Relationships between entities in datasets are often of multiple nature, like geographical distance, social relationships, or common interests among people in a social network, for example. This information can naturally be modeled by a set of weighted and undirected graphs that form a global multilayer graph, where the common vertex set represents the entities and the edges on different layers capture the similarities of the entities in term of the different modalities. In this paper, we address the problem of analyzing multi-layer graphs and propose methods for clustering the vertices by efficiently merging the information provided by the multiple modalities. To this end, we propose to combine the characteristics of individual graph layers using tools from subspace analysis on a Grassmann manifold. The resulting combination can then be viewed as a low dimensional representation of the original data which preserves the most important information from diverse relationships between entities. We use this information in new clustering methods and test our algorithm on several synthetic and real world datasets where we demonstrate superior or competitive performances compared to baseline and state-of-the-art techniques. Our generic framework further extends to numerous analysis and learning problems that involve different types of information on graphs.

The paper presents an O(N log N)-implementation of t-SNE -- an embedding technique that is commonly used for the visualization of high-dimensional data in scatter plots and that normally runs in O(N^2). The new implementation uses vantage-point trees to compute sparse pairwise similarities between the input data objects, and it uses a variant of the Barnes-Hut algorithm - an algorithm used by astronomers to perform N-body simulations - to approximate the forces between the corresponding points in the embedding. Our experiments show that the new algorithm, called Barnes-Hut-SNE, leads to substantial computational advantages over standard t-SNE, and that it makes it possible to learn embeddings of data sets with millions of objects.

We propose a general matrix-valued multiple kernel learning framework for high-dimensional nonlinear multivariate regression problems. This framework allows a broad class of mixed norm regularizers, including those that induce sparsity, to be imposed on a dictionary of vector-valued Reproducing Kernel Hilbert Spaces. We develop a highly scalable and eigendecomposition-free algorithm that orchestrates two inexact solvers for simultaneously learning both the input and output components of separable matrix-valued kernels. As a key application enabled by our framework, we show how high-dimensional causal inference tasks can be naturally cast as sparse function estimation problems, leading to novel nonlinear extensions of a class of Graphical Granger Causality techniques. Our algorithmic developments and extensive empirical studies are complemented by theoretical analyses in terms of Rademacher generalization bounds.

Introduction. Case Based Reasoning (CBR) is an emerg- ing decision making paradigm in medical research where new cases are solved relying on previously solved similar cases. Usually, a database of solved cases is provided, and every case is described through a set of attributes (inputs) and a label (output). Extracting useful information from this database can help the CBR system providing more reliable results on the yet to be solved cases. Objective. For that purpose we suggest a general frame- work where a CBR system, viz. K-Nearest Neighbor (K-NN) algorithm, is combined with various information obtained from a Logistic Regression (LR) model. Methods. LR is applied, on the case database, to assign weights to the attributes as well as the solved cases. Thus, five possible decision making systems based on K-NN and/or LR were identified: a standalone K-NN, a standalone LR and three soft K-NN algorithms that rely on the weights based on the results of the LR. The evaluation of the described approaches is performed in the field of renal transplant access waiting list. Results and conclusion. The results show that our suggested approach, where the K-NN algorithm relies on both weighted attributes and cases, can efficiently deal with non relevant attributes, whereas the four other approaches suffer from this kind of noisy setups. The robustness of this approach suggests interesting perspectives for medical problem solving tools using CBR methodology.

In this paper, we consider unsupervised partitioning problems, such as clustering, image segmentation, video segmentation and other change-point detection problems. We focus on partitioning problems based explicitly or implicitly on the minimization of Euclidean distortions, which include mean-based change-point detection, K-means, spectral clustering and normalized cuts. Our main goal is to learn a Mahalanobis metric for these unsupervised problems, leading to feature weighting and/or selection. This is done in a supervised way by assuming the availability of several potentially partially labelled datasets that share the same metric. We cast the metric learning problem as a large-margin structured prediction problem, with proper definition of regularizers and losses, leading to a convex optimization problem which can be solved efficiently with iterative techniques. We provide experiments where we show how learning the metric may significantly improve the partitioning performance in synthetic examples, bioinformatics, video segmentation and image segmentation problems.

We have developed a general Bayesian algorithm for determining the coordinates of points in a three-dimensional space. The algorithm takes as input a set of probabilistic constraints on the coordinates of the points, and an a priori distribution for each point location. The output is a maximum-likelihood estimate of the location of each point. We use the extended, iterated Kalman filter, and add a search heuristic for optimizing its solution under nonlinear conditions. This heuristic is based on the same principle as the simulated annealing heuristic for other optimization problems. Our method uses any probabilistic constraints that can be expressed as a function of the point coordinates (for example, distance, angles, dihedral angles, and planarity). It assumes that all constraints have Gaussian noise. In this paper, we describe the algorithm and show its performance on a set of synthetic data to illustrate its convergence properties, and its applicability to domains such ng molecular structure determination.

Additive asynchronous and cyclostationary impulsive noise limits communication performance in OFDM powerline communication (PLC) systems. Conventional OFDM receivers assume additive white Gaussian noise and hence experience degradation in communication performance in impulsive noise. Alternate designs assume a parametric statistical model of impulsive noise and use the model parameters in mitigating impulsive noise. These receivers require overhead in training and parameter estimation, and degrade due to model and parameter mismatch, especially in highly dynamic environments. In this paper, we model impulsive noise as a sparse vector in the time domain without any other assumptions, and apply sparse Bayesian learning methods for estimation and mitigation without training. We propose three iterative algorithms with different complexity vs. performance trade-offs: (1) we utilize the noise projection onto null and pilot tones to estimate and subtract the noise impulses; (2) we add the information in the data tones to perform joint noise estimation and OFDM detection; (3) we embed our algorithm into a decision feedback structure to further enhance the performance of coded systems. When compared to conventional OFDM PLC receivers, the proposed receivers achieve SNR gains of up to 9 dB in coded and 10 dB in uncoded systems in the presence of impulsive noise.

This article addresses the issue of representing electroencephalographic (EEG) signals in an efficient way. While classical approaches use a fixed Gabor dictionary to analyze EEG signals, this article proposes a data-driven method to obtain an adapted dictionary. To reach an efficient dictionary learning, appropriate spatial and temporal modeling is required. Inter-channels links are taken into account in the spatial multivariate model, and shift-invariance is used for the temporal model. Multivariate learned kernels are informative (a few atoms code plentiful energy) and interpretable (the atoms can have a physiological meaning). Using real EEG data, the proposed method is shown to outperform the classical multichannel matching pursuit used with a Gabor dictionary, as measured by the representative power of the learned dictionary and its spatial flexibility. Moreover, dictionary learning can capture interpretable patterns: this ability is illustrated on real data, learning a P300 evoked potential.

The task of clustering a set of objects based on multiple sources of data arises in several modern applications. We propose an integrative statistical model that permits a separate clustering of the objects for each data source. These separate clusterings adhere loosely to an overall consensus clustering, and hence they are not independent. We describe a computationally scalable Bayesian framework for simultaneous estimation of both the consensus clustering and the source-specific clusterings. We demonstrate that this flexible approach is more robust than joint clustering of all data sources, and is more powerful than clustering each data source separately. This work is motivated by the integrated analysis of heterogeneous biomedical data, and we present an application to subtype identification of breast cancer tumor samples using publicly available data from The Cancer Genome Atlas. Software is available at http://people.duke.edu/~el113/software.html.

Multilabel classification is a relatively recent subfield of machine learning. Unlike to the classical approach, where instances are labeled with only one category, in multilabel classification, an arbitrary number of categories is chosen to label an instance. Due to the problem complexity (the solution is one among an exponential number of alternatives), a very common solution (the binary method) is frequently used, learning a binary classifier for every category, and combining them all afterwards. The assumption taken in this solution is not realistic, and in this work we give examples where the decisions for all the labels are not taken independently, and thus, a supervised approach should learn those existing relationships among categories to make a better classification. Therefore, we show here a generic methodology that can improve the results obtained by a set of independent probabilistic binary classifiers, by using a combination procedure with a classifier trained on the co-occurrences of the labels. We show an exhaustive experimentation in three different standard corpora of labeled documents (Reuters-21578, Ohsumed-23 and RCV1), which present noticeable improvements in all of them, when using our methodology, in three probabilistic base classifiers.