Estimating Shapley effects for moderate-to-large input dimensions

Sobol' indices and Shapley effects are attractive methods of assessing how a function depends on its various inputs. The existing literature contains various estimators for these two classes of sensitivity indices, but few estimators of Sobol' indices and no estimators of Shapley effects are computationally tractable for moderate-to-large input dimensions. This article provides a Shapley-effect estimator that is computationally tractable for a moderate-to-large input dimension. The estimator uses a metamodel-based approach by first fitting a Bayesian Additive Regression Trees model which is then used to compute Shapley-effect estimates. This article also establishes posterior contraction rates on a large function class for this Shapley-effect estimator and for the analogous existing Sobol'-index estimator. Finally, this paper explores the performance of these Shapley-effect estimators on four different test functions for moderate-to-large input dimensions and number of observations.Comment: 19 pages, 3 figure

Tree stick-breaking priors for covariate-dependent mixture models

Stick-breaking priors are often adopted in Bayesian nonparametric mixture models for generating mixing weights. When covariates influence the sizes of clusters, stick-breaking mixtures can leverage various computational techniques for binary regression to ease posterior computation. Existing stick-breaking priors are typically based on continually breaking a single remaining piece of the unit stick. We demonstrate that this ``single-piece'' scheme can induce three highly undesirable behaviors; these behaviors are circumvented by our proposed model which continually breaks off all remaining pieces of a unit stick while keeping posterior computation essentially identical. Specifically, the new model provides more flexibility in setting cross-covariate prior correlation among the generated random measures, mitigates the impact of component label switching when posterior simulation is performed using Markov chain Monte Carlo, and removes the imposed artificial decay of posterior uncertainty on the mixing weights according to when the weight is ``broken off'' the unit stick. Unlike previous works on covariate-dependent mixtures, which focus on estimating covariate-dependent distributions, we instead focus on inferring the effects of individual covariates on the mixture weights in a fashion similar to classical regression analysis, and propose a new class of posterior predictives for summarizing covariate effects.Comment: 47 pages, 16 figures, to be submitted to Journal of the American Statistical Association Theory and Method

Virtual Experimental Environment to Support Learning by Designing Physical Experiment

Acquiring the ability to use physical laws to deal with concrete physical situations is one of the most important targets in physics learning. In the learning, however, students are usually required only to solve exercise problems by using the physical laws. The students who can solve exercise problems with the laws cannot always use the laws to deal with the concrete physical situation. We, therefore, propose a virtual experimental environment where students are required to deal with physical situations with the laws measuring several attributes in order to derive an attribute. In this paper, the implementation of the environment and the results of experimental are also described

Accelerator Analysis of Tributyltin Adsorbed onto the Surface of a Tributyltin Resistant Marine Pseudoalteromonas sp. Cell

Tributyltin (TBT) released into seawater from ship hulls is a stable marine pollutant and obviously remains in marine environments. We isolated a TBT resistant marine Pseudoalteromonas sp. TBT1 from sediment of a ship’s ballast water. The isolate (109.3 ± 0.2 colony-forming units mL−1) adsorbed TBT in proportion to the concentrations of TBTCl externally added up to 3 mM, where the number of TBT adsorbed by a single cell was estimated to be 108.2. The value was reduced to about one-fifth when the lysozyme-treated cells were used. The surface of ethanol treated cells became rough, but the capacity of TBT adsorption was the same as that for native cells. These results indicate that the function of the cell surface, rather than that structure, plays an important role to the adsorption of TBT. The adsorption state of TBT seems to be multi-layer when the number of more than 106.8 TBT molecules is adsorbed by a single cell

Impact of Tributyltin and Triphenyltin on Ivory Shell (Babylonia japonica) Populations

We histopathologically examined gonads and chemically determined organotin compounds in tissues of the ivory shell, Babylonia japonica. Imposex (a superimposition of male-type genital organs on females) occurred in approximately 80–90% of B. japonica specimens that we examined, with the penis and vas deferens both well developed. No oviduct blockage by vas deferens formation was observed. Ovarian spermatogenesis and suppressed ovarian maturation were observed in the females that exhibited imposex, although no histopathological abnormalities were found in males. Tissue distributions of organotin compounds [tributyltin (TBT), triphenyltin (TPhT), and their metabolites] were different for butyltins and phenyltins; a remarkably high accumulation of TBT was observed in the ctenidium, osphradium, and heart, whereas high concentrations of TPhT were detected in the ovary and digestive gland. More than one-third of TBT accumulated in the digestive glands of both males and females, followed by the testis, ctenidium, muscle, and heart tissues in males and in the muscle, ovary, ctenidium, and head tissues (including the central nervous system ganglia) in females. In both males and females, more than half of total TPhT accumulated in the digestive glands, followed by the gonads. The next highest values were in the muscle, ctenidium, and heart tissues in males and in the muscle, oviduct, and head tissues in females. Both TBT and TPhT concentrations in the gonads were positively correlated with penis length in females. Our findings strongly suggest that reproductive failure in adult females accompanied by imposex, possibly induced by TBT and TPhT from antifouling paints, may have caused the marked decline of B. japonica populations in Japan

Mass spectrometry of short peptides reveals common features of metazoan peptidergic neurons

The evolutionary origins of neurons remain unknown. Although recent genome data of extant early-branching animals have shown that neural genes existed in the common ancestor of animals, the physiological and genetic properties of neurons in the early evolutionary phase are still unclear. Here, we performed a mass spectrometry-based comprehensive survey of short peptides from early-branching lineages Cnidaria, Porifera and Ctenophora. We identified a number of mature ctenophore neuropeptides that are expressed in neurons associated with sensory, muscular and digestive systems. The ctenophore peptides are stored in vesicles in cell bodies and neurites, suggesting volume transmission similar to that of cnidarian and bilaterian peptidergic systems. A comparison of genetic characteristics revealed that the peptide-expressing cells of Cnidaria and Ctenophora express the vast majority of genes that have pivotal roles in maturation, secretion and degradation of neuropeptides in Bilateria. Functional analysis of neuropeptides and prediction of receptors with machine learning demonstrated peptide regulation of a wide range of target effector cells, including cells of muscular systems. The striking parallels between the peptidergic neuronal properties of Cnidaria and Bilateria and those of Ctenophora, the most basal neuron-bearing animals, suggest a common evolutionary origin of metazoan peptidergic nervous systems

Involvement of Hepatic Innate Immunity in Alcoholic Liver Disease

Excessive alcohol consumption is one of the critical causative factors leading to alcoholic liver disease (ALD). ALD is characterized by a wide spectrum of liver damage, ranging from simple uncomplicated liver steatosis (fatty liver) to steatohepatitis and liver fibrosis/cirrhosis. It has been believed that the obvious underlying cause for ALD is due to hepatocyte death induced by alcohol itself. However, recent sparkling studies have shown that diverse immune responses contribute to ALD because liver is enriched with numerous immune cells. Especially, a line of evidence has suggested that innate immune cells such as Kupffer cells and natural killer (NK)/NKT cells are significantly involved in the pathogenesis of ALD via production of pro-inflammatory cytokines and other mediators. Indeed, more interestingly, hepatic stellate cells (HSCs), known as a major cell inducing liver steatosis and fibrosis, can be killed by liver NK cells, which could be suppressed by chronic alcohol consumption. In this review, with the view of liver as predominant innate immune organ, we describe the pathogenesis of ALD in which what roles of innate immune cells are and how they are interacting with HSCs