We propose a novel technique to assess functional brain connectivity in EEG/MEG signals. Our method, called Sparsely-Connected Sources Analysis (SCSA), can overcome the problem of volume conduction by modeling neural data innovatively with the following ingredients: (a) the EEG is assumed to be a linear mixture of correlated sources following a multivariate autoregressive (MVAR) model, (b) the demixing is estimated jointly with the source MVAR parameters, (c) overfitting is avoided by using the Group Lasso penalty. This approach allows to extract the appropriate level cross-talk between the extracted sources and in this manner we obtain a sparse data-driven model of functional connectivity. We demonstrate the usefulness of SCSA with simulated data, and compare to a number of existing algorithms with excellent results.

In this paper, we consider the problem of "hyper-sparse aggregation". Namely, given a dictionary $F = \{f_1, ..., f_M \}$ of functions, we look for an optimal aggregation algorithm that writes $\tilde f = \sum_{j=1}^M \theta_j f_j$ with as many zero coefficients $\theta_j$ as possible. This problem is of particular interest when $F$ contains many irrelevant functions that should not appear in $\tilde{f}$. We provide an exact oracle inequality for $\tilde f$, where only two coefficients are non-zero, that entails $\tilde f$ to be an optimal aggregation algorithm. Since selectors are suboptimal aggregation procedures, this proves that 2 is the minimal number of elements of $F$ required for the construction of an optimal aggregation procedures in every situations. A simulated example of this algorithm is proposed on a dictionary obtained using LARS, for the problem of selection of the regularization parameter of the LASSO. We also give an example of use of aggregation to achieve minimax adaptation over anisotropic Besov spaces, which was not previously known in minimax theory (in regression on a random design).

After building a classifier with modern tools of machine learning we typically have a black box at hand that is able to predict well for unseen data. Thus, we get an answer to the question what is the most likely label of a given unseen data point. However, most methods will provide no answer why the model predicted the particular label for a single instance and what features were most influential for that particular instance. The only method that is currently able to provide such explanations are decision trees. This paper proposes a procedure which (based on a set of assumptions) allows to explain the decisions of any classification method.

Slow feature analysis (SFA) is a method for extracting slowly varying features from a quickly varying multidimensional signal. An open source Matlab-implementation sfa-tk makes SFA easily useable. We show here that under certain circumstances, namely when the covariance matrix of the nonlinearly expanded data does not have full rank, this implementation runs into numerical instabilities. We propse a modified algorithm based on singular value decomposition (SVD) which is free of those instabilities even in the case where the rank of the matrix is only less than 10% of its size. Furthermore we show that an alternative way of handling the numerical problems is to inject a small amount of noise into the multidimensional input signal which can restore a rank-deficient covariance matrix to full rank, however at the price of modifying the original data and the need for noise parameter tuning.

This survey is an introduction to positive definite kernels and the set of methods they have inspired in the machine learning literature, namely kernel methods. We first discuss some properties of positive definite kernels as well as reproducing kernel Hibert spaces, the natural extension of the set of functions $\{k(x,\cdot),x\in\mathcal{X}\}$ associated with a kernel $k$ defined on a space $\mathcal{X}$. We discuss at length the construction of kernel functions that take advantage of well-known statistical models. We provide an overview of numerous data-analysis methods which take advantage of reproducing kernel Hilbert spaces and discuss the idea of combining several kernels to improve the performance on certain tasks. We also provide a short cookbook of different kernels which are particularly useful for certain data-types such as images, graphs or speech segments.

Directed acyclic graphs (DAGs) are commonly used to represent causal relationships among random variables in graphical models. Applications of these models arise in the study of physical, as well as biological systems, where directed edges between nodes represent the influence of components of the system on each other. The general problem of estimating DAGs from observed data is computationally NP-hard, Moreover two directed graphs may be observationally equivalent. When the nodes exhibit a natural ordering, the problem of estimating directed graphs reduces to the problem of estimating the structure of the network. In this paper, we propose a penalized likelihood approach that directly estimates the adjacency matrix of DAGs. Both lasso and adaptive lasso penalties are considered and an efficient algorithm is proposed for estimation of high dimensional DAGs. We study variable selection consistency of the two penalties when the number of variables grows to infinity with the sample size. We show that although lasso can only consistently estimate the true network under stringent assumptions, adaptive lasso achieves this task under mild regularity conditions. The performance of the proposed methods is compared to alternative methods in simulated, as well as real, data examples.

Recently there has been an increasing interest in methods that deal with multiple outputs. This has been motivated partly by frameworks like multitask learning, multisensor networks or structured output data. From a Gaussian processes perspective, the problem reduces to specifying an appropriate covariance function that, whilst being positive semi-definite, captures the dependencies between all the data points and across all the outputs. One approach to account for non-trivial correlations between outputs employs convolution processes. Under a latent function interpretation of the convolution transform we establish dependencies between output variables. The main drawbacks of this approach are the associated computational and storage demands. In this paper we address these issues. We present different sparse approximations for dependent output Gaussian processes constructed through the convolution formalism. We exploit the conditional independencies present naturally in the model. This leads to a form of the covariance similar in spirit to the so called PITC and FITC approximations for a single output. We show experimental results with synthetic and real data, in particular, we show results in pollution prediction, school exams score prediction and gene expression data.

In a recent work (arXiv:0910.2517), for nonlinear models with sparse underlying linear structures, we studied the error bounds of $\ell_0$-regularized estimation. In this note, we show that $\ell_1$-regularized estimation in some important cases can achieve the same order of error bounds as those in the aforementioned work.

In query learning, the goal is to identify an unknown object while minimizing the number of "yes or no" questions (queries) posed about that object. We consider three extensions of this fundamental problem that are motivated by practical considerations in real-world, time-critical identification tasks such as emergency response. First, we consider the problem where the objects are partitioned into groups, and the goal is to identify only the group to which the object belongs. Second, we address the situation where the queries are partitioned into groups, and an algorithm may suggest a group of queries to a human user, who then selects the actual query. Third, we consider the problem of query learning in the presence of persistent query noise, and relate it to group identification. To address these problems we show that a standard algorithm for query learning, known as the splitting algorithm or generalized binary search, may be viewed as a generalization of Shannon-Fano coding. We then extend this result to the group-based settings, leading to new algorithms. The performance of our algorithms is demonstrated on simulated data and on a database used by first responders for toxic chemical identification.

Slow feature analysis (SFA) is a method for extracting slowly varying driving forces from quickly varying nonstationary time series. We show here that it is possible for SFA to detect a component which is even slower than the driving force itself (e.g. the envelope of a modulated sine wave). It is shown that it depends on circumstances like the embedding dimension, the time series predictability, or the base frequency, whether the driving force itself or a slower subcomponent is detected. We observe a phase transition from one regime to the other and it is the purpose of this work to quantify the influence of various parameters on this phase transition. We conclude that what is percieved as slow by SFA varies and that a more or less fast switching from one regime to the other occurs, perhaps showing some similarity to human perception.