National University of Defense Technology

BACKGROUND: There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions. FINDINGS: To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. CONCLUSIONS: Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.

Blockchain, the foundation of Bitcoin, has received extensive attentions recently. Blockchain serves as an immutable ledger which allows transactions take place in a decentralized manner. Blockchain-based applications are springing up, covering numerous fields including financial services, reputation system and Internet of Things (IoT), and so on. However, there are still many challenges of blockchain technology such as scalability and security problems waiting to be overcome. This paper presents a comprehensive overview on blockchain technology. We provide an overview of blockchain architechture firstly and compare some typical consensus algorithms used in different blockchains. Furthermore, technical challenges and recent advances are briefly listed. We also lay out possible future trends for blockchain.

Blockchain has numerous benefits such as decentralisation, persistency, anonymity and auditability. There is a wide spectrum of blockchain applications ranging from cryptocurrency, financial services, risk management, internet of things (IoT) to public and social services. Although a number of studies focus on using the blockchain technology in various application aspects, there is no comprehensive survey on the blockchain technology in both technological and application perspectives. To fill this gap, we conduct a comprehensive survey on the blockchain technology. In particular, this paper gives the blockchain taxonomy, introduces typical blockchain consensus algorithms, reviews blockchain applications and discusses technical challenges as well as recent advances in tackling the challenges. Moreover, this paper also points out the future directions in the blockchain technology.

Abstract Object detection, one of the most fundamental and challenging problems in computer vision, seeks to locate object instances from a large number of predefined categories in natural images. Deep learning techniques have emerged as a powerful strategy for learning feature representations directly from data and have led to remarkable breakthroughs in the field of generic object detection. Given this period of rapid evolution, the goal of this paper is to provide a comprehensive survey of the recent achievements in this field brought about by deep learning techniques. More than 300 research contributions are included in this survey, covering many aspects of generic object detection: detection frameworks, object feature representation, object proposal generation, context modeling, training strategies, and evaluation metrics. We finish the survey by identifying promising directions for future research.

Because undesirable pharmacokinetics and toxicity of candidate compounds are the main reasons for the failure of drug development, it has been widely recognized that absorption, distribution, metabolism, excretion and toxicity (ADMET) should be evaluated as early as possible. In silico ADMET evaluation models have been developed as an additional tool to assist medicinal chemists in the design and optimization of leads. Here, we announced the release of ADMETlab 2.0, a completely redesigned version of the widely used AMDETlab web server for the predictions of pharmacokinetics and toxicity properties of chemicals, of which the supported ADMET-related endpoints are approximately twice the number of the endpoints in the previous version, including 17 physicochemical properties, 13 medicinal chemistry properties, 23 ADME properties, 27 toxicity endpoints and 8 toxicophore rules (751 substructures). A multi-task graph attention framework was employed to develop the robust and accurate models in ADMETlab 2.0. The batch computation module was provided in response to numerous requests from users, and the representation of the results was further optimized. The ADMETlab 2.0 server is freely available, without registration, at https://admetmesh.scbdd.com/.

Quality control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures, and highly scalable acceleration. In this article, we demonstrate SOAPnuke as a tool with abundant functions for a "QC-Preprocess-QC" workflow and MapReduce acceleration framework. Four modules with different preprocessing functions are designed for processing datasets from genomic, small RNA, Digital Gene Expression, and metagenomic experiments, respectively. As a workflow-like tool, SOAPnuke centralizes processing functions into 1 executable and predefines their order to avoid the necessity of reformatting different files when switching tools. Furthermore, the MapReduce framework enables large scalability to distribute all the processing works to an entire compute cluster.We conducted a benchmarking where SOAPnuke and other tools are used to preprocess a ∼30× NA12878 dataset published by GIAB. The standalone operation of SOAPnuke struck a balance between resource occupancy and performance. When accelerated on 16 working nodes with MapReduce, SOAPnuke achieved ∼5.7 times the fastest speed of other tools.

Point cloud learning has lately attracted increasing attention due to its wide applications in many areas, such as computer vision, autonomous driving, and robotics. As a dominating technique in AI, deep learning has been successfully used to solve various 2D vision problems. However, deep learning on point clouds is still in its infancy due to the unique challenges faced by the processing of point clouds with deep neural networks. Recently, deep learning on point clouds has become even thriving, with numerous methods being proposed to address different problems in this area. To stimulate future research, this paper presents a comprehensive review of recent progress in deep learning methods for point clouds. It covers three major tasks, including 3D shape classification, 3D object detection and tracking, and 3D point cloud segmentation. It also presents comparative results on several publicly available datasets, together with insightful observations and inspiring future research directions.

We study the problem of efficient semantic segmentation for large-scale 3D point clouds. By relying on expensive sampling techniques or computationally heavy pre/post-processing steps, most existing approaches are only able to be trained and operate over small-scale point clouds. In this paper, we introduce RandLA-Net, an efficient and lightweight neural architecture to directly infer per-point semantics for large-scale point clouds. The key to our approach is to use random point sampling instead of more complex point selection approaches. Although remarkably computation and memory efficient, random sampling can discard key features by chance. To overcome this, we introduce a novel local feature aggregation module to progressively increase the receptive field for each 3D point, thereby effectively preserving geometric details. Extensive experiments show that our RandLA-Net can process 1 million points in a single pass with up to 200x faster than existing approaches. Moreover, our RandLA-Net clearly surpasses state-of-the-art approaches for semantic segmentation on two large-scale benchmarks Semantic3D and SemanticKITTI.

For the last two decades, intelligent transportation systems (ITS) have emerged as an efficient way of improving the performance of transportation systems, enhancing travel security, and providing more choices to travelers. A significant change in ITS in recent years is that much more data are collected from a variety of sources and can be processed into various forms for different stakeholders. The availability of a large amount of data can potentially lead to a revolution in ITS development, changing an ITS from a conventional technology-driven system into a more powerful multifunctional data-driven intelligent transportation system (D <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ITS) : a system that is vision, multisource, and learning algorithm driven to optimize its performance. Furthermore, D <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ITS is trending to become a privacy-aware people-centric more intelligent system. In this paper, we provide a survey on the development of D <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ITS, discussing the functionality of its key components and some deployment issues associated with D <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ITS Future research directions for the development of D <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ITS is also presented.

Blockchain has numerous benefits such as decentralisation, persistency, anonymity and auditability. There is a wide spectrum of blockchain applications ranging from cryptocurrency, financial services, risk management, internet of things (IoT) to public and social services. Although a number of studies focus on using the blockchain technology in various application aspects, there is no comprehensive survey on the blockchain technology in both technological and application perspectives. To fill this gap, we conduct a comprehensive survey on the blockchain technology. In particular, this paper gives the blockchain taxonomy, introduces typical blockchain consensus algorithms, reviews blockchain applications and discusses technical challenges as well as recent advances in tackling the challenges. Moreover, this paper also points out the future directions in the blockchain technology.

The global population at risk from mosquito-borne diseases-including dengue, yellow fever, chikungunya and Zika-is expanding in concert with changes in the distribution of two key vectors: Aedes aegypti and Aedes albopictus. The distribution of these species is largely driven by both human movement and the presence of suitable climate. Using statistical mapping techniques, we show that human movement patterns explain the spread of both species in Europe and the United States following their introduction. We find that the spread of Ae. aegypti is characterized by long distance importations, while Ae. albopictus has expanded more along the fringes of its distribution. We describe these processes and predict the future distributions of both species in response to accelerating urbanization, connectivity and climate change. Global surveillance and control efforts that aim to mitigate the spread of chikungunya, dengue, yellow fever and Zika viruses must consider the so far unabated spread of these mosquitos. Our maps and predictions offer an opportunity to strategically target surveillance and control programmes and thereby augment efforts to reduce arbovirus burden in human populations globally.

DESI (Dark Energy Spectroscopic Instrument) is a Stage IV ground-based dark energy experiment that will study baryon acoustic oscillations (BAO) and the growth of structure through redshift-space distortions with a wide-area galaxy and quasar redshift survey. To trace the underlying dark matter distribution, spectroscopic targets will be selected in four classes from imaging data. We will measure luminous red galaxies up to $z=1.0$. To probe the Universe out to even higher redshift, DESI will target bright [O II] emission line galaxies up to $z=1.7$. Quasars will be targeted both as direct tracers of the underlying dark matter distribution and, at higher redshifts ($ 2.1 &lt; z &lt; 3.5$), for the Ly-$α$ forest absorption features in their spectra, which will be used to trace the distribution of neutral hydrogen. When moonlight prevents efficient observations of the faint targets of the baseline survey, DESI will conduct a magnitude-limited Bright Galaxy Survey comprising approximately 10 million galaxies with a median $z\approx 0.2$. In total, more than 30 million galaxy and quasar redshifts will be obtained to measure the BAO feature and determine the matter power spectrum, including redshift space distortions.

UNLABELLED: Biological sequence diagrams are fundamental for visualizing various functional elements in protein or nucleotide sequences that enable a summarization and presentation of existing information as well as means of intuitive new discoveries. Here, we present a software package called illustrator of biological sequences (IBS) that can be used for representing the organization of either protein or nucleotide sequences in a convenient, efficient and precise manner. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Also, the final representational artwork can be directly exported into a publication-quality figure. AVAILABILITY AND IMPLEMENTATION: The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available at http://ibs.biocuckoo.org. CONTACT: renjian.sysu@gmail.com or xueyu@hust.edu.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Hybrid nanowires combining semiconductor and superconductor materials appear well suited for the creation, detection, and control of Majorana bound states (MBSs). We demonstrate the emergence of MBSs from coalescing Andreev bound states (ABSs) in a hybrid InAs nanowire with epitaxial Al, using a quantum dot at the end of the nanowire as a spectrometer. Electrostatic gating tuned the nanowire density to a regime of one or a few ABSs. In an applied axial magnetic field, a topological phase emerges in which ABSs move to zero energy and remain there, forming MBSs. We observed hybridization of the MBS with the end-dot bound state, which is in agreement with a numerical model. The ABS/MBS spectra provide parameters that are useful for understanding topological superconductivity in this system.

The massive spread of digital misinformation has been identified as a major threat to democracies. Communication, cognitive, social, and computer scientists are studying the complex causes for the viral diffusion of misinformation, while online platforms are beginning to deploy countermeasures. Little systematic, data-based evidence has been published to guide these efforts. Here we analyze 14 million messages spreading 400 thousand articles on Twitter during ten months in 2016 and 2017. We find evidence that social bots played a disproportionate role in spreading articles from low-credibility sources. Bots amplify such content in the early spreading moments, before an article goes viral. They also target users with many followers through replies and mentions. Humans are vulnerable to this manipulation, resharing content posted by bots. Successful low-credibility sources are heavily supported by social bots. These results suggest that curbing social bots may be an effective strategy for mitigating the spread of online misinformation.

Swarm intelligence algorithms are a subset of the artificial intelligence (AI) field, which is increasing popularity in resolving different optimization problems and has been widely utilized in various applications. In the past decades, numerous swarm intelligence algorithms have been developed, including ant colony optimization (ACO), particle swarm optimization (PSO), artificial fish swarm (AFS), bacterial foraging optimization (BFO), and artificial bee colony (ABC). This review tries to review the most representative swarm intelligence algorithms in chronological order by highlighting the functions and strengths from 127 research literatures. It provides an overview of the various swarm intelligence algorithms and their advanced developments, and briefly provides the description of their successful applications in optimization problems of engineering fields. Finally, opinions and perspectives on the trends and prospects in this relatively new research domain are represented to support future developments.

ADMETlab 3.0 is the second updated version of the web server that provides a comprehensive and efficient platform for evaluating ADMET-related parameters as well as physicochemical properties and medicinal chemistry characteristics involved in the drug discovery process. This new release addresses the limitations of the previous version and offers broader coverage, improved performance, API functionality, and decision support. For supporting data and endpoints, this version includes 119 features, an increase of 31 compared to the previous version. The updated number of entries is 1.5 times larger than the previous version with over 400 000 entries. ADMETlab 3.0 incorporates a multi-task DMPNN architecture coupled with molecular descriptors, a method that not only guaranteed calculation speed for each endpoint simultaneously, but also achieved a superior performance in terms of accuracy and robustness. In addition, an API has been introduced to meet the growing demand for programmatic access to large amounts of data in ADMETlab 3.0. Moreover, this version includes uncertainty estimates in the prediction results, aiding in the confident selection of candidate compounds for further studies and experiments. ADMETlab 3.0 is publicly for access without the need for registration at: https://admetlab3.scbdd.com.

Deep clustering learns deep feature representations that favor clustering task using neural networks. Some pioneering work proposes to simultaneously learn embedded features and perform clustering by explicitly defining a clustering oriented loss. Though promising performance has been demonstrated in various applications, we observe that a vital ingredient has been overlooked by these work that the defined clustering loss may corrupt feature space, which leads to non-representative meaningless features and this in turn hurts clustering performance. To address this issue, in this paper, we propose the Improved Deep Embedded Clustering (IDEC) algorithm to take care of data structure preservation. Specifically, we manipulate feature space to scatter data points using a clustering loss as guidance. To constrain the manipulation and maintain the local structure of data generating distribution, an under-complete autoencoder is applied. By integrating the clustering loss and autoencoder's reconstruction loss, IDEC can jointly optimize cluster labels assignment and learn features that are suitable for clustering with local structure preservation. The resultant optimization problem can be effectively solved by mini-batch stochastic gradient descent and backpropagation. Experiments on image and text datasets empirically validate the importance of local structure preservation and the effectiveness of our algorithm.

Time series classification is an important task in time series data mining, and has attracted great interests and tremendous efforts during last decades. However, it remains a challenging problem due to the nature of time series data: high dimensionality, large in data size and updating continuously. The deep learning techniques are explored to improve the performance of traditional feature-based approaches. Specifically, a novel convolutional neural network (CNN) framework is proposed for time series classification. Different from other feature-based classification approaches, CNN can discover and extract the suitable internal structure to generate deep features of the input time series automatically by using convolution and pooling operations. Two groups of experiments are conducted on simulated data sets and eight groups of experiments are conducted on real-world data sets from different application domains. The final experimental results show that the proposed method outperforms state-of-the-art methods for time series classification in terms of the classification accuracy and noise tolerance.

Single-frame infrared small target (SIRST) detection aims at separating small targets from clutter backgrounds. With the advances of deep learning, CNN-based methods have yielded promising results in generic object detection due to their powerful modeling capability. However, existing CNN-based methods cannot be directly applied to infrared small targets since pooling layers in their networks could lead to the loss of targets in deep layers. To handle this problem, we propose a dense nested attention network (DNA-Net) in this paper. Specifically, we design a dense nested interactive module (DNIM) to achieve progressive interaction among high-level and low-level features. With the repetitive interaction in DNIM, the information of infrared small targets in deep layers can be maintained. Based on DNIM, we further propose a cascaded channel and spatial attention module (CSAM) to adaptively enhance multi-level features. With our DNA-Net, contextual information of small targets can be well incorporated and fully exploited by repetitive fusion and enhancement. Moreover, we develop an infrared small target dataset (namely, NUDT-SIRST) and propose a set of evaluation metrics to conduct comprehensive performance evaluation. Experiments on both public and our self-developed datasets demonstrate the effectiveness of our method. Compared to other state-of-the-art methods, our method achieves better performance in terms of probability of detection ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${P}_{d}$ </tex-math></inline-formula> ), false-alarm rate ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${F}_{a}$ </tex-math></inline-formula> ), and intersection of union ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$IoU$ </tex-math></inline-formula> ).