Classroom note: The area under x α by geometry

By stretching the area under the curve x ^α it is shown to be of the form x ^{α + 1} p(α). Geometry is then used to prove p(α) = 1/(α + 1).     

Preface

<正>Biophysical chemistry is a relatively new branch of physical chemistry.Wikipedia-the free encyclopedia describes it with the following sentences(http://en.wikipedia.org/wiki/Biophysical_chemistry,cited on November 2,2014):"Biophysical chemistry is a physical science that uses the concepts of physics and physical chemistry for the study of     

Spectral representation of reduced protein models

We consider a spectrum-like two-dimensional graphical representation of proteins based on a reduced protein model in which 20 amino acids are grouped into five classes. This particular grouping of amino acids was suggested by Riddle and co-workers in 1997. The graphical representation is based on depicting sequentially the amino acids on five horizontal lines at equal separations. One-letter codes, B, O, U, X and Y, to which numerical values 1 to 5 have been assigned, are suggested as labels for the fictional amino acids that represent all the amino acids within each group. The approach is illustrated on ND6 proteins of eight species having from 168 to 175 amino acids. While visual inspection of the novel spectral graphical representations of proteins may reveal local similarities and dissimilarities of protein sequences, arithmetic manipulations of spectra offer an elegant route to graphic visualization of the degree of similarity for selected pairs of proteins.     

Prediction of an outcome using NETwork Clusters (NET-C)

Birth weight is a key consequence of environmental exposures and metabolic alterations and can influence lifelong health. While a number of methods have been used to examine associations of trace element (including essential nutrients and toxic metals) concentrations or metabolite concentrations with a health outcome, birth weight, studies evaluating how the coexistence of these factors impacts birth weight are extremely limited. Here, we present a novel algorithm NETwork Clusters (NET-C), to improve the prediction of outcome by considering the interactions of features in the network and then apply this method to predict birth weight by jointly modelling trace element and cord blood metabolite data. Specifically, by using trace element and/or metabolite subnetworks as groups, we apply group lasso to estimate birth weight. We conducted statistical simulation studies to examine how both sample size and correlations between grouped features and the outcome affect prediction performance. We showed that in terms of prediction error, our proposed method outperformed other methods such as (a) group lasso with groups defined by hierarchical clustering, (b) random forest regression and (c) neural networks. We applied our method to data ascertained as part of the New Hampshire Birth Cohort Study on trace elements, metabolites and birth outcomes, adjusting for other covariates such as maternal body mass index (BMI) and enrollment age. Our proposed method can be applied to a variety of similarly structured high-dimensional datasets to predict health outcomes.     

Aligning retention time shifts in HPLC three‐dimensional spectra by icoshift approach combined with data arrangement methods and the release of a graphical user interface

High‐performance liquid chromatography coupled with photodiode array detection has been extensively applied in many fields and the peaks among the analyzed samples can be shifted due to the variations of instrumental and experimental conditions. In multivariate analysis, retention time alignment is an important pretreatment step. Hence, the shifted peaks in high‐performance liquid chromatography coupled with photodiode array detection three‐dimensional spectra should be aligned for further analysis. Being motivated by this purpose, the interval correlated shifting method combined with the proposed data arrangement methods are recommended and employed on high‐performance liquid chromatography coupled with photodiode array detection data as a demonstration. We validate the alignment performance of the proposed method through comparison the consistency of the retention time before and after alignment. The obtained results demonstrated that the proposed method is capable of successful aligning the employed data. Additionally, the interval correlated shifting method combined with the data arrangement modes is implemented in an easy‐to‐use graphical user interface environment and so can be operated easily by users not familiar with programming languages.     

Information Network Modeling for U.S. Banking Systemic Risk

In this work we investigate whether information theory measures like mutual information and transfer entropy, extracted from a bank network, Granger cause financial stress indexes like LIBOR-OIS (London Interbank Offered Rate-Overnight Index Swap) spread, STLFSI (St. Louis Fed Financial Stress Index) and USD/CHF (USA Dollar/Swiss Franc) exchange rate. The information theory measures are extracted from a Gaussian Graphical Model constructed from daily stock time series of the top 74 listed US banks. The graphical model is calculated with a recently developed algorithm (LoGo) which provides very fast inference model that allows us to update the graphical model each market day. We therefore can generate daily time series of mutual information and transfer entropy for each bank of the network. The Granger causality between the bank related measures and the financial stress indexes is investigated with both standard Granger-causality and Partial Granger-causality conditioned on control measures representative of the general economy conditions.     

基因调控网络推断研究进展

随着高通量技术的发展,越来越多的生物医学组学数据亟需处理与分析,基于运筹优化的生物信息学方法是有效解析高维生物医学数据的重要途径之一。综述了近年来在基因调控网络推断方面的研究进展。针对不同类型的转录组学数据和研究目的,分别建立了相应的基因调控网络推断方法,主要包括先验基因调控网络数据库的建立、基于条件互信息的因果网络推断、基于微分方程的动态基因调控网络推断、转录调控和转录后调控协同作用的网络推断以及基因调控网络活性评价等,并展望了基因调控网络推断的重要研究方向。     

郑州白糖期货的因果图分析

主要探讨郑州白糖期货价、纽约白糖期货价和郑州白糖现货价格三者之间的动态关系,利用图模型方法、多维的多元线性回归等方法来分析它们之间的相互影响关系.又由于三者之间的关系受到牛市、熊市等市场因素的影响,故在熊市、牛市和震荡市三种情况下分别探讨三者的关联性.结果显示:不论市场是熊市还是牛市或者是震荡市,郑州白糖期货价都受到纽约白糖期货价的影响作用,郑州白糖现货价都受到郑州白糖期货价的影响;在市场为牛市时,纽约白糖期货价对郑州白糖现货价有显著影响.     

A Derivative-Coderivative Inclusion in Second-Order Nonsmooth Analysis

For twice smooth functions, the symmetry of the matrix of second partial derivatives is automatic and can be seen as the symmetry of the Jacobian matrix of the gradient mapping. For nonsmooth functions, possibly even extended-real-valued, the gradient mapping can be replaced by a subgradient mapping, and generalized second derivative objects can then be introduced through graphical differentiation of this mapping, but the question of what analog of symmetry might persist has remained open. An answer is provided here in terms of a derivative-coderivative inclusion.     

Schemata, Distributions and Graphical Models in Evolutionary Optimization

In this paper the optimization of additively decomposed discrete functions is investigated. For these functions genetic algorithms have exhibited a poor performance. First the schema theory of genetic algorithms is reformulated in probability theory terms. A schema defines the structure of a marginal distribution. Then the conceptual algorithm BEDA is introduced. BEDA uses a Boltzmann distribution to generate search points. From BEDA a new algorithm, FDA, is derived. FDA uses a factorization of the distribution. The factorization captures the structure of the given function. The factorization problem is closely connected to the theory of conditional independence graphs. For the test functions considered, the performance of FDA—in number of generations till convergence—is similar to that of a genetic algorithm for the OneMax function. This result is theoretically explained.