As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our aims include reducing the dimensionality of the problem that has to be dealt one at a time, improving the performance and interpretability of the models. We propose using the inherent structures in the genome; to divide the bigger problem into manageable parts. In plant and animal breeding studies a distinction is made between the commercial value (additive + epistatic genetic effects) and the breeding value (additive genetic effects) of an individual since it is expected that some of the epistatic genetic effects will be lost due to recombination. In this paper, we argue that the breeder can take advantage of some of the epistatic marker effects in regions of low recombination. The models introduced here aim to estimate local epistatic line heritability by using the genetic map information and combine the local additive and epistatic effects. To this end, we have used semi-parametric mixed models with multiple local genomic relationship matrices with hierarchical testing designs and lasso post-processing for sparsity in the final model and speed. Our models produce good predictive performance along with genetic association information.

In this work we show that, using the eigen-decomposition of the adjacency matrix, we can consistently estimate feature maps for latent position graphs with positive definite link function $\kappa$, provided that the latent positions are i.i.d. from some distribution F. We then consider the exploitation task of vertex classification where the link function $\kappa$ belongs to the class of universal kernels and class labels are observed for a number of vertices tending to infinity and that the remaining vertices are to be classified. We show that minimization of the empirical $\varphi$-risk for some convex surrogate $\varphi$ of 0-1 loss over a class of linear classifiers with increasing complexities yields a universally consistent classifier, that is, a classification rule with error converging to Bayes optimal for any distribution F.

Efron et al. (2001) proposed empirical Bayes formulation of the frequentist Benjamini and Hochbergs False Discovery Rate method (Benjamini and Hochberg,1995). This article attempts to unify the `two cultures' using concepts of comparison density and distribution function. We have also shown how almost all of the existing local fdr methods can be viewed as proposing various model specification for comparison density - unifies the vast literature of false discovery methods under one concept and notation.

In this paper, we propose a new methodology based on the Negative Selection Algorithm that belongs to the field of Computational Intelligence, specifically, Artificial Immune Systems to identify takeover targets. Although considerable research based on customary statistical techniques and some contemporary Computational Intelligence techniques have been devoted to identify takeover targets, most of the existing studies are based upon multiple previous mergers and acquisitions. Contrary to previous research, the novelty of this proposal lies in its ability to suggest takeover targets for novice firms that are at the beginning of their merger and acquisition spree. We first discuss the theoretical perspective and then provide a case study with details for practical implementation, both capitalizing from unique generalization capabilities of artificial immune systems algorithms.

This supplementary material includes three parts: some preliminary results, four examples, an experiment, three new algorithms, and all proofs of the results in the paper "Reversible MCMC on Markov equivalence classes of sparse directed acyclic graphs".

Principal components analysis (PCA) is a standard tool for identifying good low-dimensional approximations to data in high dimension. Many data sets of interest contain private or sensitive information about individuals. Algorithms which operate on such data should be sensitive to the privacy risks in publishing their outputs. Differential privacy is a framework for developing tradeoffs between privacy and the utility of these outputs. In this paper we investigate the theory and empirical performance of differentially private approximations to PCA and propose a new method which explicitly optimizes the utility of the output. We show that the sample complexity of the proposed method differs from the existing procedure in the scaling with the data dimension, and that our method is nearly optimal in terms of this scaling. We furthermore illustrate our results, showing that on real data there is a large performance gap between the existing method and our method.

We study pathwise invariances of centred random fields that can be controlled through the covariance. A result involving composition operators is obtained in second-order settings, and we show that various path properties including additivity boil down to invariances of the covariance kernel. These results are extended to a broader class of operators in the Gaussian case, via the Lo\`eve isometry. Several covariance-driven pathwise invariances are illustrated, including fields with symmetric paths, centred paths, harmonic paths, or sparse paths. The proposed approach delivers a number of promising results and perspectives in Gaussian process regression.

Consensus clustering emerges as a promising solution to find cluster structures from data. As an efficient approach for consensus clustering, the K-means based method has garnered attention in the literature, but the existing research is still preliminary and fragmented. In this paper, we provide a systematic study on the framework of K-means-based Consensus Clustering (KCC). We first formulate the general definition of KCC, and then reveal a necessary and sufficient condition for utility functions that work for KCC, on both complete and incomplete basic partitionings. Experimental results on various real-world data sets demonstrate that KCC is highly efficient and is comparable to the state-of-the-art methods in terms of clustering quality. In addition, KCC shows high robustness to incomplete basic partitionings with substantial missing values.

Cepstral features have been widely used in audio applications. Domain knowledge has played an important role in designing different types of cepstral features proposed in the literature. In this paper, we present a novel approach for learning optimized cepstral features directly from audio data to better discriminate between different categories of signals in classification tasks. We employ multi-layer feedforward neural networks to model the cepstral feature extraction process. The network weights are initialized to replicate a reference cepstral feature like the mel frequency cepstral coefficient. We then propose a embedded approach that integrates feature learning with the training of a support vector machine (SVM) classifier. A single optimization problem is formulated where the feature and classifier variables are optimized simultaneously so as to refine the initial features and minimize the classification risk. Experimental results have demonstrated the effectiveness of the proposed feature learning approach, outperforming competing methods by a large margin on benchmark data.

Bag-of-Words approach has played an important role in recent works for image classification. In consideration of efficiency, most methods use k-means clustering to generate the codebook. The obtained codebooks often lose the cluster size and shape information with distortion errors and low discriminative power. Though some efforts have been made to optimize codebook in sparse coding, they usually incur higher computational cost. Moreover, they ignore the correlations between codes in the following coding stage, that leads to low discriminative power of the final representation. In this paper, we propose a bilevel visual words coding approach in consideration of representation ability, discriminative power and efficiency. In the bilevel codebook generation stage, k-means and an efficient spectral clustering are respectively run in each level by taking both class information and the shapes of each visual word cluster into account. To obtain discriminative representation in the coding stage, we design a certain localized coding rule with bilevel codebook to select local bases. To further achieve an efficient coding referring to this rule, an online method is proposed to efficiently learn a projection of local descriptor to the visual words in the codebook. After projection, coding can be efficiently completed by a low dimensional localized soft-assignment. Experimental results show that our proposed bilevel visual words coding approach outperforms the state-of-the-art approaches for image classification.