In the template-based modeling (TBM) category of CASP10 experiment, we introduced a new protocol called protein modeling system (PMS) to generate accurate protein structures in terms of side-chains as well as backbone trace. In the new protocol, a global optimization algorithm, called conformational space annealing (CSA), is applied to the three layers of TBM procedure: multiple sequence-structure alignment, 3D chain building, and side-chain re-modeling. For 3D chain building, we developed a new energy function which includes new distance restraint terms of Lorentzian type (derived from multiple templates), and new energy terms that combine (physical) energy terms such as dynamic fragment assembly (DFA) energy, DFIRE statistical potential energy, hydrogen bonding term, etc. These physical energy terms are expected to guide the structure modeling especially for loop regions where no template structures are available. In addition, we developed a new quality assessment method based on random forest machine learning algorithm to screen templates, multiple alignments, and final models. For TBM targets of CASP10, we find that, due to the combination of three stages of CSA global optimizations and quality assessment, the modeling accuracy of PMS improves at each additional stage of the protocol. It is especially noteworthy that the side-chains of the final PMS models are far more accurate than the models in the intermediate steps.
A correction method using machine learning aims to improve the conventional linear regression (LR) based method for correction of atmospheric pressure data obtained by smartphones. The method proposed in this study conducts clustering and regression analysis with time domain classification. Data obtained in Gyeonggi-do, one of the most populous provinces in South Korea surrounding Seoul with the size of 10,000 km2, from July 2014 through December 2014, using smartphones were classified with respect to time of day (daytime or nighttime) as well as day of the week (weekday or weekend) and the user's mobility, prior to the expectation-maximization (EM) clustering. Subsequently, the results were analyzed for comparison by applying machine learning methods such as multilayer perceptron (MLP) and support vector regression (SVR). The results showed a mean absolute error (MAE) 26% lower on average when regression analysis was performed through EM clustering compared to that obtained without EM clustering. For machine learning methods, the MAE for SVR was around 31% lower for LR and about 19% lower for MLP. It is concluded that pressure data from smartphones are as good as the ones from national automatic weather station (AWS) network.
Severe weather events occur more frequently due to climate change; therefore, accurate weather forecasts are necessary, in addition to the development of numerical weather prediction (NWP) of the past several decades. A method to improve the accuracy of weather forecasts based on NWP is the collection of more meteorological data by reducing the observation interval. However, in many areas, it is economically and locally difficult to collect observation data by installing automatic weather stations (AWSs). We developed a Mini-AWS, much smaller than AWSs, to complement the shortcomings of AWSs. The installation and maintenance costs of Mini-AWSs are lower than those of AWSs; Mini-AWSs have fewer spatial constraints with respect to the installation than AWSs. However, it is necessary to correct the data collected with Mini-AWSs because they might be affected by the external environment depending on the installation area. In this paper, we propose a novel error correction of atmospheric pressure data observed with a Mini-AWS based on machine learning. Using the proposed method, we obtained corrected atmospheric pressure data, reaching the standard of the World Meteorological Organization (WMO; ±0.1 hPa), and confirmed the potential of corrected atmospheric pressure data as an auxiliary resource for AWSs.
The Monte-Carlo method is adopted to define the roughness of the mask structure. A random surface height variation described by power spectral density for the rough surfaces of an extreme ultraviolet (EUV) mask is redefined in order to calculate the field in the image plane. A general explicit formula of the scattering, which is analogous to Feynman's approach, is derived, and it is adapted to the EUV mask structure to evaluate the effect of the surface roughness of the side wall of the mask topography on the image formation. The multiple random scattering problems are dealt with the different pattern types, which are an isolated pattern and a dense pattern, in order to compare field variations in phase and amplitude with the ideal flat surface.
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