Feature vector clustering molecular pairs in computer simulations

A clustering framework is introduced to analyze the microscopic structural organization of molecular pairs in liquids and solutions. A molecular pair is represented by a representative vector (RV). To obtain RV, intermolecular atom distances in the pair are extracted from simulation trajectory as components of the key feature vector (KFV). A specific scheme is then suggested to transform KFV to RV by removing the influence of permutational molecular symmetry on the KFV as the predicted clusters should be independent of possible permutations of identical atoms in the pair. After RVs of pairs are obtained, a clustering analysis technique is finally used to classify all the RVs of molecular pairs into the clusters. The framework is applied to analyze trajectory from molecular dynamics simulations of an ionic liquid (trihexyltetradecylphosphonium bis(oxalato)borate ([P_6,6,6,14][BOB])). The molecular pairs are successfully categorized into physically meaningful clusters, and their effectiveness is evaluated by computing the product moment correlation coefficient (PMCC). (Willett, Winterman, and Bawden, J. Chem. Inf. Comput. Sci. 1986, 26, 109–118; Downs, Willett, and Fisanick, J. Chem. Inf. Comput. Sci. 1994, 34, 1094–1102) It is observed that representative configurations of two clusters are related to two energy local minimum structures optimized by density functional theory (DFT) calculation, respectively. Several widely used clustering analysis techniques of both nonhierarchical (k-means) and hierarchical clustering algorithms are also evaluated and compared with each other. The proposed KFV technique efficiently reveals local molecular pair structures in the simulated complex liquid. It is a method, which is highly useful for liquids and solutions in particular with strong intermolecular interactions. © 2019 Wiley Periodicals, Inc.     

Code2vect: An efficient heterogenous data classifier and nonlinear regression technique

The aim of this paper is to present a new classification and regression algorithm based on Artificial Intelligence. The main feature of this algorithm, which will be called Code2Vect, is the nature of the data to treat: qualitative or quantitative and continuous or discrete. Contrary to other artificial intelligence techniques based on the “Big-Data,” this new approach will enable working with a reduced amount of data, within the so-called “Smart Data” paradigm. Moreover, the main purpose of this algorithm is to enable the representation of high-dimensional data and more specifically grouping and visualizing this data according to a given target. For that purpose, the data will be projected into a vectorial space equipped with an appropriate metric, able to group data according to their affinity (with respect to a given output of interest). Furthermore, another application of this algorithm lies on its prediction capability. As it occurs with most common data-mining techniques such as regression trees, by giving an input the output will be inferred, in this case considering the nature of the data formerly described. In order to illustrate its potentialities, two different applications will be addressed, one concerning the representation of high-dimensional and categorical data and another featuring the prediction capabilities of the algorithm.     

Data assimilation and pollution forecasting in Burgers' equation with model error function

This article presents a correction method for a better resolution of the problem of estimating and predicting pollution, governed by Burgers' equations. The originality of the method consists in the introduction of an error function into the system's equations of state to model uncertainty in the model. The initial conditions and diffusion coefficients, present in the equations for pollution and concentration, and also those in the model error equations, are estimated by solving a data assimilation problem. The efficiency of the correction method is compared with that produced by the traditional method without introduction of an error function.Three test cases are presented in this study in order to compare the performances of the proposed methods. In the first two tests, the reference is the analytical solution and the last test is formulated as part of the “twin experiment”.The numerical results obtained confirm the important role of the model error equation for improving the prediction capability of the system, in terms of both accuracy and speed of convergence.     

“对比实验+现象驱动的知识挖掘”在高分子材料合成创新实验教学中的尝试与运用

高分子材料合成实验是高分子专业的核心实验课程之一，如何建立实验课程与理论课程的有效衔接，加深学生对所学知识点的深入理解和活学活用，是本课程的主要目标。为此，笔者和教学团队提出：在同一个实验中改变某个实验变量，在教学班中引入对比实验，通过这些改变引起的不同实验现象和由此产生的材料性能的迥然差异，引导学生从现象出发，联系理论课堂知识进行深入分析。这种尝试有效改变了以往实验教学中所有教学班千篇一律的操作和几乎完全相同的实验现象与结果，有效激发了学生的主动性，提高了其分析问题、解决问题的能力。2年的实验教学反馈表明，“对比实验的引入”和“现象驱动的知识挖掘”帮助学生有效巩固了理论课堂的知识点，做到了活学活用。     

苗族服饰色彩体系构建研究

色彩是民族服饰的核心要素，也是民族文化元素的重要组成部分，构建一套兼具科学性与实用性的色彩体系极具挑战性。在传统色彩地理学方法基础上，通过提取主题色和改进的关联规则挖掘方法，获取色彩数据、寻找色彩规则，并对其进行自然色彩体系（NCS）编谱分析，构建了一套苗族服饰色彩体系（Miao’s costume color system,MCCS）。该体系有助于进一步挖掘苗族服饰的配色规律，实现对苗族服饰色彩的数字化保护，为民族服饰色彩传承机理的探索与研究提供新的思路。     

Oak-Associated Negativicute Equipped with Ancestral Aromatic Polyketide Synthase Produces Antimycobacterial Dendrubins

Anaerobic bacteria have only recently been recognized as a source of antibiotics; yet, the metabolic potential of Negativicutes (Gram-negative staining Firmicutes) such as the oak-associated Dendrosporobacter quercicolus has remained unknown. Genome mining of D. quercicolus and phylogenetic analyses revealed a gene cluster for a type II polyketide synthase (PKS) complex that belongs to the most ancestral enzyme systems of this type. Metabolic profiling, NMR analyses, and stable-isotope labeling led to the discovery of a new family of anthraquinone-type polyphenols, the dendrubins, which are diversified by acylation, methylation, and dimerization. Dendrubin A and B were identified as strong antibiotics against a range of clinically relevant, human-pathogenic mycobacteria.     

Data fusion methodologies for food and beverage authentication and quality assessment – A review

The ever increasing interest of consumers for safety, authenticity and quality of food commodities has driven the attention towards the analytical techniques used for analyzing these commodities. In recent years, rapid and reliable sensor, spectroscopic and chromatographic techniques have emerged that, together with multivariate and multiway chemometrics, have improved the whole control process by reducing the time of analysis and providing more informative results. In this progression of more and better information, the combination (fusion) of outputs of different instrumental techniques has emerged as a means for increasing the reliability of classification or prediction of foodstuff specifications as compared to using a single analytical technique. Although promising results have been obtained in food and beverage authentication and quality assessment, the combination of data from several techniques is not straightforward and represents an important challenge for chemometricians. This review provides a general overview of data fusion strategies that have been used in the field of food and beverage authentication and quality assessment.     

Missing value imputation strategies for metabolomics data

The origin of missing values can be caused by different reasons and depending on these origins missing values should be considered differently and dealt with in different ways. In this research, four methods of imputation have been compared with respect to revealing their effects on the normality and variance of data, on statistical significance and on the approximation of a suitable threshold to accept missing data as truly missing. Additionally, the effects of different strategies for controlling familywise error rate or false discovery and how they work with the different strategies for missing value imputation have been evaluated. Missing values were found to affect normality and variance of data and k‐means nearest neighbour imputation was the best method tested for restoring this. Bonferroni correction was the best method for maximizing true positives and minimizing false positives and it was observed that as low as 40% missing data could be truly missing. The range between 40 and 70% missing values was defined as a “gray area” and therefore a strategy has been proposed that provides a balance between the optimal imputation strategy that was k‐means nearest neighbor and the best approximation of positioning real zeros.