Rivality index neighbourhood algorithm with density and distances weighted schemes for the building of robust QSAR classification models with high reliable applicability domain

The rivality index (RI) is a normalized distance measurement between a molecule and their first nearest neighbours providing a robust prediction of the activity of a molecule based on the known activity of their nearest neighbours. Negative values of the RI describe molecules that would be correctly classified by a statistic algorithm and, vice versa, positive values of this index describe those molecules detected as outliers by the classification algorithms. In this paper, we have described a classification algorithm based on the RI and we have proposed four weighted schemes (kernels) for its calculation based on the measuring of different characteristics of the neighbourhood of molecules for each molecule of the dataset at established values of the threshold of neighbours. The results obtained have demonstrated that the proposed classification algorithm, based on the RI, generates more reliable and robust classification models than many of the more used and well-known machine learning algorithms. These results have been validated and corroborated by using 20 balanced and unbalanced benchmark datasets of different sizes and modelability. The classification models generated provide valuable information about the molecules of the dataset, the applicability domain of the models and the reliability of the predictions.     

Variable selection for multivariate calibration using a genetic algorithm: prediction of additive concentrations in polymer films from Fourier transform-infrared spectral data

Variable selection using a genetic algorithm is combined with partial least squares (PLS) for the prediction of additive concentrations in polymer films using Fourier transform-infrared (FT-IR) spectral data. An approach using an iterative application of the genetic algorithm is proposed. This approach allows for all variables to be considered and at the same time minimizes the risk of overfitting. We demonstrate that the variables selected by the genetic algorithm are consistent with expert knowledge. This very exciting result is a convincing application that the algorithm can select correct variables in an automated fashion.     

A genetic algorithm for the automated generation of small organic molecules: Drug design using an evolutionary algorithm

Rational drug design involves finding solutions to large combinatorial problems for which an exhaustive search is impractical. Genetic algorithms provide a novel tool for the investigation of such problems. These are a class of algorithms that mimic some of the major characteristics of Darwinian evolution. LEA has been designed in order to conceive novel small organic molecules which satisfy quantitative structure-activity relationship based rules (fitness). The fitness consists of a sum of constraints that are range properties. The algorithm takes an initial set of fragments and iteratively improves them by means of crossover and mutation operators that are related to those involved in Darwinian evolution. The basis of the algorithm, its implementation and parameterization, are described together with an application in de novo molecular design of new retinoids. The results may be promising for chemical synthesis and show that this tool may find extensive applications in de novo drug design projects.     

Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency

In the replica-permutation method, an advanced version of the replica-exchange method, all combinations of replicas and parameters are considered for parameter permutation, and a list of all the combinations is prepared. Here, we report that the temperature transition probability depends on how the list is created, especially in replica permutation with solute tempering (RPST). We found that the transition probabilities decrease at large replica indices when the combinations are sequentially assigned to the state labels as in the originally proposed list. To solve this problem, we propose to modify the list by randomly assigning the combinations to the state labels. We performed molecular dynamics simulations of amyloid-β(16–22) peptides using RPST with the “randomly assigned” list (RPST-RA) and RPST with the “sequentially assigned” list (RPST-SA). The results show the decreases in the transition probabilities in RPST-SA are eliminated, and the sampling efficiency is improved in RPST-RA.     

基于改进免疫遗传算法的近红外光谱变量选择方法

该文在免疫遗传算法（IGA）的基础上,提出一种改进免疫遗传算法（iIGA）用于近红外光谱波长变量的选择。该算法舍去了原算法中固定抗体相似度阈值的思想,取而代之的是抗体相似度阈值自适应,同时引入精英保留策略和贪心算法思想,使得算法朝着正确的方向进行局部性探优。将该算法在玉米的淀粉和蛋白质含量数据集上进行实验测试,建立偏最小二乘（PLS）分析模型,并与IGA、遗传算法（GA）以及全谱方法进行了对比。结果表明,在玉米淀粉含量的预测上,iIGA相较于原IGA算法,预测集均方根误差（RMSEP）从0.312 0降至0.298 0,预测集预测精度提升4.5%;在玉米蛋白质含量的预测上,RMSEP从0.124 4降至0.110 3,预测集预测精度提升11.3%。分别对预测淀粉和蛋白质模型的RMSEP值进行显著性检验,F值分别为165.22和182.05,P值分别为9.5 × 10－23和4.5 × 10－24,P值均小于0.05,因此,iIGA能显著提升模型预测精度。     

基于内源性致香物质和化学计量学的烟草感官评价研究

采用主成分分析法结合遗传算法和神经网络,建立了基于烟草内源性致香物质的感官质量评价预测模型。利用气相色谱-质谱(GC-MS)技术对超临界萃取-分子蒸馏所得烟草精油中的内源性致香组分进行定性定量分析,汇总各类致香指标后,对其进行主成分分析;以提取所得5个主成分的得分作为输入变量,感官评吸分数作为输出变量,分别使用标准BP神经网络和遗传算法(GA)优化的BP神经网络建立预测模型。对比实验结果表明,GA优化后的模型预测效果更优,其预测值与实验值间的相关系数为0.96,预测均方根误差为1.81,说明GA-BP模型具有更好的拟合能力和预测能力,该模型能有效地预测烟草精油的感官品质。     

基于ME算法的RS译码器的原理和FPGA实现

RS（Reed—Solomon）码是具有很强纠错能力的线性分组码,广泛应用于各种通信和存储系统中。文中设计的译码器采用修正的欧几里德算法（MEA）,并在实现中采用公共项提取算法有效地优化了乘法器,以迭代、复用等方法降低了RS码译码硬件实现的复杂度。并用Verilog-HDL语言实现了RS（255,239）码的译码器各个模块的功能。     

精密温控对惯性导航平台系统性能的影响

分析惯性平台温度控制与惯性导航系统精度的关系.提出一种实用的惯性平台温度控制方法,即根据大环境温度和被控对象温度合理选择温度控制点、控制方式和控制算法.研究系统有温控、无温控、长时温控和短时温控对平台综合性能的影响.试验结果表明,系统在陀螺级具有速度快、精度高等优点,为解决惯导系统启动后缩短惯性器件热平衡过程,迅速进入稳定工作状态问题提供了一种实用方法,也为类似的惯导温度控制系统提供了有益的参考.     

基于高通量解析算法的复杂样品重叠气相色谱-质谱信号的快速分析

化学计量学算法为重叠气相色谱-质谱(GC-MS)信号的解析提供了有效手段,但其在计算过程中一般需要将数据进行分段处理,然后只对信号的某些区间进行解析,难以实现真正意义上的高通量分析。该文结合移动窗口目标转换因子分析(MWTTFA)和非负免疫算法(NNIA),建立了一种高通量解析方法。首先,根据所有可能存在的目标组分的标准质谱信息,利用MWTTFA检验复杂信号中存在的组分,并确定目标组分的质谱信息和洗脱时间区域。以得到的质谱信息作为后续计算的输入值,利用NNIA解析得到相应的色谱信息。采用快速升温程序对17种和42种农药混合标准样品的GC-MS信号进行分析,利用所建立的方法可在10 min内得到全部组分的色谱和质谱信息。     

From C58 to C62 and back: Stability,structural similarity,and ring current

An increasing number of observations show that non‐classical isomers may play an important role in the formation of fullerenes and their exo‐ and endo‐derivatives. A quantum‐mechanical study of all classical isomers of C₅₈, C₆₀, and C₆₂, and all non‐classical isomers with at most one square or heptagonal face, was carried out. Calculations at the B3LYP/6‐31G* level show that the favored isomers of C₅₈, C₆₀, and C₆₂ have closely related structures and suggest plausible inter‐conversion and growth pathways among low‐energy isomers. Similarity of the favored structures is reinforced by comparison of calculated ring currents induced on faces of these polyhedral cages by radial external magnetic fields, implying patterns of magnetic response similar to those of the stable, isolated‐pentagon C₆₀ molecule. © 2016 Wiley Periodicals, Inc.