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VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder

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Genomics, Proteomics & Bioinformatics 2018年第5期16卷 320-331页

作者： dongfang wang Jin Gu MOE Key Laboratory of Bioinformatics BNRIST Bioinformatics Division & Center for Synthetic and Systems BiologyDepartment of Automation Tsinghua University

Single-cell RNA sequencing(scRNA-seq) is a powerful technique to analyze the transcriptomic heterogeneities at the single cell level. It is an important step for studying cell subpopulations and lineages, with an effective low-dimensional representation and visualization of the original scRNA-Seq data. At the single cell level, the transcriptional fluctuations are much larger than the average of a cell population, and the low amount of RNA transcripts will increase the rate of technical dropout events. Therefore, scRNA-seq data are much noisier than traditional bulk RNA-seq data. In this study, we proposed the deep variational autoencoder for scRNA-seq data(VASC), a deep multi-layer generative model, for the unsupervised dimension reduction and visualization of scRNA-seq data. VASC can explicitly model the dropout events and find the nonlinear hierarchical feature representations of the original data. Tested on over 20 datasets, VASC shows superior performances in most cases and exhibits broader dataset compatibility compared to four state-of-the-art dimension reduction and visualization methods. In addition, VASC provides better representations for very rare cell populations in the 2D visualization. As a case study, VASC successfully re-establishes the cell dynamics in pre-implantation embryos and identifies several candidate marker genes associated with early embryo development. Moreover, VASC also performs well on a 10× Genomics dataset with more cells and higher dropout rate.

关键词： Single cell RNA sequencing Deep variational autoencoder Dimension reduction Visualization Dropout

INFLUENCE OF THE MIDDLE WEAK LAYER ON THE IMPACT BEHAVIOR OF LAMINATED STRUCTURES

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Acta Mechanica Solida Sinica 2013年第3期26卷 263-276页

作者： dongfang wang Jialing Yang Yuxin Sun The Solid Mechanics Research Center Beijing University of Aeronautics and Astronautics

In this paper, a calculation model based on the subsection displacement theory and the large deflection analysis is developed to describe the dynamic response of isotropic laminated circular plates impacted by a soft body. The model takes into account the interlaminar shear effect induced by the middle weak layer. It is proved by numerical examples that the difference between the model developed in this paper and that based on the classical laminated theory mainly depends on three factors, the elastic modulus of the glue, the radius of the circular plate and the impact force.

关键词： laminated glass interlaminar shear stress subsection displacement theory lami-nated circular plate

Lightning Activity and Its Relation to the Intensity of Typhoons over the Northwest Pacific Ocean

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Advances in Atmospheric Sciences 2014年第3期31卷 581-592页

作者： PAN Lunxiang QIE Xiushu wang dongfang Key Laboratory of the Middle Atmosphere and Global Environment Observation Institute of Atmospheric Physics Chinese Academy of Sciences Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters Nanjing University of Information Science & Technology

ABSTRACT Data from the World Wide Lightning Location Network （WWLLN） were used to analyze the lightning activity and the relationship between maximum sustained wind and lightning rate in 69 tropical cyclones over the Northwest Pacific Ocean from 2005 to 2009. The minimum lightning density was observed in the category 2 typhoon Kong-Rey （2007）, with a value of only 1.15 d-1 （100 kin）-2. The maximum lightning density occurred in the category 2 typhoon Mitag （2007）, with a value of 510.42 d-1 （100 km）-2. The average lightning density decreased with radius from the typhoon center in both weak （categories 1-3） and super （categories 4-5） typhoons. The average lightning density in the inner core of super typhoons was more than twice as large as that for weak typhoons. Both groups of typhoons showed a near-monotonic decrease in lightning density with radius. Results also showed that lightning activity was more active in typhoons that made landfall than in those that did not. The mean correlation coefficient between the accumulated flashes within a 600-kin radius and the maximum wind speed in the weak typhoons and super typhoons was 0.81 and 0.74, respectively. For more than 78% （56%） of the super （weak） typhoons, the lightning activity peaked before the maximum sustained wind speed, with the most common leading time being 30 （60） h. The results suggest that, for the Northwest Pacific Ocean, lightning activity might be used as a measurement of the intensification of typhoons.

关键词： lightning typhoon intensity WWLLN

Integrative clustering methods of multi-omics data for molecule-based cancer classifications

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Frontiers of Electrical and Electronic Engineering in China 2016年第1期4卷 58-67页

作者： dongfang wang Jin Gu Ministry of Education Key Laboratory of Bioinformatics and Bioinformatics Division Center for Synthetic and Systems BiologyTsinghua National Laboratory for Information Science and Technology/Department of Automation Tsinghua University Beijing100084 China

One goal of precise oncology is to re-classify cancer based on molecular features rather than its tissue origin. Integrative clustering of large-scale multi-omics data is an important way for molecule-based cancer classification. The data heterogeneity and the complexity of inter-omics variations are two major challenges for the integrative clustering analysis. According to the different strategies to deal with these difficulties, we summarized the clustering methods as three major categories： direct integrative clustering, clustering of clusters and regulatory integrative clustering. A few practical considerations on data pre-processing, post-clustering analysis and pathway-based analysis arc also discussed.

关键词： clustering cancer classification omics integrative analysis

Spatial Pattern Evolution and Influencing Factors of Cold Storage in China

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Chinese Geographical Science 2020年第3期30卷 505-515页

作者： LI Jinfeng XU Haicheng LIU Wanwan wang dongfang ZHOU Shuang School of Economics and Management Chang'an UniversityXi'an 710064China School of Logistics and E-Commerce Henan University of Animal Husbandry and EconomyZhengzhou 450044China School of Management Zhengzhou Institute of Technol-ogyZhengzhou 450044China School of Business Wuyi UniversityWuyishan 354300China

Cold storage is the vital infrastructure of cold chain logistics. In this study, we analyzed the spatial pattern evolution characteristics, spatial autocorrelation and influencing factors of cold storage in China by using kernel density estimation(KDE), spatial autocorrelation analysis(SAA), and spatial error model(SEM). Results showed that: 1) the spatial distribution of cold storage in China is unbalanced, and has evolved from ‘one core’ to ‘one core and many spots’, that is, ‘one core’ refers to the Bohai Rim region mainly including Beijing, Tianjin, Hebei, Shandong and Liaoning regions, and ‘many spots’ mainly include the high-density areas such as Shanghai, Fuzhou, Guangzhou, Zhengzhou, Hefei, Wuhan, ürümqi. 2) The distribution of cold storage has significant global spatial autocorrelation and local spatial autocorrelation, and the ‘High-High’ cluster area is the most stable, mainly concentrated in the Bohai Rim;the ‘Low-Low’ cluster area is grouped in the southern China. 3) Economic development level, population density, traffic accessibility, temperature and land price, all affect the location choice of cold storage in varying degrees, while the impact of market demand on it is not explicit.

关键词： cold storage spatial pattern evolution kernel density estimation(KDE) spatial autocorrelation analysis(SAA) spatial error model(SEM) China

Global sources, emissions, transport and deposition of dust and sand and their effects on the climate and environment： a review

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Frontiers of Environmental Science & Engineering 2017年第1期11卷 35-43页

作者： Feng wang Xueqiu Zhao Cynthia Gerlein-Safdi Yue Mu dongfang wang Qi Lu Institute of Desertification Studies Chinese Academy of Forestry Beijing 100091 China School of Resources and Environment Anhui Agricultural University Hefei 230036 China Department of Civil and Environmental Engineering Princeton University Princeton NJ 08544 USA

Dust and Sand Storms （DSS） originating in deserts in arid and semi-arid regions are events raising global public concern. An important component of atmospheric aerosols, dust aerosols play a key role in climatic and environmental changes at the regional and the global scale. Deserts and semi-deserts are the main source of dust and sand, but regions that undergo vegetation deterioration and desertification due to climate change and human activities also contribute significantly to DSS. Dust aerosols are mainly composed of dust particles with an average diameter of 2 ***, which can be transported over thousands of kilometers. Dust aerosols influence the radiation budget of the earth- atmosphere system by scattering solar short-wave radiation and absorbing surface long-wave radiation. They can also change albedo and rainfall patterns because they can act as cloud condensation nuclei （CCN） or ice nuclei （IN）. Dust deposition is an important source of both marine nutrients and contaminants. Dust aerosols that enter marine ecosystems after long-distance transport influence phytoplankton biomass in the oceans, and thus global climate by altering the amount of CO2 absorbed by phytoplankton. In addition, the carbonates carried by dust aerosols are an important source of carbon for the alkaline carbon pool, which can buffer atmospheric acidity and increase the alkalinity of seawater. DSS have both positive and negative impacts on human society： they can exert adverse impacts on human＇s living environment, but can also contribute to the mitigation of global warming and the reduction of atmospheric acidity.

关键词： Dust and sand storm Climate effects Radiative forcing Cloud condensation nuclei Precipitation Iron fertilizer

Space debris environment engineering model 2019:Algorithms improvement and comparison with ORDEM 3.1 and MASTER-8

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Chinese Journal of Aeronautics 2024年第5期37卷 392-409页

作者： Yuyan LIU Runqiang CHI Baojun PANG HU Diqi Wuxiong CAO dongfang wang School of Astronautics Harbin Institute of TechnologyHarbin 150001China College of Safety Science&Engineering Civil Aviation University of ChinaTianjin 300300China

As an essential tool for realistic description of the current or future debris environment,the Space Debris Environment Engineering Model(SDEEM)has been developed to provide support for risk assessment of *** contrast with SDEEM2015,SDEEM2019,the latest version,extends the orbital range from the Low Earth Orbit(LEO)to Geosynchronous Orbit(GEO)for the years *** this paper,improved modeling algorithms used by SDEEM2019 in propagating simulation,spatial density distribution,and spacecraft flux evaluation are *** debris fluxes of SDEEM2019 are compared with those of three typical models,i.e.,SDEEM2015,Orbital Debris Engineering Model 3.1(ORDEM 3.1),and Meteoroid and Space Debris Terrestrial Environment Reference(MASTER-8),in terms of two assessment *** orbital cases,including the Geostationary Transfer Orbit(GTO),Sun-Synchronous Orbit(SSO)and International Space Station(ISS)orbit,are selected for the spacecraft assessment mode,and the LEO region is selected for the spatial density assessment *** analysis indicates that compared with previous algorithms,the variable step-size orbital propagating algorithm based on semi-major axis control is more precise,the spatial density algorithm based on the second zonal harmonic of the non-spherical Earth gravity(J_(2))is more applicable,and the result of the position-centered spacecraft flux algorithm is more *** comparison shows that SDEEM2019 and MASTER-8 have consistent trends due to similar modeling processes,while the differences between SDEEM2019 and ORDEM 3.1 are mainly caused by different modeling approaches for uncatalogued debris.

关键词： SDEEM2019 Space debris propagating algorithm Spatial density algorithm ORDEM 3.1 MASTER-8

The lightning activities in super typhoons over the Northwest Pacific

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Science China Earth Sciences 2010年第8期53卷 1241-1248页

作者： PAN LunXiang QIE XiuShu LIU DongXia wang dongfang YANG Jing LAGEO Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China Graduate University of Chinese Academy of Sciences Beijing 100049China

The spatial and temporal characteristics of lightning activities have been studied in seven super typhoons from 2005 to 2008 over the Northwest Pacific, using data from the World Wide Lightning Location Network (WWLLN). The results indicated that there were three distinct lightning flash regions in mature typhoon, a significant maximum in the eyewall regions (20-80 km from the center), a minimum from 80-200 km, and a strong maximum in the outer rainbands (out of 200 km from the center). The lightning flashes in the outer rainbands were much more than those in the inner rainbands, and less than 1% of flashes occurred within 100 km of the center. Each typhoon produced eyewall lightning outbreak during the periods of its intensification, usually several hours prior to its maximum intensity, indicating that lightning activity might be used as a proxy of intensification of super typhoon. Little lightning occurred near the center after landing of the typhoon.

关键词： super typhoon lightning WWLLN the Northwest Pacific

Monitoring strata behavior due to multi-slicing top coal caving longwall mining in steeply dipping extra thick coal seam

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International Journal of Mining Science and Technology 2017年第1期27卷 179-184页

作者： Yun Dongfeng Liu Zhu Cheng Wendong Fan Zhendong wang dongfang Zhang Yuanhao CoUege of Energy Xi'an University of Science and TechnologyXi'an 710054China Ministry of Education Key Laboratory of Western Mine Exploitation and Hazard Prevention Xi'an University of Science and TechnologyXi'an 710054China College of Architecture and Civil Engineering Xi'an University of Science and TechnologyXi'an 710054China Huating Coal Group Co. Ltd.Huating 744100China Dongxia Coal Mine Huating Coal Group Co.Ltd.Huating 744100China

For studying the strata behavior due to multi-slicing top coal caving longwall mining along-the-strike direction in steeply dipping extra thick coal seams,the shield support pressures of the upper and lower slices of panel 37220 in Dongxia Coal Mine were monitored using the KJ513 dynamic monitoring *** set up rooms adopted the "horizontal line-arc segment-inclined line" form and used different types of shield *** results show that the strata pressure of upper slice panel 37220-1 changed slightly along the strike direction,while along the dip direction it exhibited strong to weak pressure from bottom to *** first weighting interval of lower slice panel 37220-2 was about 60.8 m,and the average periodic weighting interval were about 22.6 *** strata behavior of panel 37220-2 exhibited a spatiotemporal characteristic in that periodic weighting occurred first in the middle-upper part,followed by the middle and upper parts,arc segment,and finally the lower *** the periodic weighting,the weighting interval and intensity also exhibited strong space *** average dynamic load coefficient was 1.48 and the maximum lateral load of the side shield was 20-25 MPa.

关键词： Monitoring Steeply dipping seam Slicing Longwall along the strike Fully mechanized top-caving face Strata behavior