What country, university or research institute, performed the best on COVID-19? Bibliometric analysis of scientific literature

In this article, we conduct data mining to discover the countries, universities and companies, produced or collaborated the most research on Covid-19 since the pandemic started. We present some interesting findings, but despite analysing all available records on COVID-19 from the Web of Science Core Collection, we failed to reach any significant conclusions on how the world responded to the COVID-19 pandemic. Therefore, we increased our analysis to include all available data records on pandemics and epidemics from 1900 to 2020. We discover some interesting results on countries, universities and companies, that produced collaborated most the most in research on pandemic and epidemics. Then we compared the results with the analysing on COVID-19 data records. This has created some interesting findings that are explained and graphically visualised in the article

Microbial community pattern detection in human body habitats via ensemble clustering framework

The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural patterns. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. Such trends depict an integrated biography of microbial communities, which offer a new insight towards uncovering pathogenic model of human microbiome.Comment: BMC Systems Biology 201

Oversampling for Imbalanced Learning Based on K-Means and SMOTE

Learning from class-imbalanced data continues to be a common and challenging problem in supervised learning as standard classification algorithms are designed to handle balanced class distributions. While different strategies exist to tackle this problem, methods which generate artificial data to achieve a balanced class distribution are more versatile than modifications to the classification algorithm. Such techniques, called oversamplers, modify the training data, allowing any classifier to be used with class-imbalanced datasets. Many algorithms have been proposed for this task, but most are complex and tend to generate unnecessary noise. This work presents a simple and effective oversampling method based on k-means clustering and SMOTE oversampling, which avoids the generation of noise and effectively overcomes imbalances between and within classes. Empirical results of extensive experiments with 71 datasets show that training data oversampled with the proposed method improves classification results. Moreover, k-means SMOTE consistently outperforms other popular oversampling methods. An implementation is made available in the python programming language.Comment: 19 pages, 8 figure