Bayesian analysis of the differences of count data

SC 2-PCR++: Rethinking the Generation and Selection for Efficient and Robust Point Cloud Registration

Outlier removal is a critical part of feature-based point cloud registration. In this article, we revisit the model generation and selection of the classic RANSAC approach for fast and robust point cloud registration. For the model generation, we propose a second-order spatial compatibility (SC 2) measure to compute the similarity between correspondences. It takes into account global compatibility instead of local consistency, allowing for more distinctive clustering between inliers and outliers at an early stage. The proposed measure promises to find a certain number of outlier-free consensus sets using fewer samplings, making the model generation more efficient. For the model selection, we propose a new Feature and Spatial consistency constrained Truncated Chamfer Distance (FS-TCD) metric for evaluating the generated models. It considers the alignment quality, the feature matching properness, and the spatial consistency constraint simultaneously, enabling the correct model to be selected even when the inlier rate of the putative correspondence set is extremely low. Extensive experiments are carried out to investigate the performance of our method. In addition, we also experimentally prove that the proposed SC 2 measure and the FS-TCD metric are general and can be easily plugged into deep learning based frameworks.

A Trinomial Difference Distribution

<p>A trinomial difference distribution is defined and its distributional properties are illustrated. This distribution present the binomial difference distribution as a special case. The moment estimators and maximum likelihood estimators of the trinomial difference distribution are compared via simulation study. Two applications are modeled with the trinomial difference distribution and compared with other possible distributions.</p>

Can Bayesian models play a role in dental caries epidemiology? Evidence from an application to the BELCAP data set

OBJECTIVES

The aim of this study was to show the potential of Bayesian analysis in statistical modelling of dental caries data. Because of the bounded nature of the dmft (DMFT) index, zero-inflated binomial (ZIB) and beta-binomial (ZIBB) models were considered. The effects of incorporating prior information available about the parameters of models were also shown.

METHODS

The data set used in this study was the Belo Horizonte Caries Prevention (BELCAP) study (Böhning et al. (1999)), consisting of five variables collected among 797 Brazilian school children designed to evaluate four programmes for reducing caries. Only the eight primary molar teeth were considered in the data set. A data augmentation algorithm was used for estimation. Firstly, noninformative priors were used to express our lack of knowledge about the regression parameters. Secondly, prior information about the probability of being a structural zero dmft and the probability of being caries affected in the subpopulation of susceptible children was incorporated.

RESULTS

With noninformative priors, the best fitting model was the ZIBB. Education (OR = 0.76, 95% CrI: 0.59, 0.99), all interventions (OR = 0.46, 95% CrI: 0.35, 0.62), rinsing (OR = 0.61, 95% CrI: 0.47, 0.80) and hygiene (OR = 0.65, 95% CrI: 0.49, 0.86) were demonstrated to be factors protecting children from being caries affected. Being male increased the probability of being caries diseased (OR = 1.19, 95% CrI: 1.01, 1.42). However, after incorporating informative priors, ZIB models' estimates were not influenced, while ZIBB models reduced deviance and confirmed the association with all interventions and rinsing only.

DISCUSSION

In our application, Bayesian estimates showed a similar accuracy and precision than likelihood-based estimates, although they offered many computational advantages and the possibility of expressing all forms of uncertainty in terms of probability. The overdispersion parameter could expound why the introduction of prior information had significant effects on the parameters of the ZIBB model, while ZIB estimates remained unchanged. Finally, the best performance of ZIBB compared to the ZIB model was shown to catch overdispersion in data.

A parametric time series model with covariates for integers in Z

While models for integer valued time series are now abundant, there is a shortage of similar models when the time series refer to data defined on Z, i.e., in both the positive and negative integers. Such data occur in certain disciplines and the need for such models also appear when taking differences of a positive integer count time series. In addition one would often like to include covariates to explain variations in the variable of interest. In this article we construct a model doing all these assuming a specific innovation distribution and provide fully parametric inference, including prediction. Real data applications on accidents and financial returns are given. Finally we also discuss alternative models and extensions.

Differential expression analysis for paired RNA-Seq data

Background

RNA-Seq technology measures the transcript abundance by generating sequence reads and counting their frequencies across different biological conditions. To identify differentially expressed genes between two conditions, it is important to consider the experimental design as well as the distributional property of the data. In many RNA-Seq studies, the expression data are obtained as multiple pairs, e.g., pre- vs. post-treatment samples from the same individual. We seek to incorporate paired structure into analysis.

Results

We present a Bayesian hierarchical mixture model for RNA-Seq data to separately account for the variability within and between individuals from a paired data structure. The method assumes a Poisson distribution for the data mixed with a gamma distribution to account variability between pairs. The effect of differential expression is modeled by two-component mixture model. The performance of this approach is examined by simulated and real data.

Conclusions

In this setting, our proposed model provides higher sensitivity than existing methods to detect differential expression. Application to real RNA-Seq data demonstrates the usefulness of this method for detecting expression alteration for genes with low average expression levels or shorter transcript length.

Inactivation of the WASF3 gene in prostate cancer cells leads to suppression of tumorigenicity and metastases

Background:

The WASF3 protein is involved in cell movement and invasion, and to investigate its role in prostate cancer progression we studied the phenotypic effects of knockdown in primary tumors and cell lines.

Methods:

ShRNA was used to knockdown WASF3 function in prostate cell lines. Cell motility (scratch wound assay), anchorage independent growth and in vivo tumorigenicity and metastasis were then compared between knockdown and wild-type cells.

Results:

Increased levels of expression were seen in high-grade human prostate cancer and in the PC3 and DU145 cell lines. Inactivation of WASF3 using shRNAs reduced cell motility and invasion in these cells and reduced anchorage independent growth in vitro. The loss of motility was accompanied by an associated increase in stress fiber formation and focal adhesions. When injected subcutaneously into severe combined immunodeficiency (SCID) mice, tumor formation was significantly reduced for PC3 and DU145 cells with WASF3 knockdown and in vivo metastasis assays using tail vain injection showed a significant reduction for PC3 and DU145 cells. The loss of the invasion phenotype was accompanied by down-regulation of matrix metalloproteinase 9.

Conclusions:

Overall, these observations demonstrate a critical role for WASF3 in the progression of prostate cancer and identify a potential target to control tumorigenicity and metastasis.

Repeatability of paired counts

The Bland and Altman technique is widely used to assess the variation between replicates of a method of clinical measurement. It yields the repeatability, i.e. the value within which 95 per cent of repeat measurements lie. The valid use of the technique requires that the variance is constant over the data range. This is not usually the case for counts of items such as CD4 cells or parasites, nor is the log transformation applicable to zero counts. We investigate the properties of generalized differences based on Box-Cox transformations. For an example, in a data set of hookworm eggs counted by the Kato-Katz method, the square root transformation is found to stabilize the variance. We show how to back-transform the repeatability on the square root scale to the repeatability of the counts themselves, as an increasing function of the square mean root egg count, i.e. the square of the average of square roots. As well as being more easily interpretable, the back-transformed results highlight the dependence of the repeatability on the sample volume used.