It is well known that Sparse PCA (Sparse Principal Component Analysis) is NP-hard to solve exactly on worst-case instances. What is the complexity of solving Sparse PCA approximately? Our contributions include: 1) a simple and efficient algorithm that achieves an $n^{-1/3}$-approximation; 2) NP-hardness of approximation to within $(1-\varepsilon)$, for some small constant $\varepsilon > 0$; 3) SSE-hardness of approximation to within any constant factor; and 4) an $\exp\exp\left(\Omega\left(\sqrt{\log \log n}\right)\right)$ ("quasi-quasi-polynomial") gap for the standard semidefinite program.

Adaptive Monte Carlo schemes developed over the last years usually seek to ensure ergodicity of the sampling process in line with MCMC tradition. This poses constraints on what is possible in terms of adaptation. In the general case ergodicity can only be guaranteed if adaptation is diminished at a certain rate. Importance Sampling approaches offer a way to circumvent this limitation and design sampling algorithms that keep adapting. Here I present a gradient informed variant of SMC (and its special case Population Monte Carlo) for static problems.

With the wealth of high-throughput sequencing data generated by recent large-scale consortia, predictive gene expression modelling has become an important tool for integrative analysis of transcriptomic and epigenetic data. However, sequencing data-sets are characteristically large, and previously modelling frameworks are typically inefficient and unable to leverage multi-core or distributed processing architectures. In this study, we detail an efficient and parallelised MapReduce implementation of gene expression modelling. We leverage the computational efficiency of this framework to provide an integrative analysis of over fifty histone modification data-sets across a variety of cancerous and non-cancerous cell-lines. Our results demonstrate that the genome-wide relationships between histone modifications and mRNA transcription are lineage, tissue and karyotype-invariant, and that models trained on matched epigenetic/transcriptomic data from non-cancerous cell-lines are able to predict cancerous expression with equivalent genome-wide fidelity.

We consider the problem of learning a dictionary matrix from a number of observed signals, which are assumed to be generated via a linear model with a common underlying dictionary. In particular, we derive lower bounds on the minimum achievable worst case mean squared error (MSE), regardless of computational complexity of the dictionary learning (DL) schemes. By casting DL as a classical (or frequentist) estimation problem, the lower bounds on the worst case MSE are derived by following an established information-theoretic approach to minimax estimation. The main conceptual contribution of this paper is the adaption of the information-theoretic approach to minimax estimation for the DL problem in order to derive lower bounds on the worst case MSE of any DL scheme. We derive three different lower bounds applying to different generative models for the observed signals. The first bound applies to a wide range of models, it only requires the existence of a covariance matrix of the (unknown) underlying coefficient vector. By specializing this bound to the case of sparse coefficient distributions, and assuming the true dictionary satisfies the restricted isometry property, we obtain a lower bound on the worst case MSE of DL schemes in terms of a signal to noise ratio (SNR). The third bound applies to a more restrictive subclass of coefficient distributions by requiring the non-zero coefficients to be Gaussian. While, compared with the previous two bounds, the applicability of this final bound is the most limited it is the tightest of the three bounds in the low SNR regime.

Multiplex networks, a special type of multilayer networks, are increasingly applied in many domains ranging from social media analytics to biology. A common task in these applications concerns the detection of community structures. Many existing algorithms for community detection in multiplexes attempt to detect communities which are shared by all layers. In this article we propose a community detection algorithm, LART (Locally Adaptive Random Transitions), for the detection of communities that are shared by either some or all the layers in the multiplex. The algorithm is based on a random walk on the multiplex, and the transition probabilities defining the random walk are allowed to depend on the local topological similarity between layers at any given node so as to facilitate the exploration of communities across layers. Based on this random walk, a node dissimilarity measure is derived and nodes are clustered based on this distance in a hierarchical fashion. We present experimental results using networks simulated under various scenarios to showcase the performance of LART in comparison to related community detection algorithms.

We describe two nonconventional algorithms for linear regression, called GAME and CLASH. The salient characteristics of these approaches is that they exploit the convex $\ell_1$-ball and non-convex $\ell_0$-sparsity constraints jointly in sparse recovery. To establish the theoretical approximation guarantees of GAME and CLASH, we cover an interesting range of topics from game theory, convex and combinatorial optimization. We illustrate that these approaches lead to improved theoretical guarantees and empirical performance beyond convex and non-convex solvers alone.

Compressive sensing (CS) exploits sparsity to recover sparse or compressible signals from dimensionality reducing, non-adaptive sensing mechanisms. Sparsity is also used to enhance interpretability in machine learning and statistics applications: While the ambient dimension is vast in modern data analysis problems, the relevant information therein typically resides in a much lower dimensional space. However, many solutions proposed nowadays do not leverage the true underlying structure. Recent results in CS extend the simple sparsity idea to more sophisticated {\em structured} sparsity models, which describe the interdependency between the nonzero components of a signal, allowing to increase the interpretability of the results and lead to better recovery performance. In order to better understand the impact of structured sparsity, in this chapter we analyze the connections between the discrete models and their convex relaxations, highlighting their relative advantages. We start with the general group sparse model and then elaborate on two important special cases: the dispersive and the hierarchical models. For each, we present the models in their discrete nature, discuss how to solve the ensuing discrete problems and then describe convex relaxations. We also consider more general structures as defined by set functions and present their convex proxies. Further, we discuss efficient optimization solutions for structured sparsity problems and illustrate structured sparsity in action via three applications.

In this paper, we study randomized reduction methods, which reduce high-dimensional features into low-dimensional space by randomized methods (e.g., random projection, random hashing), for large-scale high-dimensional classification. Previous theoretical results on randomized reduction methods hinge on strong assumptions about the data, e.g., low rank of the data matrix or a large separable margin of classification, which hinder their applications in broad domains. To address these limitations, we propose dual-sparse regularized randomized reduction methods that introduce a sparse regularizer into the reduced dual problem. Under a mild condition that the original dual solution is a (nearly) sparse vector, we show that the resulting dual solution is close to the original dual solution and concentrates on its support set. In numerical experiments, we present an empirical study to support the analysis and we also present a novel application of the dual-sparse regularized randomized reduction methods to reducing the communication cost of distributed learning from large-scale high-dimensional data.

In this paper, we study a classification problem in which sample labels are randomly corrupted. In this scenario, there is an unobservable sample with noise-free labels. However, before being observed, the true labels are independently flipped with a probability $\rho\in[0,0.5)$, and the random label noise can be class-conditional. Here, we address two fundamental problems raised by this scenario. The first is how to best use the abundant surrogate loss functions designed for the traditional classification problem when there is label noise. We prove that any surrogate loss function can be used for classification with noisy labels by using importance reweighting, with consistency assurance that the label noise does not ultimately hinder the search for the optimal classifier of the noise-free sample. The other is the open problem of how to obtain the noise rate $\rho$. We show that the rate is upper bounded by the conditional probability $P(y|x)$ of the noisy sample. Consequently, the rate can be estimated, because the upper bound can be easily reached in classification problems. Experimental results on synthetic and real datasets confirm the efficiency of our methods.

This report is concerned with the Mondrian process and its applications in machine learning. The Mondrian process is a guillotine-partition-valued stochastic process that possesses an elegant self-consistency property. The first part of the report uses simple concepts from applied probability to define the Mondrian process and explore its properties. The Mondrian process has been used as the main building block of a clever online random forest classification algorithm that turns out to be equivalent to its batch counterpart. We outline a slight adaptation of this algorithm to regression, as the remainder of the report uses regression as a case study of how Mondrian processes can be utilized in machine learning. In particular, the Mondrian process will be used to construct a fast approximation to the computationally expensive kernel ridge regression problem with a Laplace kernel. The complexity of random guillotine partitions generated by a Mondrian process and hence the complexity of the resulting regression models is controlled by a lifetime hyperparameter. It turns out that these models can be efficiently trained and evaluated for all lifetimes in a given range at once, without needing to retrain them from scratch for each lifetime value. This leads to an efficient procedure for determining the right model complexity for a dataset at hand. The limitation of having a single lifetime hyperparameter will motivate the final Mondrian grid model, in which each input dimension is endowed with its own lifetime parameter. In this model we preserve the property that its hyperparameters can be tweaked without needing to retrain the modified model from scratch.