scholarly journals Robust principal component analysis‐based prediction of protein‐protein interaction hot spots

Author(s):  
Divya Sitani ◽  
Alejandro Giorgetti ◽  
Mercedes Alfonso‐Prieto ◽  
Paolo Carloni
2021 ◽  
Vol 3 (2) ◽  
pp. 25-34
Author(s):  
Hilmi Farhan Ramadhani ◽  
Annisa ◽  
Wisnu Ananta Kusuma

Coronavirus Disease 2019 (COVID-19) will cause disease complications and organ damage due to excessive inflammatory reactions if left untreated. Computational analysis of protein-protein interactions can be carried out in various ways, including topological analysis and clustering of protein-protein interaction networks. Topological analysis can identify significant proteins by measuring the most important nodes with centrality measurements. By using Principal Component Analysis (PCA), the types of centrality measures were extracted into the overall centrality value. The study aimed to found significant proteins in COVID-19 protein-protein interactions using PCA and ClusterONE. This study used 57 proteins associated with COVID-19 to obtain protein networks. All of these proteins are homo sapiens organism. The number of proteins and the number of interactions from 57 proteins were 357 proteins and 1686 interactions. The results of this study consisted of two clusters; the best cluster was the first cluster with a lower p-value but had an average overall centrality value that closed to the second clus-ter. There are twenty important proteins in that cluster, and all of these proteins are related to COVID-19. These proteins are expected to be used in the process of discovering medicinal compounds in COVID-19


Energies ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 196 ◽  
Author(s):  
Lihui Zhang ◽  
Riletu Ge ◽  
Jianxue Chai

China’s energy consumption issues are closely associated with global climate issues, and the scale of energy consumption, peak energy consumption, and consumption investment are all the focus of national attention. In order to forecast the amount of energy consumption of China accurately, this article selected GDP, population, industrial structure and energy consumption structure, energy intensity, total imports and exports, fixed asset investment, energy efficiency, urbanization, the level of consumption, and fixed investment in the energy industry as a preliminary set of factors; Secondly, we corrected the traditional principal component analysis (PCA) algorithm from the perspective of eliminating “bad points” and then judged a “bad spot” sample based on signal reconstruction ideas. Based on the above content, we put forward a robust principal component analysis (RPCA) algorithm and chose the first five principal components as main factors affecting energy consumption, including: GDP, population, industrial structure and energy consumption structure, urbanization; Then, we applied the Tabu search (TS) algorithm to the least square to support vector machine (LSSVM) optimized by the particle swarm optimization (PSO) algorithm to forecast China’s energy consumption. We collected data from 1996 to 2010 as a training set and from 2010 to 2016 as the test set. For easy comparison, the sample data was input into the LSSVM algorithm and the PSO-LSSVM algorithm at the same time. We used statistical indicators including goodness of fit determination coefficient (R2), the root means square error (RMSE), and the mean radial error (MRE) to compare the training results of the three forecasting models, which demonstrated that the proposed TS-PSO-LSSVM forecasting model had higher prediction accuracy, generalization ability, and higher training speed. Finally, the TS-PSO-LSSVM forecasting model was applied to forecast the energy consumption of China from 2017 to 2030. According to predictions, we found that China shows a gradual increase in energy consumption trends from 2017 to 2030 and will breakthrough 6000 million tons in 2030. However, the growth rate is gradually tightening and China’s energy consumption economy will transfer to a state of diminishing returns around 2026, which guides China to put more emphasis on the field of energy investment.


2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Isabel Scherl ◽  
Benjamin Strom ◽  
Jessica K. Shang ◽  
Owen Williams ◽  
Brian L. Polagye ◽  
...  

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