We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their underlying clustering structure. It includes feature selection and infers the most likely number of disease subtypes, given the data. We apply the method to 277 glioblastoma samples from The Cancer Genome Atlas, for which there are gene expression, copy number variation, methylation and microRNA data. We identify 8 distinct consensus subtypes and study their prognostic value for death, new tumour events, progression and recurrence. The consensus subtypes are prognostic of tumour recurrence (log-rank p-value of $3.6 \times 10^{-4}$ after correction for multiple hypothesis tests). This is driven principally by the methylation data (log-rank p-value of $2.0 \times 10^{-3}$) but the effect is strengthened by the other 3 data types, demonstrating the value of integrating multiple data types. Of particular note is a subtype of 47 patients characterised by very low levels of methylation. This subtype has very low rates of tumour recurrence and no new events in 10 years of follow up. We also identify a small gene expression subtype of 6 patients that shows particularly poor survival outcomes. Additionally, we note a consensus subtype that showly a highly distinctive data signature and suggest that it is therefore a biologically distinct subtype of glioblastoma. The code is available from https://sites.google.com/site/multipledatafusion/

An intrinsic problem of classifiers based on machine learning (ML) methods is that their learning time grows as the size and complexity of the training dataset increases. For this reason, it is important to have efficient computational methods and algorithms that can be applied on large datasets, such that it is still possible to complete the machine learning tasks in reasonable time. In this context, we present in this paper a more accurate simple process to speed up ML methods. An unsupervised clustering algorithm is combined with Expectation, Maximization (EM) algorithm to develop an efficient Hidden Markov Model (HMM) training. The idea of the proposed process consists of two steps. In the first step, training instances with similar inputs are clustered and a weight factor which represents the frequency of these instances is assigned to each representative cluster. Dynamic Time Warping technique is used as a dissimilarity function to cluster similar examples. In the second step, all formulas in the classical HMM training algorithm (EM) associated with the number of training instances are modified to include the weight factor in appropriate terms. This process significantly accelerates HMM training while maintaining the same initial, transition and emission probabilities matrixes as those obtained with the classical HMM training algorithm. Accordingly, the classification accuracy is preserved. Depending on the size of the training set, speedups of up to 2200 times is possible when the size is about 100.000 instances. The proposed approach is not limited to training HMMs, but it can be employed for a large variety of MLs methods.

We work out a classification scheme for quantum modeling in Hilbert space of any kind of composite entity violating Bell's inequalities and exhibiting entanglement. Our theoretical framework includes situations with entangled states and product measurements ('customary quantum situation'), and also situations with both entangled states and entangled measurements ('nonlocal box situation', 'nonlocal non-marginal box situation'). We show that entanglement is structurally a joint property of states and measurements. Furthermore, entangled measurements enable quantum modeling of situations that are usually believed to be 'beyond quantum'. Our results are also extended from pure states to quantum mixtures.

We consider the problem of distributed dictionary learning, where a set of nodes is required to collectively learn a common dictionary from noisy measurements. This approach may be useful in several contexts including sensor networks. Diffusion cooperation schemes have been proposed to solve the distributed linear regression problem. In this work we focus on a diffusion-based adaptive dictionary learning strategy: each node records observations and cooperates with its neighbors by sharing its local dictionary. The resulting algorithm corresponds to a distributed block coordinate descent (alternate optimization). Beyond dictionary learning, this strategy could be adapted to many matrix factorization problems and generalized to various settings. This article presents our approach and illustrates its efficiency on some numerical examples. Keywords: dictionary learning, sparse coding, distributed estimation, diffusion, matrix factorization, adaptive networks, block coordinate descent.

We consider the problem of online linear regression on arbitrary deterministic sequences when the ambient dimension d can be much larger than the number of time rounds T. We introduce the notion of sparsity regret bound, which is a deterministic online counterpart of recent risk bounds derived in the stochastic setting under a sparsity scenario. We prove such regret bounds for an online-learning algorithm called SeqSEW and based on exponential weighting and data-driven truncation. In a second part we apply a parameter-free version of this algorithm to the stochastic setting (regression model with random design). This yields risk bounds of the same flavor as in Dalalyan and Tsybakov (2012a) but which solve two questions left open therein. In particular our risk bounds are adaptive (up to a logarithmic factor) to the unknown variance of the noise if the latter is Gaussian. We also address the regression model with fixed design.

Many real world problems naturally appear as constraints satisfaction problems (CSP), for which very efficient algorithms are known. Most of these involve the combination of two techniques: some direct propagation of constraints between variables (with the goal of reducing their sets of possible values) and some kind of structured search (depth-first, breadth-first,...). But when such blind search is not possible or not allowed or when one wants a 'constructive' or a 'pattern-based' solution, one must devise more complex propagation rules instead. In this case, one can introduce the notion of a candidate (a 'still possible' value for a variable). Here, we give this intuitive notion a well defined logical status, from which we can define the concepts of a resolution rule and a resolution theory. In order to keep our analysis as concrete as possible, we illustrate each definition with the well known Sudoku example. Part I proposes a general conceptual framework based on first order logic; with the introduction of chains and braids, Part II will give much deeper results.

The change of two orders of magnitude in the 'new DCF' of NIST's SRE'10, relative to the 'old DCF' evaluation criterion, posed a difficult challenge for participants and evaluator alike. Initially, participants were at a loss as to how to calibrate their systems, while the evaluator underestimated the required number of evaluation trials. After the fact, it is now obvious that both calibration and evaluation require very large sets of trials. This poses the challenges of (i) how to decide what number of trials is enough, and (ii) how to process such large data sets with reasonable memory and CPU requirements. After SRE'10, at the BOSARIS Workshop, we built solutions to these problems into the freely available BOSARIS Toolkit. This paper explains the principles and algorithms behind this toolkit. The main contributions of the toolkit are: 1. The Normalized Bayes Error-Rate Plot, which analyses likelihood- ratio calibration over a wide range of DCF operating points. These plots also help in judging the adequacy of the sizes of calibration and evaluation databases. 2. Efficient algorithms to compute DCF and minDCF for large score files, over the range of operating points required by these plots. 3. A new score file format, which facilitates working with very large trial lists. 4. A faster logistic regression optimizer for fusion and calibration. 5. A principled way to define EER (equal error rate), which is of practical interest when the absolute error count is small.

Roborobo! is a multi-platform, highly portable, robot simulator for large-scale collective robotics experiments. Roborobo! is coded in C++, and follows the KISS guideline ("Keep it simple"). Therefore, its external dependency is solely limited to the widely available SDL library for fast 2D Graphics. Roborobo! is based on a Khepera/ePuck model. It is targeted for fast single and multi-robots simulation, and has already been used in more than a dozen published research mainly concerned with evolutionary swarm robotics, including environment-driven self-adaptation and distributed evolutionary optimization, as well as online onboard embodied evolution and embodied morphogenesis.

In experimental tests of human behavior in unstructured bargaining games, typically many joint utility outcomes are found to occur, not just one. This suggests we predict the outcome of such a game as a probability distribution. This is in contrast to what is conventionally done (e.g, in the Nash bargaining solution), which is predict a single outcome. We show how to translate Nash's bargaining axioms to provide a distribution over outcomes rather than a single outcome. We then prove that a subset of those axioms forces the distribution over utility outcomes to be a power-law distribution. Unlike Nash's original result, our result holds even if the feasible set is finite. When the feasible set is convex and comprehensive, the mode of the power law distribution is the Harsanyi bargaining solution, and if we require symmetry it is the Nash bargaining solution. However, in general these modes of the joint utility distribution are not the experimentalist's Bayes-optimal predictions for the joint utility. Nor are the bargains corresponding to the modes of those joint utility distributions the modes of the distribution over bargains in general, since more than one bargain may result in the same joint utility. After introducing distributional bargaining solution concepts, we show how an external regulator can use them to optimally design an unstructured bargaining scenario. Throughout we demonstrate our analysis in computational experiments involving flight rerouting negotiations in the National Airspace System. We emphasize that while our results are formulated for unstructured bargaining, they can also be used to make predictions for noncooperative games where the modeler knows the utility functions of the players over possible outcomes of the game, but does not know the move spaces the players use to determine those outcomes.

There has been much recent interest in application of the pool-adjacent-violators (PAV) algorithm for the purpose of calibrating the probabilistic outputs of automatic pattern recognition and machine learning algorithms. Special cost functions, known as proper scoring rules form natural objective functions to judge the goodness of such calibration. We show that for binary pattern classifiers, the non-parametric optimization of calibration, subject to a monotonicity constraint, can be solved by PAV and that this solution is optimal for all regular binary proper scoring rules. This extends previous results which were limited to convex binary proper scoring rules. We further show that this result holds not only for calibration of probabilities, but also for calibration of log-likelihood-ratios, in which case optimality holds independently of the prior probabilities of the pattern classes.