resistance pattern, agr groups (I, II, III, and IV), exfoliative toxins (eta and etb), mecA gene and SCCmec various types were carried out. Totally, 52 (34.2%) of strains were positive for PVL. Six PVL-positive strains harbored mecA gene, one strain had SCCmec I, and 5 strains SCCmec type IV. The highest ratio of agr groups belonged to group (I) and the (eta) gene was also detected in 18 isolates. The PVL-positive S. aureus strains can cause more serious infections, so identification of the genetic characteristics and antibiotic resistance monitoring of these strains is necessary