Multiobjective deep clustering and its applications in single-cell RNA-seq data

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.Single-cell RNA sequencing is a transformative technology that enables us to study the heterogeneity of the tissue at the cellular level. Clustering is used as the key computational approach to group cells under the transcriptome profiles from single-cell RNA-seq data. However, accurate identification of distinct cell types is facing the challenge of high dimensionality, and it could cause uninformative clusters when clustering is directly applied on the original transcriptome. To address such challenge, an evolutionary multiobjective deep clustering (EMDC) algorithm is proposed to identify single-cell RNA-seq data in this study. First, EMDC removes redundant and irrelevant genes by applying the differential gene expression analysis to identify differentially expressed genes across biological conditions. After that, a deep autoencoder is proposed to project the high-dimensional data into different low-dimensional nonlinear embedding subspaces under different bottleneck layers. Then, the basic clustering algorithm is applied in those nonlinear embedding subspaces to generate some basic clustering results to produce the cluster ensemble. To lessen the unnecessary cost produced by those clusterings in the ensemble, the multiobjective evolutionary optimization is designed to prune the basic clustering results in the ensemble, unleashing its cell type discovery performance under three objective functions. Multiple experiments have been conducted on 30 synthetic single-cell RNA-seq datasets and six real single-cell RNA-seq datasets, which reveal that EMDC outperforms eight other clustering methods and three multiobjective optimization algorithms in cell type identification. In addition, we have conducted extensive comparisons to effectively demonstrate the impact of each component in our proposed EMDC

Scheme for the implementation of a universal quantum cloning machine via cavity-assisted atomic collisions in cavity QED

We propose a scheme to implement the $1\to2$ universal quantum cloning machine of Buzek et.al [Phys. Rev.A 54, 1844(1996)] in the context of cavity QED. The scheme requires cavity-assisted collision processes between atoms, which cross through nonresonant cavity fields in the vacuum states. The cavity fields are only virtually excited to face the decoherence problem. That's why the requirements on the cavity quality factor can be loosened.Comment: to appear in PR

mTORC1 signaling facilitates differential stem cell differentiation to shape the developing murine lung and is associated with mitochondrial capacity

Formation of branched organs requires sequential differentiation of stem cells. In this work, we find that the conducting airways derived from SOX2+ progenitors in the murine lungs fail to form without mTOR complex 1 (mTORC1) signaling and are replaced by lung cysts. Proximal-distal patterning through transitioning of distal SOX9+ progenitors to proximal SOX2+ cells is disrupted. Mitochondria number and ATP production are reduced. Compromised mitochondrial capacity results in a similar defect as that in mTORC1-deficient lungs. This suggests that mTORC1 promotes differentiation of SOX9+ progenitors to form the conducting airways by modulating mitochondrial capacity. Surprisingly, in all mutants, saccules are produced from lung cysts at the proper developmental time despite defective branching. SOX9+ progenitors also differentiate into alveolar epithelial type I and type II cells within saccules. These findings highlight selective utilization of energy and regulatory programs during stem cell differentiation to produce distinct structures of the mammalian lungs

The valuation of contingent claims using alternative numerical methods

This study compares the computational accuracy and efficiency of three numerical methods for the valuation of contingent claims written on multiple underlying assets; these are the trinomial tree, original Markov chain and Sobol-Markov chain approaches. The major findings of this study are: (i) the original Duan and Simonato (2001) Markov chain model provides more rapid convergence than the trinomial tree method, particularly in cases where the time to maturity period is less than nine months; (ii) when pricing options with longer maturity periods or with multiple underlying assets, the Sobol-Markov chain model can solve the problem of slow convergence encountered under the original Duan and Simonato (2001) Markov chain method; and (iii) since conditional density is used, as opposed to conditional probability, we can easily extend the Sobol-Markov chain model to the pricing of derivatives which are dependent on more than two underlying assets without dealing with high-dimensional integrals. We also use 'executive stock options' (ESOs) as an example to demonstrate that the Sobol-Markov chain method can easily be applied to the valuation of such ESOs.Trinomial tree method Markov chain methods Low-discrepancy Multivariate contingent claims Executive stock options

Investigation of the interactive, intimidating relation between urbanization and the environment in an arid area based on grey system theory

Taking the Hexi Corridor in western China as an example, this paper studies the interactive intimate i relation between urbanization and the environment in arid areas based on the grey system theory. The results show that the grey relational degree between urbanization and the environment is low in the agriculture-oriented cities, modest in the tourism-oriented cities and great in the industry-oriented cities. The changing trend of coupling degree between urbanization and the environment does not entirely agree with that of urbanization or the environment. It showed fluctuating trends, which reflects the compactness and properties of the different stages of the coupling states between urbanization and the environment. In order to achieve a harmonious development with the environment in arid areas, traditional development ideas about urbanization should be revised and more attention should be paid to the effect of restriction of water resources and the ecological environment on the development of the economy and society

Phase offset method of ptychographic contrast reversal correction

Abstract: The contrast transfer function of direct ptychography methods such as the single side band (SSB) method are single signed, yet these methods still sometimes exhibit contrast reversals, most often where the projected potentials are strong. In thicker samples central focusing often provides the best ptychographic contrast as this leads to defocus variations within the sample canceling out. However focusing away from the entrance surface is often undesirable as this degrades the annular dark field (ADF) signal. Here we discuss how phase wrap asymptotes in the frequency response of SSB ptychography give rise to contrast reversals, without the need for dynamical scattering, and how these can be counteracted by manipulating the phases such that the asymptotes are either shifted to higher frequencies or damped via amplitude modulation. This is what enables post collection defocus correction of contrast reversals. However, the phase offset method of counteracting contrast reversals we introduce here is generally found to be superior to post collection application of defocus, with greater reliability and generally stronger contrast. Importantly, the phase offset method also works for thin and thick samples where central focusing does not. Finally, the independence of the method from focus is useful for optical sectioning involving ptychography, improving interpretability by better disentangling the effects of strong potentials and focus

Investigation of Traffic Loading Effects for Different Codes on Medium- and Small-Span Girder Bridges in China

With increasing traffic volume, the traffic load grade given by design codes has gradually increased. For new bridges, there is no problem, and the traffic load can be met through the requirements of the new code. However, for existing bridges, there is a lack of uniform standards on whether they can continue to be used. It is not clear whether these bridges will be judged according to the new code or the original design code. The traffic loading effects of different codes on medium- and small-span girder bridges in China are investigated in this study. Three codes are introduced: JTJ 021-89, JTG D60-2004, and JTG D60-2015. Simply supported girder bridges and continuous girder bridges are discussed. The traffic loading effects calculated based on JTG D60-2015 are significantly larger than those calculated based on JTJ 021-89. For simply supported girder bridges, most of the differences range from 20% to 40%, and the maximum value is almost larger than 60%. For continuous girder bridges, most of the differences in the positive bending moments are concentrated in the 20%∼40% range, while the differences in the negative bending moments range from 10% to 20%. Therefore, the differences in traffic loading effects calculated based on various codes cannot be ignored in actual bridge engineering. The conclusion in this study can provide a basis for bridge structure evaluation and life prediction

Marine gravimetry and Its improvements to seafloor topography estimation in the southwestern coastal area of the Baltic Sea

Marine gravimetry provides high-quality gravity measurements, particularly in coastal areas. After the update of new sensors in GFZ’s air-marine gravimeter Chekan-AM, gravimetry measurements showed a significant improvement from the first new campaign DENEB2017 with an accuracy of 0.3/2–√=0.21 mGal @ 1 km along the tracks, which is at the highest accuracy level of marine gravimetry. Then, these measurements were used to assess gravity data derived from satellite altimetry (about 3 mGal) and a new finding is that a bias of −1.5 mGal exists in the study area. Additionally, ship soundings were used to assess existing seafloor topography models. We found that the accuracy of SRTM model and SIO model is at a level of 2 m, while the accuracy of the regional model EMODnet reaches the lever of sub-meters. Furthermore, a bias of 0.7 m exists and jumps above 5 m in the SRTM model near the coast of Sweden. Finally, new combined gravity anomalies with sounding data are used to reveal the fine structure of ocean topography. Our estimated seafloor topography model is more accurate than existing digital elevation data sets such as EMODnet, SRTM and SIO models and, furthermore, shows some more detailed structure of seafloor topography. The marine gravimetry and sounding measurements as well as the estimated seafloor topography are crucial for future geoid determination, 3D-navigation and resource exploration in the Baltic Sea

Comprehensive Studies on Using the Richardson extrapolation techniques for Pricing American options under Alternative Stochastic Processes

[[abstract]]Following from the innovation of Geske and Johnson (1984), the Richardson extrapolation technique is frequently used to price American options. Therefore it is very nature for one to ask the following questions: Is it always appropriate to use the Richardson extrapolation technique to value American options? In this study, we try to answer the above critical issue by investigating the valuation of American options using the Richardson extrapolation technique under alternative stochastic processes. Additionally, following from Chang, Chung and Stapleton (2007), we apply the Repeated-Richardson extrapolation method to estimate the interval of true American option values and to determine the number of options needed for an approximation to achieve a given desired accuracy. We then test the feasibility of the estimated error bounds of the American options under alternative stochastic processes as well. Our numerical results show that on average the Repeated-Richardson extrapolation technique outperforms the Richardson extrapolation technique for the valuation of American options under alternative stochastic processes