This paper focuses on the problem of hierarchical non-overlapping clustering of a dataset. In such a clustering, each data item is associated with exactly one leaf node and each internal node is associated with all the data items stored in the sub-tree beneath it, so that each level of the hierarchy corresponds to a partition of the dataset. We develop a novel Bayesian nonparametric method combining the nested Chinese Restaurant Process (nCRP) and the Hierarchical Dirichlet Process (HDP). Compared with other existing Bayesian approaches, our solution tackles data with complex latent mixture features which has not been previously explored in the literature. We discuss the details of the model and the inference procedure. Furthermore, experiments on three datasets show that our method achieves solid empirical results in comparison with existing algorithms.
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Linear Mixed Effects (LME) models have been widely applied in clustered data analysis in many areas including marketing research, clinical trials, and biomedical studies. Inference can be conducted using maximum likelihood approach if assuming Normal distributions on the random effects. However, in many applications of economy, business and medicine, it is often essential to impose constraints on the regression parameters after taking their real-world interpretations into account. Therefore, in this paper we extend the classical (unconstrained) LME models to allow for sign constraints on its overall coefficients. We propose to assume a symmetric doubly truncated Normal (SDTN) distribution on the random effects instead of the unconstrained Normal distribution which is often found in classical literature. With the aforementioned change, difficulty has dramatically increased as the exact distribution of the dependent variable becomes analytically intractable. We then develop likelihood-based approaches to estimate the unknown model parameters utilizing the approximation of its exact distribution. Simulation studies have shown that the proposed constrained model not only improves real-world interpretations of results, but also achieves satisfactory performance on model fits as compared to the existing model.
We consider the nonparametric estimation of an S-shaped regression function. The least squares estimator provides a very natural, tuning-free approach, but results in a non-convex optimisation problem, since the inflection point is unknown. We show that the estimator may nevertheless be regarded as a projection onto a finite union of convex cones, which allows us to propose a mixed primal-dual bases algorithm for its efficient, sequential computation. After developing a projection framework that demonstrates the consistency and robustness to misspecification of the estimator, our main theoretical results provide sharp oracle inequalities that yield worst-case and adaptive risk bounds for the estimation of the regression function, as well as a rate of convergence for the estimation of the inflection point. These results reveal not only that the estimator achieves the minimax optimal rate of convergence for both the estimation of the regression function and its inflection point (up to a logarithmic factor in the latter case), but also that it is able to achieve an almost-parametric rate when the true regression function is piecewise affine with not too many affine pieces. Simulations and a real data application to air pollution modelling also confirm the desirable finite-sample properties of the estimator, and our algorithm is implemented in the R package Sshaped.
In biomedical optics, it is often of interest to statistically model the amplitude of the speckle using some distributional models with their parameters acting as biomarkers. In this paper, a paradigm shift is being advocated in which a distributional model-free approach is used. Specifically, a range of distances, evaluated in different domains, between an empirical nonparametric distribution of the normalized speckle amplitude sample and the benchmark Rayleigh distribution, is considered. Using OCT images from phantoms, two ex-vivo experiments with porcine corneas and an in-vivo experiment with human corneas, an evidence is provided that the distributional model-free approach, despite its simplicity, could lead to better results than the best-fitted (among a range of considered models) distributional model. Concluding, in practice, the distributional model-free approach should be considered as the first choice to speckle modeling before a distributional-based approach is utilized.
We develop a Bayesian nonparametric autoregressive model applied to flexibly estimate general transition densities exhibiting nonlinear lag dependence. Our approach is related to Bayesian density regression using Dirichlet process mixtures, with the Markovian likelihood defined through the conditional distribution obtained from the mixture. This results in a Bayesian nonparametric extension of a mixtures-of-experts model formulation. We address computational challenges to posterior sampling that arise from the Markovian structure in the likelihood. The base model is illustrated with synthetic data from a classical model for population dynamics, as well as a series of waiting times between eruptions of Old Faithful Geyser. We study inferences available through the base model before extending the methodology to include automatic relevance detection among a pre-specified set of lags. Inference for global and local lag selection is explored with additional simulation studies, and the methods are illustrated through analysis of an annual time series of pink salmon abundance in a stream in Alaska. We further explore and compare transition density estimation performance for alternative configurations of the proposed model.
To combat the HIV/AIDS pandemic effectively, targeted interventions among certain key populations play a critical role. Examples of such key populations include sex workers, people who inject drugs, and men who have sex with men. While having accurate estimates for the size of these key populations is important, any attempt to directly contact or count members of these populations is difficult. As a result, indirect methods are used to produce size estimates. Multiple approaches for estimating the size of such populations have been suggested but often give conflicting results. It is therefore necessary to have a principled way to combine and reconcile these estimates. To this end, we present a Bayesian hierarchical model for estimating the size of key populations that combines multiple estimates from different sources of information. The proposed model makes use of multiple years of data and explicitly models the systematic error in the data sources used. We use the model to estimate the size of people who inject drugs in Ukraine. We evaluate the appropriateness of the model and compare the contribution of each data source to the final estimates.
This paper aims to explore models based on the extreme gradient boosting (XGBoost) approach for business risk classification. Feature selection (FS) algorithms and hyper-parameter optimizations are simultaneously considered during model training. The five most commonly used FS methods including weight by Gini, weight by Chi-square, hierarchical variable clustering, weight by correlation, and weight by information are applied to alleviate the effect of redundant features. Two hyper-parameter optimization approaches, random search (RS) and Bayesian tree-structured Parzen Estimator (TPE), are applied in XGBoost. The effect of different FS and hyper-parameter optimization methods on the model performance are investigated by the Wilcoxon Signed Rank Test. The performance of XGBoost is compared to the traditionally utilized logistic regression (LR) model in terms of classification accuracy, area under the curve (AUC), recall, and F1 score obtained from the 10-fold cross validation. Results show that hierarchical clustering is the optimal FS method for LR while weight by Chi-square achieves the best performance in XG-Boost. Both TPE and RS optimization in XGBoost outperform LR significantly. TPE optimization shows a superiority over RS since it results in a significantly higher accuracy and a marginally higher AUC, recall and F1 score. Furthermore, XGBoost with TPE tuning shows a lower variability than the RS method. Finally, the ranking of feature importance based on XGBoost enhances the model interpretation. Therefore, XGBoost with Bayesian TPE hyper-parameter optimization serves as an operative while powerful approach for business risk modeling.
The availability of large microarray data has led to a growing interest in biclustering methods in the past decade. Several algorithms have been proposed to identify subsets of genes and conditions according to different similarity measures and under varying constraints. In this paper we focus on the exclusive row biclustering problem for gene expression data sets, in which each row can only be a member of a single bicluster while columns can participate in multiple ones. This type of biclustering may be adequate, for example, for clustering groups of cancer patients where each patient (row) is expected to be carrying only a single type of cancer, while each cancer type is associated with multiple (and possibly overlapping) genes (columns). We present a novel method to identify these exclusive row biclusters through a combination of existing biclustering algorithms and combinatorial auction techniques. We devise an approach for tuning the threshold for our algorithm based on comparison to a null model in the spirit of the Gap statistic approach. We demonstrate our approach on both synthetic and real-world gene expression data and show its power in identifying large span non-overlapping rows sub matrices, while considering their unique nature. The Gap statistic approach succeeds in identifying appropriate thresholds in all our examples.
We consider the task of learning the parameters of a {\em single} component of a mixture model, for the case when we are given {\em side information} about that component, we call this the "search problem" in mixture models. We would like to solve this with computational and sample complexity lower than solving the overall original problem, where one learns parameters of all components. Our main contributions are the development of a simple but general model for the notion of side information, and a corresponding simple matrix-based algorithm for solving the search problem in this general setting. We then specialize this model and algorithm to four common scenarios: Gaussian mixture models, LDA topic models, subspace clustering, and mixed linear regression. For each one of these we show that if (and only if) the side information is informative, we obtain parameter estimates with greater accuracy, and also improved computation complexity than existing moment based mixture model algorithms (e.g. tensor methods). We also illustrate several natural ways one can obtain such side information, for specific problem instances. Our experiments on real data sets (NY Times, Yelp, BSDS500) further demonstrate the practicality of our algorithms showing significant improvement in runtime and accuracy.
Discrete random structures are important tools in Bayesian nonparametrics and the resulting models have proven effective in density estimation, clustering, topic modeling and prediction, among others. In this paper, we consider nested processes and study the dependence structures they induce. Dependence ranges between homogeneity, corresponding to full exchangeability, and maximum heterogeneity, corresponding to (unconditional) independence across samples. The popular nested Dirichlet process is shown to degenerate to the fully exchangeable case when there are ties across samples at the observed or latent level. To overcome this drawback, inherent to nesting general discrete random measures, we introduce a novel class of latent nested processes. These are obtained by adding common and group-specific completely random measures and, then, normalising to yield dependent random probability measures. We provide results on the partition distributions induced by latent nested processes, and develop an Markov Chain Monte Carlo sampler for Bayesian inferences. A test for distributional homogeneity across groups is obtained as a by product. The results and their inferential implications are showcased on synthetic and real data.
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