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A unifying review of linear gaussian models.

Factor analysis, principal component analysis, mixtures of gaussian clusters, vector quantization, Kalman filter models, and hidden Markov models can all be unified as variations of unsupervised learning under a single basic generative model. This is achieved by collecting together disparate observations and derivations made by many previous authors and introducing a new way of linking discrete and continuous state models using a simple nonlinearity. Through the use of other nonlinearities, we show how independent component analysis is also a variation of the same basic generative model. We show that factor analysis and mixtures of gaussians can be implemented in autoencoder neural networks and learned using squared error plus the same regularization term. We introduce a new model for static data, known as sensible principal component analysis, as well as a novel concept of spatially adaptive observation noise. We also review some of the literature involving global and local mixtures of the basic models and provide pseudocode for inference and learning for all the basic models.

Algorithms↗

Reassessment of the PAS patterns in uveal melanoma.

BACKGROUND: Previous work has highlighted the prognostic importance of patterns of periodic acid Schiff (PAS) staining (the Folberg patterns) in uveal melanoma. These patterns have been ascribed to blood vessels but the patterns are different from those seen with other staining techniques for blood vessels. It has recently been shown that microvessel density is the dominant prognostic factor in uveal melanoma. This study reinvestigates the nature and significance of the PAS patterns. METHODS: The PAS patterns were compared with the patterns seen with conventional connective tissue stains and with the patterns seen in sections stained for the presence of blood vessels (by immunohistochemistry for factor VIII related antigen). The PAS patterns were determined on a panel of 117 cases of uveal melanoma. The prognostic significance of each of these patterns was determined and, as more than one pattern can exist in a tumour, principal components analysis was performed to determine the number of underlying factors. RESULTS: Comparison of the PAS patterns with other stains demonstrates that they are based on connective tissue including fibrovascular tissue. Five of the nine PAS patterns carried prognostic significance on univariate analysis. Principal components analysis suggested that these patterns represented three underlying factors, which were tentatively identified as representing disordered growth (factor 1), emergence of rapidly growing subclones (factor 2), and section orientation (factor 3). CONCLUSIONS: The PAS patterns are based on fibrovascular tissue and can be ascribed to three underlying factors. The first two of these factors carried prognostic significance and the first (disordered growth) retained independent prognostic significance in a multivariate Cox model which included microvessel density and tumour size.

Biomarkers, Tumor↗

Development of a scale to measure directive guidance by pharmacists.

OBJECTIVE: To develop and test a questionnaire that can be used to measure directive guidance behaviors by pharmacists. QUESTIONNAIRE DESIGN: The Purdue Pharmacist Directive Guidance (PPDG) scale was developed based on the directive guidance dimension of socially supportive behaviors, as described by Barrera and Ainlay. The final scale consists of 10 items. SUBJECTS: Individuals on the Walker Test Crew database who were 18 years of age or older and self-reported taking medications for asthma, hypertension, and/or diabetes in the past 3 months were eligible for inclusion. All data were collected through telephone interviews. A total of 464 contacts were made, resulting in 300 responses. DATA ANALYSIS: Principal components analysis was performed to determine the construct subscales of the PPDG. Internal consistency of the PPDG and its subscales was assessed using Cronbach's alpha and corrected item-total correlations. Pearson product-moment correlations of the PPDG with measures of family and friend support (FFS) and self-reported medication adherence were used to determine convergent validity. Spearman rank-order correlations of the PPDG with the total number of prescription medications as well as those for asthma, hypertension, and diabetes taken in the past 3 months were obtained. ANOVA and Student's t-tests were used to determine differences in PPDG across demographic characteristics. RESULTS: Principal components analysis yielded two subscales for the PPDG. These were named Instruction and Feedback and Goal Setting, based on their content. The PPDG scale had good internal consistency (Cronbach's alpha = 0.86), and correlated positively and significantly with FFS (r = 0.27), giving some evidence of convergent validity. The PPDG scale and its subscales also had logically intuitive positive and significant correlations with the total number of prescription drugs taken in the past 3 months. CONCLUSIONS: The PPDG is short and easy to administer, and showed validity and reliability. The PPDG scale should be useful in developing a better understanding of the process by which pharmacists influence healthcare outcomes, assessing variations in pharmaceutical care, and as a tool in identifying means of overcoming barriers to higher levels of pharmaceutical care.

Adult↗

Multivariate analysis of heavy metal contamination in urban dusts of Xi'an, Central China.

Though there are many studies of heavy metal contaminations of urban dusts in developed countries, little attention has been paid to this kind of study in developing countries, including China. Therefore, a series of investigations were performed to provide heavy metal signatures of urban dusts and to evaluate potential sources in Xi'an, Shaanxi Province. Sixty-five samples of urban dusts were collected in Xi'an. Then Ag, Cr, Cu, Mn, Pb and Zn concentrations were determined by using atomic absorption spectrophotometry, and As, Hg and Sb concentrations by atomic fluorescence spectroscopy. The results indicate that, in comparison with Chinese soil, urban dusts in Xi'an have elevated metal concentrations as a whole, except those of arsenic and manganese. These concentration levels are comparable to those in other studies. Correlation coefficient analysis, principal component analysis (PCA) and cluster analysis (CA) were performed and three main sources with corresponding cluster elements were identified: (1) Ag and Hg have commercial and domestic sources; (2) Cr, Cu, Pb, Sb and Zn are mainly derived from industrial sources, combined with traffic sources as well for Pb and Zn; (3) As and Mn come mainly from soil sources, and As also has an industrial source. Based on PCA and CA analyses, manganese was selected as the reference element, and heavy metal enrichment factors (Efs) were calculated, which in turn further confirms the source identification. Also, Efs give an insight of human influence degree of urban dusts.

Arsenic↗

Transcriptional profiles in liver from rats treated with tumorigenic and non-tumorigenic triazole conazole fungicides: Propiconazole, triadimefon, and myclobutanil.

Conazoles are a class of fungicides used as pharmaceutical and agricultural agents. In chronic bioassays in rats, triadimefon was hepatotoxic and induced follicular cell adenomas in the thyroid gland, whereas, propiconazole and myclobutanil were hepatotoxic but had no effect on the thyroid gland. These conazoles administered in the feed to male Wistar/Han rats were found to induce hepatomegaly, induce high levels of pentoxyresorufin-O-dealkylase, increase cell proliferation in the liver, increase serum cholesterol, decrease serum T3 and T4, and increase hepatic uridine diphosphoglucuronosyl transferase activity. The goal of the present study was to define pathways that explain the biologic outcomes. Male Wistar/Han rats (3 per group), were exposed to the 3 conazoles in the feed for 4, 30, or 90 days of treatment at tumorigenic and nontumorigenic doses. Hepatic gene expression was determined using high-density Affymetrix GeneChips (Rat 230_2). Differential gene expression was assessed at the probe level using Robust Multichip Average analysis. Principal component analysis by treatment and time showed within group sample similarity and that the treatment groups were distinct from each other. The number of altered genes varied by treatment, dose, and time. The greatest number of altered genes was induced by triadimefon and propiconazole after 90 days of treatment, while myclobutanil had minimal effects at that time point. Pathway level analyses revealed that after 90 days of treatment the most significant numbers of altered pathways were related to cell signaling, growth, and metabolism. Pathway level analysis for triadimefon and propiconazole resulted in 71 altered pathways common to both chemicals. These pathways controlled cholesterol metabolism, activation of nuclear receptors, and N-ras and K-ras signaling. There were 37 pathways uniquely changed by propiconazole, and triadimefon uniquely altered 34 pathways. Pathway level analysis of altered gene expression resulted in a more complete description of the associated toxicological effects that can distinguish triadimefon from propiconazole and myclobutanil.

Animals↗

Multivariate analysis of infrared spectra for monitoring and understanding the kinetics and mechanisms of adsorption processes.

Water adsorption onto thin zeolite 3A wafers has been investigated as a function of time, water vapor concentration, and zeolite sample mass using mid-infrared spectroscopy coupled with multivariate data analysis. Principal component analysis (PCA) of the spectral region of the water combination band was used for quantitative characterization of water adsorption onto the zeolite. The kinetics of the adsorption of water are found to be very reproducible and nearly linear with time. The kinetics of water adsorption based on data from different masses of zeolite are consistent with a diffusion/immobilization model for which the interparticle diffusion rate is comparable to the rate of adsorption. The infrared zeolite bands (1340-1550 cm(-1)) change during the adsorption process and yield more detail about the adsorption sites of the material. PCA applied to the zeolite bands was not directly interpretable. However, multivariate curve resolution applied to the spectral region containing the zeolite bands readily demonstrates that zeolite 3A has three water adsorption sites or environments that are sequentially occupied. Potential explanations for the observations of the multivariate curve resolution (MCR) analysis of these infrared (IR) kinetic adsorption experiments are presented. The explanation most consistent with our data suggests that water adsorbs sequentially on the zeolite to form single, double, and triple water adsorption on single zeolite adsorption sites. The combination of infrared spectroscopy and multivariate analysis is therefore demonstrated to be a powerful method to study detailed adsorption kinetics and mechanisms of the adsorption of molecules onto surfaces.

Adsorption↗

In search of secreted protein biomarkers for the anti-inflammatory effect of beta2-adrenergic receptor agonists: application of DIGE technology in combination with multivariate and univariate data analysis tools.

Two-dimensional difference gel electrophoresis (DIGE) in combination with univariate (Student's t-test) and multivariate data analysis, principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were used to study the anti-inflammatory effects of the beta(2)-adrenergic receptor (beta(2)-AR) agonist zilpaterol. U937 macrophages were exposed to the endotoxin lipopolysaccharide (LPS) to induce an inflammatory reaction, which was inhibited by the addition of zilpaterol (LZ). This inhibition was counteracted by addition of the beta(2)-AR antagonist propranolol (LZP). The extracellular proteome of the U937 cells induced by the three treatments were examined by DIGE. PCA was used as an explorative tool to investigate the clustering of the proteome dataset. Using this tool, the dataset obtained from cells treated with LPS and LZP were separated from those obtained from LZ treated cells. PLS-DA, a multivariate data analysis tool that also takes correlations between protein spots and class assignment into account, correctly classified the different extracellular proteomes and showed that many proteins were differentially expressed between the proteome of inflamed cells (LPS and LZP) and cells in which the inflammatory response was inhibited (LZ). The Student's t-test revealed 8 potential protein biomarkers, each of which was expressed at a similar level in the LPS and LZP treated cells, but differently expressed in the LZ treated cells. Two of the identified proteins, macrophage inflammatory protein-1beta (MIP-1beta) and macrophage inflammatory protein-1alpha (MIP-1alpha) are known secreted proteins. The inhibition of MIP-1beta by zilpaterol and the involvement of the beta(2)-AR and cAMP were confirmed using a specific immunoassay.

Adrenergic Agonists↗

Analysis of principal component based quantitative phenotypes for alcoholism.

Principal component analysis was used to construct quantitative phenotypes for alcoholism. These were analyzed for linkage to genomic regions with a variance components approach. The four phenotypes considered were a factor describing medical symptoms of alcohol dependency, a factor describing a psychological profile correlated with susceptibility to alcoholism, monoamine oxidase B (MAOB) activity and an average measurement of the P3 component of event-related potentials (ERP) at the Fp electrode placements. One region (around marker GATA123C09 on chromosome 3) with suggestive evidence for linkage was detected for the P3 (Fp) measurement. For three of the four distinct phenotypes, modest evidence for linkage to a similar region (around marker ADH3 on chromosome 4) was found.

Alcoholism↗

Patterns of multiple resistance to antibiotics in gram-negative bacteria demonstrated by factor analysis.

Principal component analysis was used to demonstrate the main associations between patterns of resistance to antibiotic drugs in 670 gram-negative bacteria consecutively isolated from blood cultures over a period of two years. Six factors were derived, which accounted for 84% of the total variance of the original matrix. Each factor represented an association between resistance to certain antibiotics as follows: factor 1: aztreonam, third generation cephalosporins and aminoglycosides; factor 2: first and second generation cephalosporins; factor 3: tetracycline and chloramphenicol; factor 4: ampicillin and ureidopenicillins; factor 5: trimethoprim/sulfamethoxazole; factor 6: fluoroquinolones. On two-way analysis of variance the difference in the factor scores was significant between bacteria for all factors except factor 5. The difference in factor scores between community and hospital acquired strains was significant only for factors 1, 2 and 6. Only the score of factor 6 showed a clear trend to increase with time during the two-year study period. Patients who were treated with antibiotics prior to bacteremia had higher scores for all factors, the difference being most marked in patients treated with fluoroquinolones. Factor analysis can be used to describe phenotypic associations between resistance to antibiotics, and the factor score used to compare groups of isolates and to demonstrate temporal and other trends.

Ampicillin↗

Exploratory behavior of F2 crosses of mouse lines selected for different brain weight: a multivariate analysis.

Principal component analysis of behavioural measures together with body and brain weight of hybrid F2 mice crosses between two lines selected for large (LB) and small (SB) brain weight yielded eight-factor solution explaining 75.1% of total variance. Two of eight factors had sufficient loading on brain weight and several behavioural measures. The factor analysis showed that, among F2 hybrids, mice with larger brain weight were characterised, in open-field test, by higher scores of locomotion in the periphery of arena and of rearing, as well as less frequent grooming and freezing than mice with smaller brain weight. F2 hybrids with larger brain weight moved faster and displayed stereotyped behaviour in the cross-maze test more frequently. In general, this diversity is in accord with the behaviour differences between parent LB and SB lines. The results show that, in mice fear-anxiety and stereotypic behaviours, which are known to interfere with normal exploration and learning of the environment, are causally connected with brain weight.

Animals↗

Feature selection and nearest centroid classification for protein mass spectrometry.

BACKGROUND: The use of mass spectrometry as a proteomics tool is poised to revolutionize early disease diagnosis and biomarker identification. Unfortunately, before standard supervised classification algorithms can be employed, the "curse of dimensionality" needs to be solved. Due to the sheer amount of information contained within the mass spectra, most standard machine learning techniques cannot be directly applied. Instead, feature selection techniques are used to first reduce the dimensionality of the input space and thus enable the subsequent use of classification algorithms. This paper examines feature selection techniques for proteomic mass spectrometry. RESULTS: This study examines the performance of the nearest centroid classifier coupled with the following feature selection algorithms. Student-t test, Kolmogorov-Smirnov test, and the P-test are univariate statistics used for filter-based feature ranking. From the wrapper approaches we tested sequential forward selection and a modified version of sequential backward selection. Embedded approaches included shrunken nearest centroid and a novel version of boosting based feature selection we developed. In addition, we tested several dimensionality reduction approaches, namely principal component analysis and principal component analysis coupled with linear discriminant analysis. To fairly assess each algorithm, evaluation was done using stratified cross validation with an internal leave-one-out cross-validation loop for automated feature selection. Comprehensive experiments, conducted on five popular cancer data sets, revealed that the less advocated sequential forward selection and boosted feature selection algorithms produce the most consistent results across all data sets. In contrast, the state-of-the-art performance reported on isolated data sets for several of the studied algorithms, does not hold across all data sets. CONCLUSION: This study tested a number of popular feature selection methods using the nearest centroid classifier and found that several reportedly state-of-the-art algorithms in fact perform rather poorly when tested via stratified cross-validation. The revealed inconsistencies provide clear evidence that algorithm evaluation should be performed on several data sets using a consistent (i.e., non-randomized, stratified) cross-validation procedure in order for the conclusions to be statistically sound.

Algorithms↗

Environmetric modeling and interpretation of river water monitoring data.

This environmetric study deals with modeling and interpretation of river water monitoring data from the basin of the Saale river and its tributaries the Ilm and the Unstrut. For a period of one year of observation between September 1993 and August 1994 a data set from twelve campaigns at twenty-nine sampling sites from the Saale river and six campaigns from the river Ilm at seven sampling sites and from river Unstrut at ten sampling sites was collected. Twenty-seven chemical and physicochemical properties were measured to estimate the water quality. The application of cluster analysis, principal components analysis, and apportioning modeling on absolute principal components scores revealed important information about the ecological status of the region of interest:identification of two separate patterns of pollution (upper and lower stream of the rivers);identification of six latent factors responsible for the data structure with different content for the two identified pollution patterns; anddetermination of the contribution of each latent factor (source of emission) to the formation of the total concentration of the chemical burden of the river water. As a result more objective ecological policy and decision making is possible.

Bulgaria↗

Application of two-dimensional nuclear magnetic resonance spectroscopy to quality control of ginseng commercial products.

Ginseng has been used as a powder or a crude extract of the plant roots. The quality control of commercial ginseng preparations is difficult due to the diverse compounds present. Most previous quality control methods using TLC or HPLC-UV (or -MS) cannot be expected to cover a wide range of compounds in the commercial ginseng preparations. In this study, the metabolic fingerprinting of ginseng preparations was performed by (1)H-NMR spectroscopy. Although (1)H-NMR spectroscopy could provide information about the total profile of the compounds present, low resolution and overlapping signals make it difficult for further identification of each compound. For overcoming the problem two-dimensional J-resolved NMR spectra and multivariate data analysis techniques was applied for the analysis. Principal component analysis (PCA) of projected J-resolved NMR spectra shows a clear discrimination among those samples by principal component 1 and principal component 3. The loading plot of PC values obtained from all NMR signals indicates that alanine, arginine, choline, fumaric acid, inositol, sucrose as well as ginsenosides are important metabolites to differentiate the preparations from each other. This method allows an efficient discrimination of a ginseng preparation in less than 15 minutes without any pre-purification steps.

Humans↗

A gentle guide to the analysis of metabolomic data.

Modern molecular biology crucially relies on computational tools to handle and interpret the large amounts of data that are generated by high-throughput measurements. To this end, much effort is dedicated to devise novel sophisticated methods that allow one to integrate, evaluate, and analyze biological data. However, prior to an application of specifically designed methods, simple and well-known statistical approaches often provide a more appropriate starting point for further analysis. This chapter seeks to describe several well-established approaches to data analysis, including various clustering techniques, discriminant function analysis, principal component analysis, multidimensional scaling, and classification trees. The chapter is accompanied by a webpage, describing the application of all algorithms in a ready-to-use format.

Arabidopsis↗

On the slow convergence of EM and VBEM in low-noise linear models.

We analyze convergence of the expectation maximization (EM) and variational Bayes EM (VBEM) schemes for parameter estimation in noisy linear models. The analysis shows that both schemes are inefficient in the low-noise limit. The linear model with additive noise includes as special cases independent component analysis, probabilistic principal component analysis, factor analysis, and Kalman filtering. Hence, the results are relevant for many practical applications.

Algorithms↗

Selecting a battery of bioassays for ecotoxicological characterization of wastes.

This study was conducted in France within the context of waste classification (Hazardous Waste Council Directive 91/689/EEC), and focused on "ecotoxic" property (H14). In 1998, an experimental test strategy was developed to assess ecotoxicological properties of wastes using a battery of six standardized bioassays. This combined direct and indirect approaches integrating two solid-phase tests: emergence and growth inhibition of Lactuca sativa (14 days), mortality of Eisenia fetida (14 days) and four standardized tests performed on water extracts from wastes: growth inhibition of Pseudokirchneriella subcapitata (3 days), inhibition of mobility of Daphnia magna (48 h), inhibition of reproduction of Ceriodaphnia dubia (7 days), inhibition of light emission of Vibrio fischeri (30 min). This study aimed to set up preliminary conclusions on relevancy of this experimental test strategy, based on data obtained since 1998. Results were analyzed from the combined use of Hierarchical Cluster Analysis, Principal Component Analysis and Nonlinear Mapping. These multivariate analyses clearly showed that it was possible to reduce this number of tests without changing the typology of the wastes. A battery of bioassays including one solid phase test and two tests performed on water extracts (L. sativa, V. fischeri and C. dubia) was found as an optimal solution for characterizing the toxicity of the studied wastes. This optimal battery represents a good basis for determining the H14 property.

Aliivibrio fischeri↗

Strategies for reducing large fMRI data sets for independent component analysis.

In independent component analysis (ICA), principal component analysis (PCA) is generally used to reduce the raw data to a few principal components (PCs) through eigenvector decomposition (EVD) on the data covariance matrix. Although this works for spatial ICA (sICA) on moderately sized fMRI data, it is intractable for temporal ICA (tICA), since typical fMRI data have a high spatial dimension, resulting in an unmanageable data covariance matrix. To solve this problem, two practical data reduction methods are presented in this paper. The first solution is to calculate the PCs of tICA from the PCs of sICA. This approach works well for moderately sized fMRI data; however, it is highly computationally intensive, even intractable, when the number of scans increases. The second solution proposed is to perform PCA decomposition via a cascade recursive least squared (CRLS) network, which provides a uniform data reduction solution for both sICA and tICA. Without the need to calculate the covariance matrix, CRLS extracts PCs directly from the raw data, and the PC extraction can be terminated after computing an arbitrary number of PCs without the need to estimate the whole set of PCs. Moreover, when the whole data set becomes too large to be loaded into the machine memory, CRLS-PCA can save data retrieval time by reading the data once, while the conventional PCA requires numerous data retrieval steps for both covariance matrix calculation and PC extractions. Real fMRI data were used to evaluate the PC extraction precision, computational expense, and memory usage of the presented methods.

Algorithms↗

Three microarray platforms: an analysis of their concordance in profiling gene expression.

BACKGROUND: Microarrays for the analysis of gene expression are of three different types: short oligonucleotide (25-30 base), long oligonucleotide (50-80 base), and cDNA (highly variable in length). The short oligonucleotide and cDNA arrays have been the mainstay of expression analysis to date, but long oligonucleotide platforms are gaining in popularity and will probably replace cDNA arrays. As part of a validation study for the long oligonucleotide arrays, we compared and contrasted expression profiles from the three formats, testing RNA from six different cell lines against a universal reference standard. RESULTS: The three platforms had 6430 genes in common. In general, correlation of gene expression levels across the platforms was good when defined by concordance in the direction of expression difference (upregulation or downregulation), scatter plot analysis, principal component analysis, cell line correlation or quantitative RT-PCR. The overall correlations (r values) between platforms were in the range 0.7 to 0.8, as determined by analysis of scatter plots. When concordance was measured for expression ratios significant at p-values of <0.05 and at expression threshold levels of 1.5 and 2-fold, the agreement among the platforms was very high, ranging from 93% to 100%. CONCLUSION: Our results indicate that the long oligonucleotide platform is highly suitable for expression analysis and compares favorably with the cDNA and short oligonucleotide varieties. All three platforms can give similar and reproducible results if the criterion is the direction of change in gene expression and minimal emphasis is placed on the magnitude of change.

Cell Line↗