Studying phenotypic evolution using multivariate quantitative genetics

Quantitative genetics provides a powerful framework for studying phenotypic evolution and the evolution of adaptive genetic variation. Central to the approach is G, the matrix of additive genetic variances and covariances. G summarizes the genetic basis of the traits and can be used to predict the phenotypic response to multivariate selection or to drift. Recent analytical and computational advances have improved both the power and the accessibility of the necessary multivariate statistics. It is now possible to study the relationships between G and other evolutionary parameters, such as those describing the mutational input, the shape and orientation of the adaptive landscape, and the phenotypic divergence among populations. At the same time, we are moving towards a greater understanding of how the genetic variation summarized by G evolves. Computer simulations of the evolution of G, innovations in matrix comparison methods, and rapid development of powerful molecular genetic tools have all opened the way for dissecting the interaction between allelic variation and evolutionary process. Here I discuss some current uses of G, problems with the application of these approaches, and identify avenues for future research.

Delay estimation for multivariate time series

Most traditional methods for extracting the relationships between two time series are based on cross-correlation. In a non-linear non-stationary environment, these techniques are not sufficient. We show in this paper how to use hidden Markov models (HMMs) to identify the lag (or delay) between different variables for such data. We first present a method using maximum likelihood estimation and propose a simple algorithm which is capable of identifying associations between variables. We also adopt an information-theoretic approach and develop a novel procedure for training HMMs to maximise the mutual information between delayed time series. Both methods are successfully applied to real data. We model the oil drilling process with HMMs and estimate a crucial parameter, namely the lag for return.

Evaluating the effectiveness of Bayesian feature selection

A practical Bayesian approach for inference in neural network models has been available for ten years, and yet it is not used frequently in medical applications. In this chapter we show how both regularisation and feature selection can bring significant benefits in diagnostic tasks through two case studies: heart arrhythmia classification based on ECG data and the prognosis of lupus. In the first of these, the number of variables was reduced by two thirds without significantly affecting performance, while in the second, only the Bayesian models had an acceptable accuracy. In both tasks, neural networks outperformed other pattern recognition approaches.

Performance of small and medium enterprises and the impact of environmental variables: evidence from Vietnam

thesis is developed from a real life application of performance evaluation of small and medium-sized enterprises (SMEs) in Vietnam. The thesis presents two main methodological developments on evaluation of dichotomous environment variable impacts on technical efficiency. Taking into account the selection bias the thesis proposes a revised frontier separation approach for the seminal Data Envelopment Analysis (DEA) model which was developed by Charnes, Cooper, and Rhodes (1981). The revised frontier separation approach is based on a nearest neighbour propensity score matching pairing treated SMEs with their counterfactuals on the propensity score. The thesis develops order-m frontier conditioning on propensity score from the conditional order-m approach proposed by Cazals, Florens, and Simar (2002), advocated by Daraio and Simar (2005). By this development, the thesis allows the application of the conditional order-m approach with a dichotomous environment variable taking into account the existence of the self-selection problem of impact evaluation. Monte Carlo style simulations have been built to examine the effectiveness of the aforementioned developments. Methodological developments of the thesis are applied in empirical studies to evaluate the impact of training programmes on the performance of food processing SMEs and the impact of exporting on technical efficiency of textile and garment SMEs of Vietnam. The analysis shows that training programmes have no significant impact on the technical efficiency of food processing SMEs. Moreover, the analysis confirms the conclusion of the export literature that exporters are self selected into the sector. The thesis finds no significant impact from exporting activities on technical efficiency of textile and garment SMEs. However, large bias has been eliminated by the proposed approach. Results of empirical studies contribute to the understanding of the impact of different environmental variables on the performance of SMEs. It helps policy makers to design proper policy supporting the development of Vietnamese SMEs.

Emulation of dynamic computer models with multivariate output

This preliminary report describes work carried out as part of work package 1.2 of the MUCM research project. The report is split in two parts: the ?rst part (Sections 1 and 2) summarises the state of the art in emulation of computer models, while the second presents some initial work on the emulation of dynamic models. In the ?rst part, we describe the basics of emulation, introduce the notation and put together the key results for the emulation of models with single and multiple outputs, with or without the use of mean function. In the second part, we present preliminary results on the chaotic Lorenz 63 model. We look at emulation of a single time step, and repeated application of the emulator for sequential predic- tion. After some design considerations, the emulator is compared with the exact simulator on a number of runs to assess its performance. Several general issues related to emulating dynamic models are raised and discussed. Current work on the larger Lorenz 96 model (40 variables) is presented in the context of dimension reduction, with results to be provided in a follow-up report. The notation used in this report are summarised in appendix.

Higher-order co-occurrences for exploratory point pattern analysis and decision tree clustering on spatial data

Analyzing geographical patterns by collocating events, objects or their attributes has a long history in surveillance and monitoring, and is particularly applied in environmental contexts, such as ecology or epidemiology. The identification of patterns or structures at some scales can be addressed using spatial statistics, particularly marked point processes methodologies. Classification and regression trees are also related to this goal of finding "patterns" by deducing the hierarchy of influence of variables on a dependent outcome. Such variable selection methods have been applied to spatial data, but, often without explicitly acknowledging the spatial dependence. Many methods routinely used in exploratory point pattern analysis are2nd-order statistics, used in a univariate context, though there is also a wide literature on modelling methods for multivariate point pattern processes. This paper proposes an exploratory approach for multivariate spatial data using higher-order statistics built from co-occurrences of events or marks given by the point processes. A spatial entropy measure, derived from these multinomial distributions of co-occurrences at a given order, constitutes the basis of the proposed exploratory methods. © 2010 Elsevier Ltd.

The use of multivariate methods in the identification of subtypes of Alzheimer's disease: a comparison of principal components and cluster analysis

Two contrasting multivariate statistical methods, viz., principal components analysis (PCA) and cluster analysis were applied to the study of neuropathological variations between cases of Alzheimer's disease (AD). To compare the two methods, 78 cases of AD were analyzed, each characterised by measurements of 47 neuropathological variables. Both methods of analysis revealed significant variations between AD cases. These variations were related primarily to differences in the distribution and abundance of senile plaques (SP) and neurofibrillary tangles (NFT) in the brain. Cluster analysis classified the majority of AD cases into five groups which could represent subtypes of AD. However, PCA suggested that variation between cases was more continuous with no distinct subtypes. Hence, PCA may be a more appropriate method than cluster analysis in the study of neuropathological variations between AD cases.

Higher-order co-occurrences for exploratory point pattern analysis and decision tree clustering on spatial data

Analyzing geographical patterns by collocating events, objects or their attributes has a long history in surveillance and monitoring, and is particularly applied in environmental contexts, such as ecology or epidemiology. The identification of patterns or structures at some scales can be addressed using spatial statistics, particularly marked point processes methodologies. Classification and regression trees are also related to this goal of finding "patterns" by deducing the hierarchy of influence of variables on a dependent outcome. Such variable selection methods have been applied to spatial data, but, often without explicitly acknowledging the spatial dependence. Many methods routinely used in exploratory point pattern analysis are2nd-order statistics, used in a univariate context, though there is also a wide literature on modelling methods for multivariate point pattern processes. This paper proposes an exploratory approach for multivariate spatial data using higher-order statistics built from co-occurrences of events or marks given by the point processes. A spatial entropy measure, derived from these multinomial distributions of co-occurrences at a given order, constitutes the basis of the proposed exploratory methods. © 2010 Elsevier Ltd.

Fair testing in employment selection

This project represents the collaboration of Charta Mede Ltd and the Interdisciplinary Higher Degrees Scheme at the University of Aston. The aim of the project was to monitor the effects of the Civil Service's Executive Officer Qualifying Test Battery on minority group applicants. Prior to monitoring the EO Test Battery, however, an ethnic classification had to be developed which was reliable, acceptable to respondents and appropriate for monitoring. Three pilot studies were conducted to examine these issues, during which different classifications and different ways of asking the question were trialled. The results indicated that by providing more precise instructions as to the meanings of categories, it was possible to obtain classifications which were acceptable and reliable. However, there were also certain terms and expressions which should be avoided such as those referring to colour and anthropological racial groups. Two classifications were used in the Executive Officer Study - one derived from an Office of Population Censuses and Surveys classification and one developed for this project - the MultiCultural British Classification. The results indicated that some minority groups (Asians, West Indians and Africans in particular) pass the tests in significantly lower proportions than the majority group and also score significantly less well on the tests. Factors which were significantly related to pass/fail and test scores included educational qualifications and age on entering the UK (the latter being negatively correlated). Using variables in this study, however, it was only possible to account for 5% of the variance in pass/fail rates and 11% of the variance in test scores. Analyses of covariance carried out indicated that the differences in test scores still remained even though the effects of significantly correlated variables were removed. Although indirect discrimination could not be inferred from the data, further research into differential validity and fairer methods of select ion is needed.

A method for systematic artifact selection decision making

Artifact selection decisions typically involve the selection of one from a number of possible/candidate options (decision alternatives). In order to support such decisions, it is important to identify and recognize relevant key issues of problem solving and decision making (Albers, 1996; Harris, 1998a, 1998b; Jacobs & Holten, 1995; Loch & Conger, 1996; Rumble, 1991; Sauter, 1999; Simon, 1986). Sauter classifies four problem solving/decision making styles: (1) left-brain style, (2) right-brain style, (3) accommodating, and (4) integrated (Sauter, 1999). The left-brain style employs analytical and quantitative techniques and relies on rational and logical reasoning. In an effort to achieve predictability and minimize uncertainty, problems are explicitly defined, solution methods are determined, orderly information searches are conducted, and analysis is increasingly refined. Left-brain style decision making works best when it is possible to predict/control, measure, and quantify all relevant variables, and when information is complete. In direct contrast, right-brain style decision making is based on intuitive techniques—it places more emphasis on feelings than facts. Accommodating decision makers use their non-dominant style when they realize that it will work best in a given situation. Lastly, integrated style decision makers are able to combine the left- and right-brain styles—they use analytical processes to filter information and intuition to contend with uncertainty and complexity.

Comparing methods to separate treatment from self-selection effects in an online banking setting

The literature discusses several methods to control for self-selection effects but provides little guidance on which method to use in a setting with a limited number of variables. The authors theoretically compare and empirically assess the performance of different matching methods and instrumental variable and control function methods in this type of setting by investigating the effect of online banking on product usage. Hybrid matching in combination with the Gaussian kernel algorithm outperforms the other methods with respect to predictive validity. The empirical finding of large self-selection effects indicates the importance of controlling for these effects when assessing the effectiveness of marketing activities.

A multivariate spatial analysis of vowel formants in American English

This paper presents the results of a multivariate spatial analysis of 38 vowel formant variables in the language of 402 informants from 236 cities from across the contiguous United States, based on the acoustic data from the Atlas of North American English (Labov, Ash & Boberg, 2006). The results of the analysis both confirm and challenge the results of the Atlas. Most notably, while the analysis identifies similar patterns as the Atlas in the West and the Southeast, the analysis finds that the Midwest and the Northeast are distinct dialect regions that are considerably stronger than the traditional Midland and Northern dialect region indentified in the Atlas. The analysis also finds evidence that a western vowel shift is actively shaping the language of the Western United States.

A method for systematic artifact selection decision making

Artifact selection decisions typically involve the selection of one from a number of possible/candidate options (decision alternatives). In order to support such decisions, it is important to identify and recognize relevant key issues of problem solving and decision making (Albers, 1996; Harris, 1998a, 1998b; Jacobs & Holten, 1995; Loch & Conger, 1996; Rumble, 1991; Sauter, 1999; Simon, 1986). Sauter classifies four problem solving/decision making styles: (1) left-brain style, (2) right-brain style, (3) accommodating, and (4) integrated (Sauter, 1999). The left-brain style employs analytical and quantitative techniques and relies on rational and logical reasoning. In an effort to achieve predictability and minimize uncertainty, problems are explicitly defined, solution methods are determined, orderly information searches are conducted, and analysis is increasingly refined. Left-brain style decision making works best when it is possible to predict/control, measure, and quantify all relevant variables, and when information is complete. In direct contrast, right-brain style decision making is based on intuitive techniques—it places more emphasis on feelings than facts. Accommodating decision makers use their non-dominant style when they realize that it will work best in a given situation. Lastly, integrated style decision makers are able to combine the left- and right-brain styles—they use analytical processes to filter information and intuition to contend with uncertainty and complexity.

Correlating liposomal adjuvant characteristics to in-vivo cell-mediated immunity using a novel Mycobacterium tuberculosis fusion protein:a multivariate analysis study

Objective In this study, we have used a chemometrics-based method to correlate key liposomal adjuvant attributes with in-vivo immune responses based on multivariate analysis. Methods The liposomal adjuvant composed of the cationic lipid dimethyldioctadecylammonium bromide (DDA) and trehalose 6,6-dibehenate (TDB) was modified with 1,2-distearoyl-sn-glycero-3-phosphocholine at a range of mol% ratios, and the main liposomal characteristics (liposome size and zeta potential) was measured along with their immunological performance as an adjuvant for the novel, postexposure fusion tuberculosis vaccine, Ag85B-ESAT-6-Rv2660c (H56 vaccine). Partial least square regression analysis was applied to correlate and cluster liposomal adjuvants particle characteristics with in-vivo derived immunological performances (IgG, IgG1, IgG2b, spleen proliferation, IL-2, IL-5, IL-6, IL-10, IFN-γ). Key findings While a range of factors varied in the formulations, decreasing the 1,2-distearoyl-sn-glycero-3-phosphocholine content (and subsequent zeta potential) together built the strongest variables in the model. Enhanced DDA and TDB content (and subsequent zeta potential) stimulated a response skewed towards a cell mediated immunity, with the model identifying correlations with IFN-γ, IL-2 and IL-6. Conclusion This study demonstrates the application of chemometrics-based correlations and clustering, which can inform liposomal adjuvant design.

Laser-induced breakdown spectroscopy quantitative analysis method via adaptive analytical line selection and relevance vector machine regression model

Abstract A new LIBS quantitative analysis method based on analytical line adaptive selection and Relevance Vector Machine (RVM) regression model is proposed. First, a scheme of adaptively selecting analytical line is put forward in order to overcome the drawback of high dependency on a priori knowledge. The candidate analytical lines are automatically selected based on the built-in characteristics of spectral lines, such as spectral intensity, wavelength and width at half height. The analytical lines which will be used as input variables of regression model are determined adaptively according to the samples for both training and testing. Second, an LIBS quantitative analysis method based on RVM is presented. The intensities of analytical lines and the elemental concentrations of certified standard samples are used to train the RVM regression model. The predicted elemental concentration analysis results will be given with a form of confidence interval of probabilistic distribution, which is helpful for evaluating the uncertainness contained in the measured spectra. Chromium concentration analysis experiments of 23 certified standard high-alloy steel samples have been carried out. The multiple correlation coefficient of the prediction was up to 98.85%, and the average relative error of the prediction was 4.01%. The experiment results showed that the proposed LIBS quantitative analysis method achieved better prediction accuracy and better modeling robustness compared with the methods based on partial least squares regression, artificial neural network and standard support vector machine.