Linear mixed models (LMMs) are widely used for heritability estimation in genome-wide association studies (GWAS). In standard approaches to heritability estimation with LMMs, a genetic relationship matrix (GRM) must be specified. In GWAS, the GRM is frequently a correlation matrix estimated from the study population's genotypes, which corresponds to a normalized Euclidean distance kernel. In this paper, we show that reliance on the Euclidean distance kernel contributes to several unresolved modeling inconsistencies in heritability estimation for GWAS. These inconsistencies can cause biased heritability estimates in the presence of linkage disequilibrium (LD), depending on the distribution of causal variants. We show that these biases can be resolved (at least at the modeling level) if one adopts a Mahalanobis distance-based GRM for LMM analysis. Additionally, we propose a new definition of partitioned heritability -- the heritability attributable to a subset of genes or single nucleotide polymorphisms (SNPs) -- using the Mahalanobis GRM, and show that it inherits many of the nice consistency properties identified in our original analysis. Partitioned heritability is a relatively new area for GWAS analysis, where inconsistency issues related to LD have previously been known to be especially pernicious.
Recently, in independent work, @cite_0 proposed using the Mahalanobis kernel in a similar way for heritability esitmation with GWAS data. 's paper primarily focuses on empirical analysis, using both simulated and real datasets to illsutrate advantages of the Mahalanobis kernel. The present work contains more precise mathematical and statistical justification for much of the work in @cite_0 , and introduces statistical principles (e.g. @math -heritability in Section ) that can be extended to other targeted application areas and genetics (like partitioning heritability).
@cite_0
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We are interested in the large-scale learning of Mahalanobis distances, with a particular focus on person re-identification. We propose a metric learning formulation called Weighted Approximate Rank Component Analysis (WARCA). WARCA optimizes the precision at top ranks by combining the WARP loss with a regularizer that favors orthonormal linear mappings and avoids rank-deficient embeddings. Using this new regularizer allows us to adapt the large-scale WSABIE procedure and to leverage the Adam stochastic optimization algorithm, which results in an algorithm that scales gracefully to very large data-sets. Also, we derive a kernelized version which allows to take advantage of state-of-the-art features for re-identification when data-set size permits kernel computation. Benchmarks on recent and standard re-identification data-sets show that our method beats existing state-of-the-art techniques both in terms of accuracy and speed. We also provide experimental analysis to shade lights on the properties of the regularizer we use, and how it improves performance. Single nucleotide polymorphism (SNP)-heritability estimation is an important topic in several research fields, including animal, plant and human genetics, as well as in ecology. Linear mixed model estimation of SNP-heritability uses the structures of genomic relationships between individuals, which is constructed from genome-wide sets of SNP-markers that are generally weighted equally in their contributions. Proposed methods to handle dependence between SNPs include, “thinning” the marker set by linkage disequilibrium (LD)-pruning, the use of haplotype-tagging of SNPs, and LD-weighting of the SNP-contributions. For improved estimation, we propose a new conceptual framework for genomic relationship matrix, in which Mahalanobis distance-based LD-correction is used in a linear mixed model estimation of SNP-heritability. The superiority of the presented method is illustrated and compared to mixed-model analyses using a VanRaden genomic relationship matrix, a matrix used by GCTA and a matrix employing LD-weighting (as implemented in the LDAK software) in simulated (using real human, rice and cattle genotypes) and real (maize, rice and mice) datasets. Despite of the computational difficulties, our results suggest that by using the proposed method one can improve the accuracy of SNP-heritability estimates in datasets with high LD. Measures of genomic similarity are often the basis of flexible statistical analyses, and when based on kernel methods, they provide a powerful platform to take advantage of a broad and deep statistical theory, and a wide range of existing software; see the companion paper for a review of this material [1]. The kernel method converts information – perhaps complex or high-dimensional information – for a pair of subjects to a quantitative value representing either similarity or dissimilarity, with the requirement that it must create a positive semidefinite matrix when applied to all pairs of subjects. This approach provides enormous opportunities to enhance genetic analyses by including a wide range of publically-available data as structured kernel ‘prior’ information. Kernel methods are appealing for their generality, yet this generality can make it challenging to formulate measures of similarity that directly address a specific scientific aim, or that are most powerful to detect a specific genetic mechanism. Although it is difficult to create a cook book of kernels for genetic studies, useful guidelines can be gleaned from a variety of novel published approaches. We review some novel developments of kernels for specific analyses and speculate on how to build kernels for complex genomic attributes based on publically available data. The creativity of analysts, with rigorous evaluations by applications to real and simulated data, will ultimately provide a much stronger array of kernel ‘tools’ for genetic analyses. We treat the use of more complex higher degree polynomial curves and surfaces of degree higher than 2, which have many desirable properties for object recognition and position estimation, and attack the instability problem arising in their use with partial and noisy data. The scenario discussed in this paper is one where we have a set of objects that are modeled as implicit polynomial functions, or a set of representations of classes of objects with each object in a class modeled as an implicit polynomial function, stored in the database. Then, given partial data from one of the objects, we want to recognize the object (or the object class) or collect more data in order to get better parameter estimates for more reliable recognition. Two problems arising in this scenario are discussed: 1) the problem of recognizing these polynomials by comparing them in terms of their coefficients; and 2) the problem of where to collect data so as to improve the parameter estimates as quickly as possible. We use an asymptotic Bayesian approximation for solving the two problems. The intrinsic dimensionality of polynomials and the use of the Mahalanobis distance are discussed. We address the problem of learning distance metrics using side-information in the form of groups of "similar" points. We propose to use the RCA algorithm, which is a simple and efficient algorithm for learning a full ranked Mahalanobis metric (, 2002). We first show that RCA obtains the solution to an interesting optimization problem, founded on an information theoretic basis. If the Mahalanobis matrix is allowed to be singular, we show that Fisher's linear discriminant followed by RCA is the optimal dimensionality reduction algorithm under the same criterion. We then show how this optimization problem is related to the criterion optimized by another recent algorithm for metric learning (, 2002), which uses the same kind of side information. We empirically demonstrate that learning a distance metric using the RCA algorithm significantly improves clustering performance, similarly to the alternative algorithm. Since the RCA algorithm is much more efficient and cost effective than the alternative, as it only uses closed form expressions of the data, it seems like a preferable choice for the learning of full rank Mahalanobis distances. We are interested in supervised metric learning of Mahalanobis like distances. Existing approaches mainly focus on learning a new distance using similarity and dissimilarity constraints between examples. In this paper, instead of bringing closer examples of the same class and pushing far away examples of different classes we propose to move the examples with respect to virtual points. Hence, each example is brought closer to a a priori defined virtual point reducing the number of constraints to satisfy. We show that our approach admits a closed form solution which can be kernelized. We provide a theoretical analysis showing the consistency of the approach and establishing some links with other classical metric learning methods. Furthermore we propose an efficient solution to the difficult problem of selecting virtual points based in part on recent works in optimal transport. Lastly, we evaluate our approach on several state of the art datasets. One approach to improving the running time of kernel-based methods is to build a small sketch of the kernel matrix and use it in lieu of the full matrix in the machine learning task of interest. Here, we describe a version of this approach that comes with running time guarantees as well as improved guarantees on its statistical performance. By extending the notion of statistical leverage scores to the setting of kernel ridge regression, we are able to identify a sampling distribution that reduces the size of the sketch (i.e., the required number of columns to be sampled) to the effective dimensionality of the problem. This latter quantity is often much smaller than previous bounds that depend on the maximal degrees of freedom. We give an empirical evidence supporting this fact. Our second contribution is to present a fast algorithm to quickly compute coarse approximations to these scores in time linear in the number of samples. More precisely, the running time of the algorithm is O(np2) with p only depending on the trace of the kernel matrix and the regularization parameter. This is obtained via a variant of squared length sampling that we adapt to the kernel setting. Lastly, we discuss how this new notion of the leverage of a data point captures a fine notion of the difficulty of the learning problem. In this paper, we raise important issues on scalability and the required degree of supervision of existing Mahalanobis metric learning methods. Often rather tedious optimization procedures are applied that become computationally intractable on a large scale. Further, if one considers the constantly growing amount of data it is often infeasible to specify fully supervised labels for all data points. Instead, it is easier to specify labels in form of equivalence constraints. We introduce a simple though effective strategy to learn a distance metric from equivalence constraints, based on a statistical inference perspective. In contrast to existing methods we do not rely on complex optimization problems requiring computationally expensive iterations. Hence, our method is orders of magnitudes faster than comparable methods. Results on a variety of challenging benchmarks with rather diverse nature demonstrate the power of our method. These include faces in unconstrained environments, matching before unseen object instances and person re-identification across spatially disjoint cameras. In the latter two benchmarks we clearly outperform the state-of-the-art. We introduce a kernel approximation strategy that enables computation of the Gaussian process log marginal likelihood and all hyperparameter derivatives in @math time. Our GRIEF kernel consists of @math eigenfunctions found using a Nystrom approximation from a dense Cartesian product grid of inducing points. By exploiting algebraic properties of Kronecker and Khatri-Rao tensor products, computational complexity of the training procedure can be practically independent of the number of inducing points. This allows us to use arbitrarily many inducing points to achieve a globally accurate kernel approximation, even in high-dimensional problems. The fast likelihood evaluation enables type-I or II Bayesian inference on large-scale datasets. We benchmark our algorithms on real-world problems with up to two-million training points and @math inducing points. We develop and apply a previously undescribed framework that is designed to extract information in the form of a positive definite kernel matrix from possibly crude, noisy, incomplete, inconsistent dissimilarity information between pairs of objects, obtainable in a variety of contexts. Any positive definite kernel defines a consistent set of distances, and the fitted kernel provides a set of coordinates in Euclidean space that attempts to respect the information available while controlling for complexity of the kernel. The resulting set of coordinates is highly appropriate for visualization and as input to classification and clustering algorithms. The framework is formulated in terms of a class of optimization problems that can be solved efficiently by using modern convex cone programming software. The power of the method is illustrated in the context of protein clustering based on primary sequence data. An application to the globin family of proteins resulted in a readily visualizable 3D sequence space of globins, where several subfamilies and subgroupings consistent with the literature were easily identifiable. We propose an independence criterion based on the eigenspectrum of covariance operators in reproducing kernel Hilbert spaces (RKHSs), consisting of an empirical estimate of the Hilbert-Schmidt norm of the cross-covariance operator (we term this a Hilbert-Schmidt Independence Criterion, or HSIC). This approach has several advantages, compared with previous kernel-based independence criteria. First, the empirical estimate is simpler than any other kernel dependence test, and requires no user-defined regularisation. Second, there is a clearly defined population quantity which the empirical estimate approaches in the large sample limit, with exponential convergence guaranteed between the two: this ensures that independence tests based on HSIC do not suffer from slow learning rates. Finally, we show in the context of independent component analysis (ICA) that the performance of HSIC is competitive with that of previously published kernel-based criteria, and of other recently published ICA methods. In this paper, we address the person re-identification problem, discovering the correct matches for a probe person image from a set of gallery person images. We follow the learning-to-rank methodology and learn a similarity function to maximize the difference between the similarity scores of matched and unmatched images for a same person. We introduce at least three contributions to person re-identification. First, we present an explicit polynomial kernel feature map, which is capable of characterizing the similarity information of all pairs of patches between two images, called soft-patch-matching, instead of greedily keeping only the best matched patch, and thus more robust. Second, we introduce a mixture of linear similarity functions that is able to discover different soft-patch-matching patterns. Last, we introduce a negative semi-definite regularization over a subset of the weights in the similarity function, which is motivated by the connection between explicit polynomial kernel feature map and the Mahalanobis distance, as well as the sparsity constraint over the parameters to avoid over-fitting. Experimental results over three public benchmarks demonstrate the superiority of our approach. We present a new method for clustering based on compression. The method does not use subject-specific features or background knowledge, and works as follows: First, we determine a parameter-free, universal, similarity distance, the normalized compression distance or NCD, computed from the lengths of compressed data files (singly and in pairwise concatenation). Second, we apply a hierarchical clustering method. The NCD is not restricted to a specific application area, and works across application area boundaries. A theoretical precursor, the normalized information distance, co-developed by one of the authors, is provably optimal. However, the optimality comes at the price of using the noncomputable notion of Kolmogorov complexity. We propose axioms to capture the real-world setting, and show that the NCD approximates optimality. To extract a hierarchy of clusters from the distance matrix, we determine a dendrogram (ternary tree) by a new quartet method and a fast heuristic to implement it. The method is implemented and available as public software, and is robust under choice of different compressors. To substantiate our claims of universality and robustness, we report evidence of successful application in areas as diverse as genomics, virology, languages, literature, music, handwritten digits, astronomy, and combinations of objects from completely different domains, using statistical, dictionary, and block sorting compressors. In genomics, we presented new evidence for major questions in Mammalian evolution, based on whole-mitochondrial genomic analysis: the Eutherian orders and the Marsupionta hypothesis against the Theria hypothesis. In this paper, a novel approximate solution of the criterion used in non-linear class-specific discriminant subspace learning is proposed. We build on the class-specific kernel spectral regression method, which is a two-step process formed by an eigenanalysis step and a kernel regression step. Based on the structure of the intra-class and out-of-class scatter matrices, we provide a fast solution for the first step. For the second step, we propose the use of approximate kernel space definitions. We analytically show that the adoption of randomized and class-specific kernels has the effect of regularization and Nystrom-based approximation, respectively. We evaluate the proposed approach in face verification problems and compare it with the existing approaches. Experimental results show the effectiveness and efficiency of the proposed approximate class-specific kernel spectral regression method, since it can provide satisfactory performance and scale well with the size of the data. Modern learning problems in computer vision, natural language processing, computational biology, and other areas are often based on large data sets of tens of thousands to millions of training instances. However, several standard learning algorithms, such as kernel-based algorithms, e.g., Support Vector Machines, Kernel Ridge Regression, Kernel PCA, do not easily scale to such orders of magnitude. This thesis focuses on sampling-based matrix approximation techniques that help scale kernel-based algorithms to large-scale datasets. We address several fundamental theoretical and empirical questions including: (1) What approximation should be used? We discuss two common sampling-based methods, providing novel theoretical insights regarding their suitability for various applications and experimental results motivated by this theory. Our results show that one of these methods, the Nystrom method, is superior in the context of large-scale learning. (2) Do these approximations work in practice? We show the effectiveness of approximation techniques on a variety of problems. In the largest study to-date for manifold learning, we use the Nystrom method to extract low-dimensional structure from high-dimensional data to effectively cluster face images. We also report good empirical results for Kernel Ridge Regression and Kernel Logistic Regression. (3) How should we sample columns? A key aspect of sampling-based algorithms is the distribution according to which columns are sampled. We study both fixed and adaptive sampling schemes as well as a promising ensemble technique that can be easily parallelized and generates superior approximations, both in theory and in practice. (4) How well do these approximations work in theory? We provide theoretical analyses of the Nystrom method to understand when this technique should be used. We present guarantees on approximation accuracy based on various matrix properties and analyze the effect of matrix approximation on actual kernel-based algorithms. This work has important consequences for the machine learning community since it extends to large-scale applications the benefits of kernel-based algorithms. The crucial aspect of this research, involving low-rank matrix approximation, is of independent interest within the field of linear algebra. Domain specific (dis-)similarity or proximity measures used e.g. in alignment algorithms of sequence data are popular to analyze complicated data objects and to cover domain specific data properties. Without an underlying vector space these data are given as pairwise (dis-)similarities only. The few available methods for such data focus widely on similarities and do not scale to large datasets. Kernel methods are very effective for metric similarity matrices, also at large scale, but costly transformations are necessary starting with non-metric (dis-) similarities. We propose an integrative combination of Nystrom approximation, potential double centering and eigenvalue correction to obtain valid kernel matrices at linear costs in the number of samples. By the proposed approach effective kernel approaches become accessible. Experiments with several larger (dis-)similarity datasets show that the proposed method achieves much better runtime performance than the standard strategy while keeping competitive model accuracy. The main contribution is an efficient and accurate technique, to convert (potentially non-metric) large scale dissimilarity matrices into approximated positive semi-definite kernel matrices at linear costs. HighlightsWe propose a linear time and memory efficient approach for converting low rank dissimilarity matrices to similarity matrices and vice versa.Our approach is applicable for proximities obtained from non-metric proximity measures (indefinite kernels, non-standard dissimilarity measures).The presented approach also comprises a generalization of Landmark MDS - the presented approach is in general more accurate and flexible than Landmark MDS.We provide an alternative derivation of the Nystrom approximation together with a convergence proof, also for indefinite kernels not given in the workshop paper as a core element of the approach. In this paper, we present an information-theoretic approach to learning a Mahalanobis distance function. We formulate the problem as that of minimizing the differential relative entropy between two multivariate Gaussians under constraints on the distance function. We express this problem as a particular Bregman optimization problem---that of minimizing the LogDet divergence subject to linear constraints. Our resulting algorithm has several advantages over existing methods. First, our method can handle a wide variety of constraints and can optionally incorporate a prior on the distance function. Second, it is fast and scalable. Unlike most existing methods, no eigenvalue computations or semi-definite programming are required. We also present an online version and derive regret bounds for the resulting algorithm. Finally, we evaluate our method on a recent error reporting system for software called Clarify, in the context of metric learning for nearest neighbor classification, as well as on standard data sets. We introduce a method that enables scalable image search for learned metrics. Given pairwise similarity and dissimilarity constraints between some images, we learn a Mahalanobis distance function that captures the imagespsila underlying relationships well. To allow sub-linear time similarity search under the learned metric, we show how to encode the learned metric parameterization into randomized locality-sensitive hash functions. We further formulate an indirect solution that enables metric learning and hashing for vector spaces whose high dimensionality make it infeasible to learn an explicit weighting over the feature dimensions. We demonstrate the approach applied to a variety of image datasets. Our learned metrics improve accuracy relative to commonly-used metric baselines, while our hashing construction enables efficient indexing with learned distances and very large databases. Motivated by the idea that the correlation structure of the entire training set can disclose the relationship between the test sample and the training samples, we propose the combined sparse representation (CSR) classifier for disease recognition. The CSR classifier minimizes the correlation structure of the entire training set multiplied by its transposition and the sparse coefficient together for classification. Including the kernel concept, we propose the kernel combined sparse representation classifier utilizing the high-dimensional nonlinear information instead of the linear information in the CSR classifier. Furthermore, considering the information of the training samples and the class center, we then propose the center-based kernel combined sparse representation (CKCSR) classifier. CKCSR uses the center-based kernel matrix to increase the center-based information that is helpful for classification. The proposed classifiers have been evaluated by extensive experiments on several well-known databases including the EXACT09 database, Emphysema-CT database, mini-MIAS database, Wisconsin breast cancer database, and HD-PECTF database. The experimental results demonstrate that the proposed classifiers achieve better recognition rates than the sparse representation-based classification, collaborative representation based classification, and several state-of-the-art methods. In this paper, we propose to learn a Mahalanobis distance to perform alignment of multivariate time series. The learning examples for this task are time series for which the true alignment is known. We cast the alignment problem as a structured prediction task, and propose realistic losses between alignments for which the optimization is tractable. We provide experiments on real data in the audio to audio context, where we show that the learning of a similarity measure leads to improvements in the performance of the alignment task. We also propose to use this metric learning framework to perform feature selection and, from basic audio features, build a combination of these with better performance for the alignment.