Experimental life sciences like biology or chemistry have seen in the recent decades an explosion of the data available from experiments. Laboratory instruments become more and more complex and report hundreds or thousands measurements for a single experiment and therefore the statistical methods face challenging tasks when dealing with such high dimensional data. However, much of the data is highly redundant and can be efficiently brought down to a much smaller number of variables without a significant loss of information. The mathematical procedures making possible this reduction are called dimensionality reduction techniques; they have widely been developed by fields like Statistics or Machine Learning, and are currently a hot research topic. In this review we categorize the plethora of dimension reduction techniques available and give the mathematical insight behind them.

A low-rank transformation learning framework for subspace clustering and classification is here proposed. Many high-dimensional data, such as face images and motion sequences, approximately lie in a union of low-dimensional subspaces. The corresponding subspace clustering problem has been extensively studied in the literature to partition such high-dimensional data into clusters corresponding to their underlying low-dimensional subspaces. However, low-dimensional intrinsic structures are often violated for real-world observations, as they can be corrupted by errors or deviate from ideal models. We propose to address this by learning a linear transformation on subspaces using matrix rank, via its convex surrogate nuclear norm, as the optimization criteria. The learned linear transformation restores a low-rank structure for data from the same subspace, and, at the same time, forces a a maximally separated structure for data from different subspaces. In this way, we reduce variations within subspaces, and increase separation between subspaces for a more robust subspace clustering. This proposed learned robust subspace clustering framework significantly enhances the performance of existing subspace clustering methods. Basic theoretical results here presented help to further support the underlying framework. To exploit the low-rank structures of the transformed subspaces, we further introduce a fast subspace clustering technique, which efficiently combines robust PCA with sparse modeling. When class labels are present at the training stage, we show this low-rank transformation framework also significantly enhances classification performance. Extensive experiments using public datasets are presented, showing that the proposed approach significantly outperforms state-of-the-art methods for subspace clustering and classification.

Multi-label classification has attracted an increasing amount of attention in recent years. To this end, many algorithms have been developed to classify multi-label data in an effective manner. However, they usually do not consider the pairwise relations indicated by sample labels, which actually play important roles in multi-label classification. Inspired by this, we naturally extend the traditional pairwise constraints to the multi-label scenario via a flexible thresholding scheme. Moreover, to improve the generalization ability of the classifier, we adopt a boosting-like strategy to construct a multi-label ensemble from a group of base classifiers. To achieve these goals, this paper presents a novel multi-label classification framework named Variable Pairwise Constraint projection for Multi-label Ensemble (VPCME). Specifically, we take advantage of the variable pairwise constraint projection to learn a lower-dimensional data representation, which preserves the correlations between samples and labels. Thereafter, the base classifiers are trained in the new data space. For the boosting-like strategy, we employ both the variable pairwise constraints and the bootstrap steps to diversify the base classifiers. Empirical studies have shown the superiority of the proposed method in comparison with other approaches.

We present the FuSSO, a functional analogue to the LASSO, that efficiently finds a sparse set of functional input covariates to regress a real-valued response against. The FuSSO does so in a semi-parametric fashion, making no parametric assumptions about the nature of input functional covariates and assuming a linear form to the mapping of functional covariates to the response. We provide a statistical backing for use of the FuSSO via proof of asymptotic sparsistency under various conditions. Furthermore, we observe good results on both synthetic and real-world data.

We propose a method for inferring the conditional indepen- dence graph (CIG) of a high-dimensional discrete-time Gaus- sian vector random process from finite-length observations. Our approach does not rely on a parametric model (such as, e.g., an autoregressive model) for the vector random process; rather, it only assumes certain spectral smoothness proper- ties. The proposed inference scheme is compressive in that it works for sample sizes that are (much) smaller than the number of scalar process components. We provide analytical conditions for our method to correctly identify the CIG with high probability.

We study the problem of distribution to real-value regression, where one aims to regress a mapping $f$ that takes in a distribution input covariate $P\in \mathcal{I}$ (for a non-parametric family of distributions $\mathcal{I}$) and outputs a real-valued response $Y=f(P) + \epsilon$. This setting was recently studied, and a "Kernel-Kernel" estimator was introduced and shown to have a polynomial rate of convergence. However, evaluating a new prediction with the Kernel-Kernel estimator scales as $\Omega(N)$. This causes the difficult situation where a large amount of data may be necessary for a low estimation risk, but the computation cost of estimation becomes infeasible when the data-set is too large. To this end, we propose the Double-Basis estimator, which looks to alleviate this big data problem in two ways: first, the Double-Basis estimator is shown to have a computation complexity that is independent of the number of of instances $N$ when evaluating new predictions after training; secondly, the Double-Basis estimator is shown to have a fast rate of convergence for a general class of mappings $f\in\mathcal{F}$.

It is widely known in the machine learning community that class noise can be (and often is) detrimental to inducing a model of the data. Many current approaches use a single, often biased, measurement to determine if an instance is noisy. A biased measure may work well on certain data sets, but it can also be less effective on a broader set of data sets. In this paper, we present noise identification using classifier diversity (NICD) -- a method for deriving a less biased noise measurement and integrating it into the learning process. To lessen the bias of the noise measure, NICD selects a diverse set of classifiers (based on their predictions of novel instances) to determine which instances are noisy. We examine NICD as a technique for filtering, instance weighting, and selecting the base classifiers of a voting ensemble. We compare NICD with several other noise handling techniques that do not consider classifier diversity on a set of 54 data sets and 5 learning algorithms. NICD significantly increases the classification accuracy over the other considered approaches and is effective across a broad set of data sets and learning algorithms.

We address the problem of retrieving relevant experiments given a query experiment, motivated by the public databases of datasets in molecular biology and other experimental sciences, and the need of scientists to relate to earlier work on the level of actual measurement data. Since experiments are inherently noisy and databases ever accumulating, we argue that a retrieval engine should possess two particular characteristics. First, it should compare models learnt from the experiments rather than the raw measurements themselves: this allows incorporating experiment-specific prior knowledge to suppress noise effects and focus on what is important. Second, it should be updated sequentially from newly published experiments, without explicitly storing either the measurements or the models, which is critical for saving storage space and protecting data privacy: this promotes life long learning. We formulate the retrieval as a ``supermodelling'' problem, of sequentially learning a model of the set of posterior distributions, represented as sets of MCMC samples, and suggest the use of Particle-Learning-based sequential Dirichlet process mixture (DPM) for this purpose. The relevance measure for retrieval is derived from the supermodel through the mixture representation. We demonstrate the performance of the proposed retrieval method on simulated data and molecular biological experiments.

In this paper, we consider a popular model for collaborative filtering in recommender systems where some users of a website rate some items, such as movies, and the goal is to recover the ratings of some or all of the unrated items of each user. In particular, we consider both the clustering model, where only users (or items) are clustered, and the co-clustering model, where both users and items are clustered, and further, we assume that some users rate many items (information-rich users) and some users rate only a few items (information-sparse users). When users (or items) are clustered, our algorithm can recover the rating matrix with $\omega(MK \log M)$ noisy entries while $MK$ entries are necessary, where $K$ is the number of clusters and $M$ is the number of items. In the case of co-clustering, we prove that $K^2$ entries are necessary for recovering the rating matrix, and our algorithm achieves this lower bound within a logarithmic factor when $K$ is sufficiently large. We compare our algorithms with a well-known algorithms called alternating minimization (AM), and a similarity score-based algorithm known as the popularity-among-friends (PAF) algorithm by applying all three to the MovieLens and Netflix data sets. Our co-clustering algorithm and AM have similar overall error rates when recovering the rating matrix, both of which are lower than the error rate under PAF. But more importantly, the error rate of our co-clustering algorithm is significantly lower than AM and PAF in the scenarios of interest in recommender systems: when recommending a few items to each user or when recommending items to users who only rated a few items (these users are the majority of the total user population). The performance difference increases even more when noise is added to the datasets.

This paper introduces a robust mixing model to describe hyperspectral data resulting from the mixture of several pure spectral signatures. This new model not only generalizes the commonly used linear mixing model, but also allows for possible nonlinear effects to be easily handled, relying on mild assumptions regarding these nonlinearities. The standard nonnegativity and sum-to-one constraints inherent to spectral unmixing are coupled with a group-sparse constraint imposed on the nonlinearity component. This results in a new form of robust nonnegative matrix factorization. The data fidelity term is expressed as a beta-divergence, a continuous family of dissimilarity measures that takes the squared Euclidean distance and the generalized Kullback-Leibler divergence as special cases. The penalized objective is minimized with a block-coordinate descent that involves majorization-minimization updates. Simulation results obtained on synthetic and real data show that the proposed strategy competes with state-of-the-art linear and nonlinear unmixing methods.