Tulaya Limpiti

Study of large and highly stratified population datasets by combining iterative pruning principal component analysis and structure.

BackgroundThe ever increasing sizes of population genetic datasets pose great challenges for population structure analysis. The Tracy-Widom (TW) statistical test is widely used for detecting structure. However, it has not been adequately investigated whether the TW statistic is susceptible to type I error, especially in large, complex datasets. Non-parametric, Principal Component Analysis (PCA) based methods for resolving structure have been developed which rely on the TW test. Although PCA-based methods can resolve structure, they cannot infer ancestry. Model-based methods are still needed for ancestry analysis, but they are not suitable for large datasets. We propose a new structure analysis framework for large datasets. This includes a new heuristic for detecting structure and incorporation of the structure patterns inferred by a PCA method to complement STRUCTURE analysis.ResultsA new heuristic called EigenDev for detecting population structure is presented. When tested on simulated data, this heuristic is robust to sample size. In contrast, the TW statistic was found to be susceptible to type I error, especially for large population samples. EigenDev is thus better-suited for analysis of large datasets containing many individuals, in which spurious patterns are likely to exist and could be incorrectly interpreted as population stratification. EigenDev was applied to the iterative pruning PCA (ipPCA) method, which resolves the underlying subpopulations. This subpopulation information was used to supervise STRUCTURE analysis to infer patterns of ancestry at an unprecedented level of resolution. To validate the new approach, a bovine and a large human genetic dataset (3945 individuals) were analyzed. We found new ancestry patterns consistent with the subpopulations resolved by ipPCA.ConclusionsThe EigenDev heuristic is robust to sampling and is thus superior for detecting structure in large datasets. The application of EigenDev to the ipPCA algorithm improves the estimation of the number of subpopulations and the individual assignment accuracy, especially for very large and complex datasets. Furthermore, we have demonstrated that the structure resolved by this approach complements parametric analysis, allowing a much more comprehensive account of population structure. The new version of the ipPCA software with EigenDev incorporated can be downloaded from http://www4a.biotec.or.th/GI/tools/ippca.

A Spatiotemporal Framework for MEG/EEG Evoked Response Amplitude and Latency Variability Estimation

This paper presents a spatiotemporal framework for estimating single-trial response latencies and amplitudes from evoked response magnetoencephalographic/electroencephalographic data. Spatial and temporal bases are employed to capture the aspects of the evoked response that are consistent across trials. Trial amplitudes are assumed independent but have the same underlying normal distribution with unknown mean and variance. The trial latency is assumed to be deterministic but unknown. We assume that the noise is spatially correlated with unknown covariance matrix. We introduce a generalized expectation-maximization algorithm called Trial Variability in Amplitude and Latency (TriViAL) that computes the maximum likelihood (ML) estimates of the amplitudes, latencies, basis coefficients, and noise covariance matrix. The proposed approach also performs ML source localization by scanning the TriViAL algorithm over spatial bases corresponding to different locations on the cortical surface. Source locations are identified as the locations corresponding to large likelihood values. The effectiveness of the TriViAL algorithm is demonstrated using simulated data and human evoked response experiments. The localization performance is validated using tactile stimulation of the finger. The efficacy of the algorithm in estimating latency variability is shown using the known dependence of the M100 auditory response latency to stimulus tone frequency. We also demonstrate that estimation of response amplitude is improved when latency is included in the signal model.

Iterative PCA for population structure analysis

An extension of principal component analysis called ipPCA has been proposed earlier for analyzing structure in genetic data. This non-parametric framework iteratively classifies individuals into subpopulations. However, it is prone to false positives when dealing with large datasets and mixed-type genetic markers. We address these shortcomings by introducing a unified encoding scheme and suggesting a new terminating criterion for ipPCA. To validate the improvements, simulated datasets as well as real bovine and large human genetic datasets are analyzed. It is observed that the estimation of the number of subpopulations and the individual assignment accuracy have been improved. Furthermore, the structure resolved by this approach can be used to identify subset of individuals for further parametric population structure analysis.

Chromatin Detection in Malaria Thick Blood Film Using Automated Image Processing

Malaria is a serious global health problem and rapid, accurate diagnosis is required to control the disease. An image processing algorithm to aid the diagnosis of malaria on thick blood films is developed. Morphological and automatic threshold selection techniques are applied on two color components from the HSI color model to identify chromatins of P. Falciparum and P. Vivax malaria species on the images. Chromatins are positively identified with good sensitivities for both species. After identifying the position of chromatins, the algorithm splits the image into small sub-images, each with a chromatin in the center. These small images can subsequently be used by technician to classify malaria species more conveniently.

A study on Ka-band site switching using advanced prediction for rain-induced attenuation

High frequency satellite communications suffers from rain-induced attenuations, which may cause service discontinuity during high-intensity rain events. To combat this, we propose a novel site switching technique that anticipates signal attenuations using a linear dynamical system response model and performs site switching in advance. Using only the rainfall data measured at a ground station for attenuation prediction, we demonstrate that our method is able to lessen signal attenuation while maintaining link availability.

iNJclust: iterative neighbor-joining tree clustering framework for inferring population structure

Understanding genetic differences among populations is one of the most important issues in population genetics. Genetic variations, e.g., single nucleotide polymorphisms, are used to characterize commonality and difference of individuals from various populations. This paper presents an efficient graph-based clustering framework which operates iteratively on the Neighbor-Joining (NJ) tree called the iNJclust algorithm. The framework uses well-known genetic measurements, namely the allele-sharing distance, the neighbor-joining tree, and the fixation index. The behavior of the fixation index is utilized in the algorithms stopping criterion. The algorithm provides an estimated number of populations, individual assignments, and relationships between populations as outputs. The clustering result is reported in the form of a binary tree, whose terminal nodes represent the final inferred populations and the tree structure preserves the genetic relationships among them. The clustering performance and the robustness of the proposed algorithm are tested extensively using simulated and real data sets from bovine, sheep, and human populations. The result indicates that the number of populations within each data set is reasonably estimated, the individual assignment is robust, and the structure of the inferred population tree corresponds to the intrinsic relationships among populations within the data.

PCA-based Informative SNP Selection for Analyzing Population Structure

Phenotypic differences among individuals of the same species are the result of a set of genetic variations which can be observed in the DNA sequence. To conduct a population genetic study, a high throughput genotyping platform such as Single Nucleotide Polymorphism (SNP) array is popularly used to obtain a large set of SNPs for each individual. However, analyzing todays genotypic data can be computationally expensive due to its large size and complexity. Faulty substructure may also be detected if the data is noisy from redundant or non-informative SNPs. Considerable efforts have been done to extract a smaller informative SNP subset that still represents the same intrinsic structure of populations within a data set as the full panel of SNPs. This work describes a foundation of a PCA-based informative marker selection technique. The proposed technique is simple and efficient. It improves upon another spectral analysis technique called PCA-correlated SNPs. A new informativeness score based on a basis function expansion of the SNP variation patterns across individuals is introduced. Such score is computed for each SNP to select a subset of SNPs with the best scores. Using a bovine data set, we demonstrate that our technique is superior to the PCA-correlated SNPs method, which requires accurate rank estimation to perform well. In contrast, our method is robust to the assumed rank of the data. High data representation accuracy is also achieved after a significant reduction of the number of SNPs while retaining information about the underlying population structure from the original data.

Estimating an optimal setpoint to lessen errors in filling weighing system based on Kalman filtering

A weighing system in which a sensor is not mounted to a discharger especially in vertical filling gives rise to an excess of weight added to the given target of weight. In addition, the excess is not constant on account of some factors, such as vibration of the machine, flow of the substance, and cycle time of the system. These factors cause the surplus to oscillate. To overcome this problem, Kalman filtering is performed to predict the optimal setpoint to meet the defined target. To illustrate the performance of the proposed technique, the resulting outcome is compared with that of using the conventional statistical method. The results have shown that the proposed approach has significantly increased the speed and lowered the error. It is pointed out that the proposed algorithm may be preferable to the traditional statistical technique due to its effectiveness and its simple implementation.