DeepOrgan: Multi-level Deep Convolutional Networks for Automated Pancreas Segmentation

Automatic organ segmentation is an important yet challenging problem for medical image analysis. The pancreas is an abdominal organ with very high anatomical variability. This inhibits previous segmentation methods from achieving high accuracies, especially compared to other organs such as the liver, heart or kidneys. In this paper, we present a probabilistic bottom-up approach for pancreas segmentation in abdominal computed tomography (CT) scans, using multi-level deep convolutional networks (ConvNets). We propose and evaluate several variations of deep ConvNets in the context of hierarchical, coarse-to-fine classification on image patches and regions, i.e. superpixels. We first present a dense labeling of local image patches via $P{-}\mathrm{ConvNet}$ and nearest neighbor fusion. Then we describe a regional ConvNet ($R_1{-}\mathrm{ConvNet}$) that samples a set of bounding boxes around each image superpixel at different scales of contexts in a "zoom-out" fashion. Our ConvNets learn to assign class probabilities for each superpixel region of being pancreas. Last, we study a stacked $R_2{-}\mathrm{ConvNet}$ leveraging the joint space of CT intensities and the $P{-}\mathrm{ConvNet}$ dense probability maps. Both 3D Gaussian smoothing and 2D conditional random fields are exploited as structured predictions for post-processing. We evaluate on CT images of 82 patients in 4-fold cross-validation. We achieve a Dice Similarity Coefficient of 83.6$\pm$6.3% in training and 71.8$\pm$10.7% in testing.Comment: To be presented at MICCAI 2015 - 18th International Conference on Medical Computing and Computer Assisted Interventions, Munich, German

Mining Fix Patterns for FindBugs Violations

In this paper, we first collect and track a large number of fixed and unfixed violations across revisions of software. The empirical analyses reveal that there are discrepancies in the distributions of violations that are detected and those that are fixed, in terms of occurrences, spread and categories, which can provide insights into prioritizing violations. To automatically identify patterns in violations and their fixes, we propose an approach that utilizes convolutional neural networks to learn features and clustering to regroup similar instances. We then evaluate the usefulness of the identified fix patterns by applying them to unfixed violations. The results show that developers will accept and merge a majority (69/116) of fixes generated from the inferred fix patterns. It is also noteworthy that the yielded patterns are applicable to four real bugs in the Defects4J major benchmark for software testing and automated repair.Comment: Accepted for IEEE Transactions on Software Engineerin

Tiresias: Predicting Security Events Through Deep Learning

With the increased complexity of modern computer attacks, there is a need for defenders not only to detect malicious activity as it happens, but also to predict the specific steps that will be taken by an adversary when performing an attack. However this is still an open research problem, and previous research in predicting malicious events only looked at binary outcomes (e.g., whether an attack would happen or not), but not at the specific steps that an attacker would undertake. To fill this gap we present Tiresias, a system that leverages Recurrent Neural Networks (RNNs) to predict future events on a machine, based on previous observations. We test Tiresias on a dataset of 3.4 billion security events collected from a commercial intrusion prevention system, and show that our approach is effective in predicting the next event that will occur on a machine with a precision of up to 0.93. We also show that the models learned by Tiresias are reasonably stable over time, and provide a mechanism that can identify sudden drops in precision and trigger a retraining of the system. Finally, we show that the long-term memory typical of RNNs is key in performing event prediction, rendering simpler methods not up to the task

Anatomy-specific classification of medical images using deep convolutional nets

Automated classification of human anatomy is an important prerequisite for many computer-aided diagnosis systems. The spatial complexity and variability of anatomy throughout the human body makes classification difficult. "Deep learning" methods such as convolutional networks (ConvNets) outperform other state-of-the-art methods in image classification tasks. In this work, we present a method for organ- or body-part-specific anatomical classification of medical images acquired using computed tomography (CT) with ConvNets. We train a ConvNet, using 4,298 separate axial 2D key-images to learn 5 anatomical classes. Key-images were mined from a hospital PACS archive, using a set of 1,675 patients. We show that a data augmentation approach can help to enrich the data set and improve classification performance. Using ConvNets and data augmentation, we achieve anatomy-specific classification error of 5.9 % and area-under-the-curve (AUC) values of an average of 0.998 in testing. We demonstrate that deep learning can be used to train very reliable and accurate classifiers that could initialize further computer-aided diagnosis.Comment: Presented at: 2015 IEEE International Symposium on Biomedical Imaging, April 16-19, 2015, New York Marriott at Brooklyn Bridge, NY, US

Chiral perturbation theory, finite size effects and the three-dimensional XYXY model

We study finite size effects of the d=3 $XY$ model in terms of the chiral perturbation theory. We calculate by Monte Carlo simulations physical quantities which are, to order of $(1/L)^2$, uniquely determined only by two low energy constants. They are the magnetization and the helicity modulus (or the Goldstone boson decay constant) in infinite volume. We also pay a special attention to the region of the validity of the two possible expansions in the theory.Comment: 34 pages ( 9 PS files are included. harvmac and epsf macros are needed. ), KYUSHU-HET-17, SAGA-HE-6