In this paper, we propose an online algorithm to compute matrix factorizations. Proposed algorithm updates the dictionary matrix and associated coefficients using a single observation at each time. The algorithm performs low-rank updates to dictionary matrix. We derive the algorithm by defining a simple objective function to minimize whenever an observation is arrived. We extend the algorithm further for handling missing data. We also provide a mini-batch extension which enables to compute the matrix factorization on big datasets. We demonstrate the efficiency of our algorithm on a real dataset and give comparisons with well-known algorithms such as stochastic gradient matrix factorization and nonnegative matrix factorization (NMF).

In applications such as recommendation systems and revenue management, it is important to predict preferences on items that have not been seen by a user or predict outcomes of comparisons among those that have never been compared. A popular discrete choice model of multinomial logit model captures the structure of the hidden preferences with a low-rank matrix. In order to predict the preferences, we want to learn the underlying model from noisy observations of the low-rank matrix, collected as revealed preferences in various forms of ordinal data. A natural approach to learn such a model is to solve a convex relaxation of nuclear norm minimization. We present the convex relaxation approach in two contexts of interest: collaborative ranking and bundled choice modeling. In both cases, we show that the convex relaxation is minimax optimal. We prove an upper bound on the resulting error with finite samples, and provide a matching information-theoretic lower bound.

We introduce, test and discuss a method for classifying and clustering data modeled as directed graphs. The idea is to start diffusion processes from any subset of a data collection, generating corresponding distributions for reaching points in the network. These distributions take the form of high-dimensional numerical vectors and capture essential topological properties of the original dataset. We show how these diffusion vectors can be successfully applied for getting state-of-the-art accuracies in the problem of extracting pathways from metabolic networks. We also provide a guideline to illustrate how to use our method for classification problems, and discuss important details of its implementation. In particular, we present a simple dimensionality reduction technique that lowers the computational cost of classifying diffusion vectors, while leaving the predictive power of the classification process substantially unaltered. Although the method has very few parameters, the results we obtain show its flexibility and power. This should make it helpful in many other contexts.

The recent explosion in the amount and dimensionality of data has exacerbated the need of trading off computational and statistical efficiency carefully, so that inference is both tractable and meaningful. We propose a framework that provides an explicit opportunity for practitioners to specify how much statistical risk they are willing to accept for a given computational cost, and leads to a theoretical risk-computation frontier for any given inference problem. We illustrate the tradeoff between risk and computation and illustrate the frontier in three distinct settings. First, we derive analytic forms for the risk of estimating parameters in the classical setting of estimating the mean and variance for normally distributed data and for the more general setting of parameters of an exponential family. The second example concentrates on computationally constrained Hodges-Lehmann estimators. We conclude with an evaluation of risk associated with early termination of iterative matrix inversion algorithms in the context of linear regression.

Non-linear manifold learning enables high-dimensional data analysis, but requires out-of-sample-extension methods to process new data points. In this paper, we propose a manifold learning algorithm based on deep learning to create an encoder, which maps a high-dimensional dataset and its low-dimensional embedding, and a decoder, which takes the embedded data back to the high-dimensional space. Stacking the encoder and decoder together constructs an autoencoder, which we term a diffusion net, that performs out-of-sample-extension as well as outlier detection. We introduce new neural net constraints for the encoder, which preserves the local geometry of the points, and we prove rates of convergence for the encoder. Also, our approach is efficient in both computational complexity and memory requirements, as opposed to previous methods that require storage of all training points in both the high-dimensional and the low-dimensional spaces to calculate the out-of-sample-extension and the pre-image.

Fairness-aware learning is a novel framework for classification tasks. Like regular empirical risk minimization (ERM), it aims to learn a classifier with a low error rate, and at the same time, for the predictions of the classifier to be independent of sensitive features, such as gender, religion, race, and ethnicity. Existing methods can achieve low dependencies on given samples, but this is not guaranteed on unseen samples. The existing fairness-aware learning algorithms employ different dependency measures, and each algorithm is specifically designed for a particular one. Such diversity makes it difficult to theoretically analyze and compare them. In this paper, we propose a general framework for fairness-aware learning that uses f-divergences and that covers most of the dependency measures employed in the existing methods. We introduce a way to estimate the f-divergences that allows us to give a unified analysis for the upper bound of the estimation error; this bound is tighter than that of the existing convergence rate analysis of the divergence estimation. With our divergence estimate, we propose a fairness-aware learning algorithm, and perform a theoretical analysis of its generalization error. Our analysis reveals that, under mild assumptions and even with enforcement of fairness, the generalization error of our method is $O(\sqrt{1/n})$, which is the same as that of the regular ERM. In addition, and more importantly, we show that, for any f-divergence, the upper bound of the estimation error of the divergence is $O(\sqrt{1/n})$. This indicates that our fairness-aware learning algorithm guarantees low dependencies on unseen samples for any dependency measure represented by an f-divergence.

We take a new look at parameter estimation for Gaussian Mixture Models (GMMs). In particular, we propose using \emph{Riemannian manifold optimization} as a powerful counterpart to Expectation Maximization (EM). An out-of-the-box invocation of manifold optimization, however, fails spectacularly: it converges to the same solution but vastly slower. Driven by intuition from manifold convexity, we then propose a reparamerization that has remarkable empirical consequences. It makes manifold optimization not only match EM---a highly encouraging result in itself given the poor record nonlinear programming methods have had against EM so far---but also outperform EM in many practical settings, while displaying much less variability in running times. We further highlight the strengths of manifold optimization by developing a somewhat tuned manifold LBFGS method that proves even more competitive and reliable than existing manifold optimization tools. We hope that our results encourage a wider consideration of manifold optimization for parameter estimation problems.

We present a framework for clustering with cluster-specific feature selection. The framework, CRAFT, is derived from asymptotic log posterior formulations of nonparametric MAP-based clustering models. CRAFT handles assorted data, i.e., both numeric and categorical data, and the underlying objective functions are intuitively appealing. The resulting algorithm is simple to implement and scales nicely, requires minimal parameter tuning, obviates the need to specify the number of clusters a priori, and compares favorably with other methods on real datasets.

Gene expression levels in a population vary extensively across tissues. Such heterogeneity is caused by genetic variability and environmental factors, and is expected to be linked to disease development. The abundance of experimental data now enables the identification of features of gene expression profiles that are shared across tissues, and those that are tissue-specific. While most current research is concerned with characterising differential expression by comparing mean expression profiles across tissues, it is also believed that a significant difference in a gene expression's variance across tissues may also be associated to molecular mechanisms that are important for tissue development and function. We propose a sparse multi-view matrix factorisation (sMVMF) algorithm to jointly analyse gene expression measurements in multiple tissues, where each tissue provides a different "view" of the underlying organism. The proposed methodology can be interpreted as an extension of principal component analysis in that it provides the means to decompose the total sample variance in each tissue into the sum of two components: one capturing the variance that is shared across tissues, and one isolating the tissue-specific variances. sMVMF has been used to jointly model mRNA expression profiles in three tissues - adipose, skin and LCL - which are available for a large and well-phenotyped twins cohort, TwinsUK. Using sMVMF, we are able to prioritise genes based on whether their variation patterns are specific to each tissue. Furthermore, using DNA methylation profiles available, we provide supporting evidence that adipose-specific gene expression patterns may be driven by epigenetic effects.

We present a novel approach to automatically segment magnetic resonance (MR) images of the human brain into anatomical regions. Our methodology is based on a deep artificial neural network that assigns each voxel in an MR image of the brain to its corresponding anatomical region. The inputs of the network capture information at different scales around the voxel of interest: 3D and orthogonal 2D intensity patches capture the local spatial context while large, compressed 2D orthogonal patches and distances to the regional centroids enforce global spatial consistency. Contrary to commonly used segmentation methods, our technique does not require any non-linear registration of the MR images. To benchmark our model, we used the dataset provided for the MICCAI 2012 challenge on multi-atlas labelling, which consists of 35 manually segmented MR images of the brain. We obtained competitive results (mean dice coefficient 0.725, error rate 0.163) showing the potential of our approach. To our knowledge, our technique is the first to tackle the anatomical segmentation of the whole brain using deep neural networks.