Identification and discovery of viruses using next-generation sequencing technology is a fast-developing area with potential wide application in clinical diagnostics, public health monitoring and novel virus discovery. However, tremendous sequence data from NGS study has posed great challenge both in accuracy and velocity for application of NGS study. Here we describe VIP (“Virus Identification Pipeline”), a one-touch computational pipeline for virus identification and discovery from metagenomic NGS data. VIP performs the following steps to achieve its goal: (i) map and filter out background-related reads, (ii) extensive classification of reads on the basis of nucleotide and remote amino acid homology, (iii) multiple k-mer based de novo assembly and phylogenetic analysis to provide evolutionary insight. We validated the feasibility and veracity of this pipeline with sequencing results of various types of clinical samples and public datasets. VIP has also contributed to timely virus diagnosis (~10 min) in acutely ill patients, demonstrating its potential in the performance of unbiased NGS-based clinical studies with demand of short turnaround time. VIP is released under GPLv3 and is available for free download at: https://github.com/keylabivdc/VIP.

We describe an active contour framework with accurate shape and size constraints on the vessel cross-sectional planes to produce the vessel segmentation. It starts with a multiscale vessel axis tracing in a 3D computed tomography (CT) data, followed by vessel boundary delineation on the cross-sectional planes derived from the extracted axis. The vessel boundary surface is deformed under constrained movements on the cross sections and is voxelized to produce the final vascular segmentation. The novelty of this paper lies in the accurate contour point detection of thin vessels based on the CT scanning model, in the efficient implementation of missing contour points in the problematic regions and in the active contour model with accurate shape and size constraints. The main advantage of our framework is that it avoids disconnected and incomplete segmentation of the vessels in the problematic regions that contain touching vessels (vessels in close proximity to each other), diseased portions (pathologic structure attached to a vessel), and thin vessels. It is particularly suitable for accurate segmentation of thin and low contrast vessels. Our method is evaluated and demonstrated on CT data sets from our partner site, and its results are compared with three related methods. Our method is also tested on two publicly available databases and its results are compared with the recently published method. The applicability of the proposed method to some challenging clinical problems, the segmentation of the vessels in the problematic regions, is demonstrated with good results on both quantitative and qualitative experimentations; our segmentation algorithm can delineate vessel boundaries that have level of variability similar to those obtained manually.

One-stage object detectors are trained by optimizing classification-loss and localization-loss simultaneously, with the former suffering much from extreme foreground-background class imbalance issue due to the large number of anchors. This paper alleviates this issue by proposing a novel framework to replace the classification task in one-stage detectors with a ranking task, and adopting the Average-Precision loss (AP-loss) for the ranking problem. Due to its non-differentiability and non-convexity, the AP-loss cannot be optimized directly. For this purpose, we develop a novel optimization algorithm, which seamlessly combines the error-driven update scheme in perceptron learning and backpropagation algorithm in deep networks. We provide in-depth analyses on the good convergence property and computational complexity of the proposed algorithm, both theoretically and empirically. Experimental results demonstrate notable improvement in addressing the imbalance issue in object detection over existing AP-based optimization algorithms. An improved state-of-the-art performance is achieved in one-stage detectors based on AP-loss over detectors using classification-losses on various standard benchmarks. The proposed framework is also highly versatile in accommodating different network architectures.

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Network security has always been a hot topic as security and reliability are vital to software and hardware. Network intrusion detection system (NIDS) is an effective solution to the identification of attacks in computer and communication systems. A necessary condition for high-quality intrusion detection is the gathering of useful and precise intrusion information. Machine learning, particularly deep learning, has achieved a lot of success in various fields of industry and academic due to its good ability of feature representation and extraction. In this paper, deep learning methods are integrated into the NIDS. The intrusion activity is regarded as a time-series event and a bidirectional gated recurrent unit (GRU) based network intrusion detection model with hierarchical attention mechanism is presented. The influence of different lengths of previous traffic on the performance is then studied. Some experiments are performed on the dataset UNSW-NB15, in which the proposed hierarchical attention model achieves satisfactory detection accuracy of more than 98.76% and a false alarm rate (FAR) of lower than 1.2%. An attention probability map to reflect the importance of features is then visualized using the attention mechanism. The visualization ability assists in providing an understanding of the varied importance of the same features for different traffic classes and to determine feature selection in the future.