In this paper, a new descriptor selection method for selecting an optimal combination of important descriptors of sulfonamide derivatives data, named self tuned reweighted sampling (STRS), is developed. descriptors are defined as the descriptors with large absolute coefficients in a multivariate linear regression model such as partial least squares(PLS). In this study, the absolute values of regression coefficients of PLS model are used as an index for evaluating the importance of each descriptor Then, based on the importance level of each descriptor, STRS sequentially selects N subsets of descriptors from N Monte Carlo (MC) sampling runs in an iterative and competitive manner. In each sampling run, a fixed ratio (e.g. 80%) of samples is first randomly selected to establish a regresson model. Next, based on the regression coefficients, a two-step procedure including rapidly decreasing function (RDF) based enforced descriptor selection and self tuned sampling (STS) based competitive descriptor selection is adopted to select the important descriptorss. After running the loops, a number of subsets of descriptors are obtained and root mean squared error of cross validation (RMSECV) of PLS models established with subsets of descriptors is computed. The subset of descriptors with the lowest RMSECV is considered as the optimal descriptor subset. The performance of the proposed algorithm is evaluated by sulfanomide derivative dataset. The results reveal an good characteristic of STRS that it can usually locate an optimal combination of some important descriptors which are interpretable to the biologically of interest. Additionally, our study shows that better prediction is obtained by STRS when compared to full descriptor set PLS modeling, Monte Carlo uninformative variable elimination (MC-UVE).

We apply the OSCAR (octagonal selection and clustering algorithms for regression) in recovering group-sparse matrices (two-dimensional---2D---arrays) from compressive measurements. We propose a 2D version of OSCAR (2OSCAR) consisting of the $\ell_1$ norm and the pair-wise $\ell_{\infty}$ norm, which is convex but non-differentiable. We show that the proximity operator of 2OSCAR can be computed based on that of OSCAR. The 2OSCAR problem can thus be efficiently solved by state-of-the-art proximal splitting algorithms. Experiments on group-sparse 2D array recovery show that 2OSCAR regularization solved by the SpaRSA algorithm is the fastest choice, while the PADMM algorithm (with debiasing) yields the most accurate results.

We propose a novel SPARsity and Clustering (SPARC) regularizer, which is a modified version of the previous octagonal shrinkage and clustering algorithm for regression (OSCAR), where, the proposed regularizer consists of a $K$-sparse constraint and a pair-wise $\ell_{\infty}$ norm restricted on the $K$ largest components in magnitude. The proposed regularizer is able to separably enforce $K$-sparsity and encourage the non-zeros to be equal in magnitude. Moreover, it can accurately group the features without shrinking their magnitude. In fact, SPARC is closely related to OSCAR, so that the proximity operator of the former can be efficiently computed based on that of the latter, allowing using proximal splitting algorithms to solve problems with SPARC regularization. Experiments on synthetic data and with benchmark breast cancer data show that SPARC is a competitive group-sparsity inducing regularizer for regression and classification.

We consider new formulations and methods for sparse quantile regression in the high-dimensional setting. Quantile regression plays an important role in many applications, including outlier-robust exploratory analysis in gene selection. In addition, the sparsity consideration in quantile regression enables the exploration of the entire conditional distribution of the response variable given the predictors and therefore yields a more comprehensive view of the important predictors. We propose a generalized OMP algorithm for variable selection, taking the misfit loss to be either the traditional quantile loss or a smooth version we call quantile Huber, and compare the resulting greedy approaches with convex sparsity-regularized formulations. We apply a recently proposed interior point methodology to efficiently solve all convex formulations as well as convex subproblems in the generalized OMP setting, pro- vide theoretical guarantees of consistent estimation, and demonstrate the performance of our approach using empirical studies of simulated and genomic datasets.

Hierarchical statistical models are widely employed in information science and data engineering. The models consist of two types of variables: observable variables that represent the given data and latent variables for the unobservable labels. An asymptotic analysis of the models plays an important role in evaluating the learning process; the result of the analysis is applied not only to theoretical but also to practical situations, such as optimal model selection and active learning. There are many studies of generalization errors, which measure the prediction accuracy of the observable variables. However, the accuracy of estimating the latent variables has not yet been elucidated. For a quantitative evaluation of this, the present paper formulates distribution-based functions for the errors in the estimation of the latent variables. The asymptotic behavior is analyzed for both the maximum likelihood and the Bayes methods.

Determinantal point processes (DPPs) are well-suited for modeling repulsion and have proven useful in many applications where diversity is desired. While DPPs have many appealing properties, such as efficient sampling, learning the parameters of a DPP is still considered a difficult problem due to the non-convex nature of the likelihood function. In this paper, we propose using Bayesian methods to learn the DPP kernel parameters. These methods are applicable in large-scale and continuous DPP settings even when the exact form of the eigendecomposition is unknown. We demonstrate the utility of our DPP learning methods in studying the progression of diabetic neuropathy based on spatial distribution of nerve fibers, and in studying human perception of diversity in images.

Statistical and machine-learning algorithms are frequently applied to high-dimensional data. In many of these applications data is scarce, and often much more costly than computation time. We provide the first sample-efficient polynomial-time estimator for high-dimensional spherical Gaussian mixtures. For mixtures of any $k$ $d$-dimensional spherical Gaussians, we derive an intuitive spectral-estimator that uses $\mathcal{O}_k\bigl(\frac{d\log^2d}{\epsilon^4}\bigr)$ samples and runs in time $\mathcal{O}_{k,\epsilon}(d^3\log^5 d)$, both significantly lower than previously known. The constant factor $\mathcal{O}_k$ is polynomial for sample complexity and is exponential for the time complexity, again much smaller than what was previously known. We also show that $\Omega_k\bigl(\frac{d}{\epsilon^2}\bigr)$ samples are needed for any algorithm. Hence the sample complexity is near-optimal in the number of dimensions. We also derive a simple estimator for one-dimensional mixtures that uses $\mathcal{O}\bigl(\frac{k \log \frac{k}{\epsilon} }{\epsilon^2} \bigr)$ samples and runs in time $\widetilde{\mathcal{O}}\left(\bigl(\frac{k}{\epsilon}\bigr)^{3k+1}\right)$. Our other technical contributions include a faster algorithm for choosing a density estimate from a set of distributions, that minimizes the $\ell_1$ distance to an unknown underlying distribution.

An experiment is an organized procedure for validating a hypothesis, and usually comprises measurements over a set of variables that are either varied (covariates or independent variables) or studied (outcomes or dependent variables). For example, in the study of genome-wide association, one explores the association between'traits' (controlled variable) and common genetic variations (response variables) [1], or in the study of functional genomics covariates can be the species, disease state, and cell type, whereas outcome can be microarray measurements [2]. Traditionally, similar experiments have been retrieved from qualitative assessment of related scientific documents without explicitly handling the experimental data. Recent technological advances have allowed researchers to both acquire measurements in an unprecedented scale throughout the globe, and to release these measurements for public use after curation, e.g., [3]. However, exploring similar experiments still relies on comparing the manual annotations which suffer extensively from variations in terminology, and incompleteness in annotations, e.g., [4]. The global effort of availing researchers with wealth of data invites the need for sophisticated retrieval systems that look beyond annotations in comparing related experiments to improve accessibility. The next step toward this goal is to compare the knowledge acquired from experimental measurements rather than just annotations.

We investigate the Student-t process as an alternative to the Gaussian process as a nonparametric prior over functions. We derive closed form expressions for the marginal likelihood and predictive distribution of a Student-t process, by integrating away an inverse Wishart process prior over the covariance kernel of a Gaussian process model. We show surprising equivalences between different hierarchical Gaussian process models leading to Student-t processes, and derive a new sampling scheme for the inverse Wishart process, which helps elucidate these equivalences. Overall, we show that a Student-t process can retain the attractive properties of a Gaussian process -- a nonparametric representation, analytic marginal and predictive distributions, and easy model selection through covariance kernels -- but has enhanced flexibility, and predictive covariances that, unlike a Gaussian process, explicitly depend on the values of training observations. We verify empirically that a Student-t process is especially useful in situations where there are changes in covariance structure, or in applications like Bayesian optimization, where accurate predictive covariances are critical for good performance. These advantages come at no additional computational cost over Gaussian processes.

We propose a new high dimensional semiparametric principal component analysis (PCA) method, named Copula Component Analysis (COCA). The semiparametric model assumes that, after unspecified marginally monotone transformations, the distributions are multivariate Gaussian. COCA improves upon PCA and sparse PCA in three aspects: (i) It is robust to modeling assumptions; (ii) It is robust to outliers and data contamination; (iii) It is scale-invariant and yields more interpretable results. We prove that the COCA estimators obtain fast estimation rates and are feature selection consistent when the dimension is nearly exponentially large relative to the sample size. Careful experiments confirm that COCA outperforms sparse PCA on both synthetic and real-world datasets.