We describe a Groebner basis of relations among conditional probabilities in a discrete probability space, with any set of conditioned-upon events. They may be specialized to the partially-observed random variable case, the purely conditional case, and other special cases. We also investigate the connection to generalized permutohedra and describe a conditional probability simplex.

The local linear embedding algorithm (LLE) is a non-linear dimension-reducing technique, widely used due to its computational simplicity and intuitive approach. LLE first linearly reconstructs each input point from its nearest neighbors and then preserves these neighborhood relations in the low-dimensional embedding. We show that the reconstruction weights computed by LLE capture the high-dimensional structure of the neighborhoods, and not the low-dimensional manifold structure. Consequently, the weight vectors are highly sensitive to noise. Moreover, this causes LLE to converge to a linear projection of the input, as opposed to its non-linear embedding goal. To overcome both of these problems, we propose to compute the weight vectors using a low-dimensional neighborhood representation. We prove theoretically that this straightforward and computationally simple modification of LLE reduces LLE's sensitivity to noise. This modification also removes the need for regularization when the number of neighbors is larger than the dimension of the input. We present numerical examples demonstrating both the perturbation and linear projection problems, and the improved outputs using the low-dimensional neighborhood representation.

This paper provides the reader with a very brief introduction to some of the theory and methods of text data mining. The intent of this article is to introduce the reader to some of the current methodologies that are employed within this discipline area while at the same time making the reader aware of some of the interesting challenges that remain to be solved within the area. Finally, the articles serves as a very rudimentary tutorial on some of techniques while also providing the reader with a list of references for additional study.

Gaussian processes retain the linear model either as a special case, or in the limit. We show how this relationship can be exploited when the data are at least partially linear. However from the perspective of the Bayesian posterior, the Gaussian processes which encode the linear model either have probability of nearly zero or are otherwise unattainable without the explicit construction of a prior with the limiting linear model in mind. We develop such a prior, and show that its practical benefits extend well beyond the computational and conceptual simplicity of the linear model. For example, linearity can be extracted on a per-dimension basis, or can be combined with treed partition models to yield a highly efficient nonstationary model. Our approach is demonstrated on synthetic and real datasets of varying linearity and dimensionality.

Bayesian model averaging, model selection and its approximations such as BIC are generally statistically consistent, but sometimes achieve slower rates og convergence than other methods such as AIC and leave-one-out cross-validation. On the other hand, these other methods can br inconsistent. We identify the "catch-up phenomenon" as a novel explanation for the slow convergence of Bayesian methods. Based on this analysis we define the switch distribution, a modification of the Bayesian marginal distribution. We show that, under broad conditions,model selection and prediction based on the switch distribution is both consistent and achieves optimal convergence rates, thereby resolving the AIC-BIC dilemma. The method is practical; we give an efficient implementation. The switch distribution has a data compression interpretation, and can thus be viewed as a "prequential" or MDL method; yet it is different from the MDL methods that are usually considered in the literature. We compare the switch distribution to Bayes factor model selection and leave-one-out cross-validation.

Art historians and archaeologists have long grappled with the regional classification of ancient Near Eastern ivory carvings. Based on the visual similarity of sculptures, individuals within these fields have proposed object assemblages linked to hypothesized regional production centers. Using quantitative rather than visual methods, we here approach this classification task by exploiting computational methods from machine learning currently used with success in a variety of statistical problems in science and engineering. We first construct a prediction function using 66 categorical features as inputs and regional style as output. The model assigns regional style group (RSG), with 98 percent prediction accuracy. We then rank these features by their mutual information with RSG, quantifying single-feature predictive power. Using the highest- ranking features in combination with nomographic visualization, we have found previously unknown relationships that may aid in the regional classification of these ivories and their interpretation in art historical context.

We present an efficient, principled, and interpretable technique for inferring module assignments and for identifying the optimal number of modules in a given network. We show how several existing methods for finding modules can be described as variant, special, or limiting cases of our work, and how the method overcomes the resolution limit problem, accurately recovering the true number of modules. Our approach is based on Bayesian methods for model selection which have been used with success for almost a century, implemented using a variational technique developed only in the past decade. We apply the technique to synthetic and real networks and outline how the method naturally allows selection among competing models.

Statistical modeling of nuclear data provides a novel approach to nuclear systematics complementary to established theoretical and phenomenological approaches based on quantum theory. Continuing previous studies in which global statistical modeling is pursued within the general framework of machine learning theory, we implement advances in training algorithms designed to improved generalization, in application to the problem of reproducing and predicting the halflives of nuclear ground states that decay 100% by the beta^- mode. More specifically, fully-connected, multilayer feedforward artificial neural network models are developed using the Levenberg-Marquardt optimization algorithm together with Bayesian regularization and cross-validation. The predictive performance of models emerging from extensive computer experiments is compared with that of traditional microscopic and phenomenological models as well as with the performance of other learning systems, including earlier neural network models as well as the support vector machines recently applied to the same problem. In discussing the results, emphasis is placed on predictions for nuclei that are far from the stability line, and especially those involved in the r-process nucleosynthesis. It is found that the new statistical models can match or even surpass the predictive performance of conventional models for beta-decay systematics and accordingly should provide a valuable additional tool for exploring the expanding nuclear landscape.

The problem of supervised classification (or discrimination) with functional data is considered, with a special interest on the popular k-nearest neighbors (k-NN) classifier. First, relying on a recent result by Cerou and Guyader (2006), we prove the consistency of the k-NN classifier for functional data whose distribution belongs to a broad family of Gaussian processes with triangular covariance functions. Second, on a more practical side, we check the behavior of the k-NN method when compared with a few other functional classifiers. This is carried out through a small simulation study and the analysis of several real functional data sets. While no global "uniform" winner emerges from such comparisons, the overall performance of the k-NN method, together with its sound intuitive motivation and relative simplicity, suggests that it could represent a reasonable benchmark for the classification problem with functional data.

We present the Procrustes measure, a novel measure based on Procrustes rotation that enables quantitative comparison of the output of manifold-based embedding algorithms (such as LLE (Roweis and Saul, 2000) and Isomap (Tenenbaum et al, 2000)). The measure also serves as a natural tool when choosing dimension-reduction parameters. We also present two novel dimension-reduction techniques that attempt to minimize the suggested measure, and compare the results of these techniques to the results of existing algorithms. Finally, we suggest a simple iterative method that can be used to improve the output of existing algorithms.