Principal components analysis of Alzheimer’s disease based on neuropathological data: A study of 79 patients

A Principal Components Analysis of neuropathological data from 79 Alzheimer’s disease (AD) cases was performed to determine whether there was evidence for subtypes of the disease. Two principal components were extracted from the data which accounted for 72% and 12% of the total variance respectively. The results suggested that 1) AD was heterogeneous but subtypes could not be clearly defined; 2) the heterogeneity, in part, reflected disease onset; 3) familial cases did not constitute a distinct subtype of AD and 4) there were two forms of late onset AD, one of which was associated with less senile plaque and neurofibrillary tangle development but with a greater degree of brain atherosclerosis.

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.

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.

Principal components analysis of Alzheimer's disease based on neuropathological data: a study of 79 patients

A principal components analysis was carried out on neuropathological data collected from 79 cases of Alzheimer's disease (AD) diagnosed in a single centre. The purpose of the study was to determine whether on neuropathological criteria there was evidence for clearly defined subtypes of the disease. Two principal components (PC1 and PC2) were extracted from the data. PC1 was considerable more important than PC2 accounting for 72% of the total variance. When plotted in relation to the first two principal components the majority of cases (65/79) were distributed in a single cluster within which subgroupings were not clearly evident. In addition, there were a number of individual, mainly early-onset cases, which were neither related to each other nor to the main cluster. The distribution of each neuropathological feature was examined in relation to PC1 and 2, Disease onset, rhe degree of gross brain atrophy, neuronal loss and the devlopment of senile plaques (SP) and neurofibrillary tangles (NFT) were negatively correlated with PC1. The devlopment of SP and NFT and the degree of brain athersclerosis were positively correlated with PC2. These results suggested: 1) that there were different forms of AD but no clear division of the cases into subclasses could be made based on the neuropathological criteria used; the cases showing a more continuous distribution from one form to another, 2) that disease onset was an important variable and was associated with a greater development of pathological changes, 3) familial cases were not a distinct subclass of AD; the cases being widely distributed in relation to PC1 and PC2 and 4) that there may be two forms of late-onset AD whic grade into each other, one of which was associated with less SP and NFT development but with a greater degree of brain atherosclerosis.

Bagging model with cost sensitive analysis on diabetes data

Diabetes patients might suffer from an unhealthy life, long-term treatment and chronic complicated diseases. The decreasing hospitalization rate is a crucial problem for health care centers. This study combines the bagging method with base classifier decision tree and costs-sensitive analysis for diabetes patients' classification purpose. Real patients' data collected from a regional hospital in Thailand were analyzed. The relevance factors were selected and used to construct base classifier decision tree models to classify diabetes and non-diabetes patients. The bagging method was then applied to improve accuracy. Finally, asymmetric classification cost matrices were used to give more alternative models for diabetes data analysis.

Semantics, knowledge and grids on big data

Semantics, knowledge and Grids represent three spaces where people interact, understand, learn and create. Grids represent the advanced cyber-infrastructures and evolution. Big data influence the evolution of semantics, knowledge and Grids. Exploring semantics, knowledge and Grids on big data helps accelerate the shift of scientific paradigm, the fourth industrial revolution, and the transformational innovation of technologies.

Point-wise confidence interval estimation by neural networks: A comparative study based on automotive engine calibration.

In developing neural network techniques for real world applications it is still very rare to see estimates of confidence placed on the neural network predictions. This is a major deficiency, especially in safety-critical systems. In this paper we explore three distinct methods of producing point-wise confidence intervals using neural networks. We compare and contrast Bayesian, Gaussian Process and Predictive error bars evaluated on real data. The problem domain is concerned with the calibration of a real automotive engine management system for both air-fuel ratio determination and on-line ignition timing. This problem requires real-time control and is a good candidate for exploring the use of confidence predictions due to its safety-critical nature.

Impact of liberalization on efficiency and productivity of sugar industry in Kenya

Purpose – The data used in this study is for the period 1980-2000. Almost midway through this period (in 1992), the Kenyan government liberalized the sugar industry and the role of the market increased, while the government's role with respect to control of prices, imports and other aspects in the sector declined. This exposed the local sugar manufacturers to external competition from other sugar producers, especially from the COMESA region. This study aims to find whether there were any changes in efficiency of production between the two periods (pre and post-liberalization). Design/methodology/approach – The study utilized two methodologies to efficiency estimation: data envelopment analysis (DEA) and the stochastic frontier. DEA uses mathematical programming techniques and does not impose any functional form on the data. However, it attributes all deviation from the mean function to inefficiencies. The stochastic frontier utilizes econometric techniques. Findings – The test for structural differences in the two periods does not show any statistically significant differences between the two periods. However, both methodologies show a decline in efficiency levels from 1992, with the lowest period experienced in 1998. From then on, efficiency levels began to increase. Originality/value – To the best of the authors' knowledge, this is the first paper to use both methodologies in the sugar industry in Kenya. It is shown that in industries where the noise (error) term is minimal (such as manufacturing), the DEA and stochastic frontier give similar results.

Estimation of functional connectivity from electromagnetic signals and the amount of empirical data required

An increasing number of neuroimaging studies are concerned with the identification of interactions or statistical dependencies between brain areas. Dependencies between the activities of different brain regions can be quantified with functional connectivity measures such as the cross-correlation coefficient. An important factor limiting the accuracy of such measures is the amount of empirical data available. For event-related protocols, the amount of data also affects the temporal resolution of the analysis. We use analytical expressions to calculate the amount of empirical data needed to establish whether a certain level of dependency is significant when the time series are autocorrelated, as is the case for biological signals. These analytical results are then contrasted with estimates from simulations based on real data recorded with magnetoencephalography during a resting-state paradigm and during the presentation of visual stimuli. Results indicate that, for broadband signals, 50-100 s of data is required to detect a true underlying cross-correlations coefficient of 0.05. This corresponds to a resolution of a few hundred milliseconds for typical event-related recordings. The required time window increases for narrow band signals as frequency decreases. For instance, approximately 3 times as much data is necessary for signals in the alpha band. Important implications can be derived for the design and interpretation of experiments to characterize weak interactions, which are potentially important for brain processing.

Visual data mining: integrating machine learning with information visualization

Today, the data available to tackle many scientific challenges is vast in quantity and diverse in nature. The exploration of heterogeneous information spaces requires suitable mining algorithms as well as effective visual interfaces. Most existing systems concentrate either on mining algorithms or on visualization techniques. Though visual methods developed in information visualization have been helpful, for improved understanding of a complex large high-dimensional dataset, there is a need for an effective projection of such a dataset onto a lower-dimension (2D or 3D) manifold. This paper introduces a flexible visual data mining framework which combines advanced projection algorithms developed in the machine learning domain and visual techniques developed in the information visualization domain. The framework follows Shneiderman’s mantra to provide an effective user interface. The advantage of such an interface is that the user is directly involved in the data mining process. We integrate principled projection methods, such as Generative Topographic Mapping (GTM) and Hierarchical GTM (HGTM), with powerful visual techniques, such as magnification factors, directional curvatures, parallel coordinates, billboarding, and user interaction facilities, to provide an integrated visual data mining framework. Results on a real life high-dimensional dataset from the chemoinformatics domain are also reported and discussed. Projection results of GTM are analytically compared with the projection results from other traditional projection methods, and it is also shown that the HGTM algorithm provides additional value for large datasets. The computational complexity of these algorithms is discussed to demonstrate their suitability for the visual data mining framework.

Statnote 5: Is one set of data more variable than another?

There may be circumstances where it is necessary for microbiologists to compare variances rather than means, e,g., in analysing data from experiments to determine whether a particular treatment alters the degree of variability or testing the assumption of homogeneity of variance prior to other statistical tests. All of the tests described in this Statnote have their limitations. Bartlett’s test may be too sensitive but Levene’s and the Brown-Forsythe tests also have problems. We would recommend the use of the variance-ratio test to compare two variances and the careful application of Bartlett’s test if there are more than two groups. Considering that these tests are not particularly robust, it should be remembered that the homogeneity of variance assumption is usually the least important of those considered when carrying out an ANOVA. If there is concern about this assumption and especially if the other assumptions of the analysis are also not likely to be met, e.g., lack of normality or non additivity of treatment effects then it may be better either to transform the data or to carry out a non-parametric test on the data.

Data visualisation and exploration with prior knowledge

Visualising data for exploratory analysis is a major challenge in many applications. Visualisation allows scientists to gain insight into the structure and distribution of the data, for example finding common patterns and relationships between samples as well as variables. Typically, visualisation methods like principal component analysis and multi-dimensional scaling are employed. These methods are favoured because of their simplicity, but they cannot cope with missing data and it is difficult to incorporate prior knowledge about properties of the variable space into the analysis; this is particularly important in the high-dimensional, sparse datasets typical in geochemistry. In this paper we show how to utilise a block-structured correlation matrix using a modification of a well known non-linear probabilistic visualisation model, the Generative Topographic Mapping (GTM), which can cope with missing data. The block structure supports direct modelling of strongly correlated variables. We show that including prior structural information it is possible to improve both the data visualisation and the model fit. These benefits are demonstrated on artificial data as well as a real geochemical dataset used for oil exploration, where the proposed modifications improved the missing data imputation results by 3 to 13%.

A study of thermodynamic characteristics and predictive computer modelling of an air to water heat pump system

A study on heat pump thermodynamic characteristics has been made in the laboratory on a specially designed and instrumented air to water heat pump system. The design, using refrigerant R12, was based on the requirement to produce domestic hot water at a temperature of about 50 °C and was assembled in the laboratory. All the experimental data were fed to a microcomputer and stored on disk automatically from appropriate transducers via amplifier and 16 channel analogue to digital converters. The measurements taken were R12 pressures and temperatures, water and R12 mass flow rates, air speed, fan and compressor input powers, water and air inlet and outlet temperatures, wet and dry bulb temperatures. The time interval between the observations could be varied. The results showed, as expected, that the COP was higher at higher air inlet temperatures and at lower hot water output temperatures. The optimum air speed was found to be at a speed when the fan input power was about 4% of the condenser heat output. It was also found that the hot water can be produced at a temperature higher than the appropriate R12 condensing temperature corresponding to condensing pressure. This was achieved by condenser design to take advantage of discharge superheat and by further heating the water using heat recovery from the compressor. Of the input power to the compressor, typically about 85% was transferred to the refrigerant, 50 % by the compression work and 35% due to the heating of the refrigerant by the cylinder wall, and the remaining 15% (of the input power) was rejected to the cooling medium. The evaporator effectiveness was found to be about 75% and sensitive to the air speed. Using the data collected, a steady state computer model was developed. For given input conditions s air inlet temperature, air speed, the degree of suction superheat , water inlet and outlet temperatures; the model is capable of predicting the refrigerant cycle, compressor efficiency, evaporator effectiveness, condenser water flow rate and system Cop.

The use of ERS-1 crossovers and TOPEX/Poseidon repeat pass data for global sea surface variability studies

In previous sea-surface variability studies, researchers have failed to utilise the full ERS-1 mission due to the varying orbital characteristics in each mission phase, and most have simply ignored the Ice and Geodetic phases. This project aims to introduce a technique which will allow the straightforward use of all orbital phases, regardless of orbit type. This technique is based upon single satellite crossovers. Unfortunately the ERS-1 orbital height is still poorly resolved (due to higher air drag and stronger gravitational effects) when compared with that of TOPEX/Poseidon (T/P), so to make best use of the ERS-1 crossover data corrections to the ERS-1 orbital heights are calculated by fitting a cubic-spline to dual-crossover residuals with T/P. This correction is validated by comparison of dual satellite crossovers with tide gauge data. The crossover processing technique is validated by comparing the extracted sea-surface variability information with that from T/P repeat pass data. The two data sets are then combined into a single consistent data set for analysis of sea-surface variability patterns. These patterns are simplified by the use of an empirical orthogonal function decomposition which breaks the signals into spatial modes which are then discussed separately. Further studies carried out on these data include an analysis of the characteristics of the annual signal, discussion of evidence for Rossby wave propagation on a global basis, and finally analysis of the evidence for global mean sea level rise.

Exploratory data analysis with non-linear and missing data in geochemistry

Exploratory analysis of data seeks to find common patterns to gain insights into the structure and distribution of the data. In geochemistry it is a valuable means to gain insights into the complicated processes making up a petroleum system. Typically linear visualisation methods like principal components analysis, linked plots, or brushing are used. These methods can not directly be employed when dealing with missing data and they struggle to capture global non-linear structures in the data, however they can do so locally. This thesis discusses a complementary approach based on a non-linear probabilistic model. The generative topographic mapping (GTM) enables the visualisation of the effects of very many variables on a single plot, which is able to incorporate more structure than a two dimensional principal components plot. The model can deal with uncertainty, missing data and allows for the exploration of the non-linear structure in the data. In this thesis a novel approach to initialise the GTM with arbitrary projections is developed. This makes it possible to combine GTM with algorithms like Isomap and fit complex non-linear structure like the Swiss-roll. Another novel extension is the incorporation of prior knowledge about the structure of the covariance matrix. This extension greatly enhances the modelling capabilities of the algorithm resulting in better fit to the data and better imputation capabilities for missing data. Additionally an extensive benchmark study of the missing data imputation capabilities of GTM is performed. Further a novel approach, based on missing data, will be introduced to benchmark the fit of probabilistic visualisation algorithms on unlabelled data. Finally the work is complemented by evaluating the algorithms on real-life datasets from geochemical projects.