Accumulation of standardized data collections is opening up novel opportunities for holistic characterization of genome function. The limited scalability of current preprocessing techniques has, however, formed a bottleneck for full utilization of contemporary microarray collections. While short oligonucleotide arrays constitute a major source of genome-wide profiling data, scalable probe-level preprocessing algorithms have been available only for few measurement platforms based on pre-calculated model parameters from restricted reference training sets. To overcome these key limitations, we introduce a fully scalable online-learning algorithm that provides tools to process large microarray atlases including tens of thousands of arrays. Unlike the alternatives, the proposed algorithm scales up in linear time with respect to sample size and is readily applicable to all short oligonucleotide platforms. This is the only available preprocessing algorithm that can learn probe-level parameters based on sequential hyperparameter updates at small, consecutive batches of data, thus circumventing the extensive memory requirements of the standard approaches and opening up novel opportunities to take full advantage of contemporary microarray data collections. Moreover, using the most comprehensive data collections to estimate probe-level effects can assist in pinpointing individual probes affected by various biases and provide new tools to guide array design and quality control. The implementation is freely available in R/Bioconductor at http://www.bioconductor.org/packages/devel/bioc/html/RPA.html

Given a current news event, we tackle the problem of generating plausible predictions of future events it might cause. We present a new methodology for modeling and predicting such future news events using machine learning and data mining techniques. Our Pundit algorithm generalizes examples of causality pairs to infer a causality predictor. To obtain precisely labeled causality examples, we mine 150 years of news articles and apply semantic natural language modeling techniques to headlines containing certain predefined causality patterns. For generalization, the model uses a vast number of world knowledge ontologies. Empirical evaluation on real news articles shows that our Pundit algorithm performs as well as non-expert humans.

For robots to be accommodated in human spaces and in humans daily activities, robots should be able to understand messages from the human conversation partner. In the same light, humans must also understand the messages that are being communicated by robots, including the non-verbal ones. We conducted a web-based video study wherein participants gave interpretations on the iconic gestures and emblems that were produced by an anthropomorphic robot. Out of the 15 gestures presented, we found 6 robotic gestures that can be accurately recognized by the human observer. These were nodding, clapping, hugging, expressing anger, walking, and flying. We reviewed these gestures for their meaning from literatures in human and animal behavior. We conclude by discussing the possible implications of these gestures for the design of social robots that are aimed to have engaging interactions with humans.

Gaussian Process (GP) regression models typically assume that residuals are Gaussian and have the same variance for all observations. However, applications with input-dependent noise (heteroscedastic residuals) frequently arise in practice, as do applications in which the residuals do not have a Gaussian distribution. In this paper, we propose a GP Regression model with a latent variable that serves as an additional unobserved covariate for the regression. This model (which we call GPLC) allows for heteroscedasticity since it allows the function to have a changing partial derivative with respect to this unobserved covariate. With a suitable covariance function, our GPLC model can handle (a) Gaussian residuals with input-dependent variance, or (b) non-Gaussian residuals with input-dependent variance, or (c) Gaussian residuals with constant variance. We compare our model, using synthetic datasets, with a model proposed by Goldberg, Williams and Bishop (1998), which we refer to as GPLV, which only deals with case (a), as well as a standard GP model which can handle only case (c). Markov Chain Monte Carlo methods are developed for both modelsl. Experiments show that when the data is heteroscedastic, both GPLC and GPLV give better results (smaller mean squared error and negative log-probability density) than standard GP regression. In addition, when the residual are Gaussian, our GPLC model is generally nearly as good as GPLV, while when the residuals are non-Gaussian, our GPLC model is better than GPLV.

In the last decade, a new computational paradigm was introduced in the field of Machine Learning, under the name of Reservoir Computing (RC). RC models are neural networks which a recurrent part (the reservoir) that does not participate in the learning process, and the rest of the system where no recurrence (no neural circuit) occurs. This approach has grown rapidly due to its success in solving learning tasks and other computational applications. Some success was also observed with another recently proposed neural network designed using Queueing Theory, the Random Neural Network (RandNN). Both approaches have good properties and identified drawbacks. In this paper, we propose a new RC model called Echo State Queueing Network (ESQN), where we use ideas coming from RandNNs for the design of the reservoir. ESQNs consist in ESNs where the reservoir has a new dynamics inspired by recurrent RandNNs. The paper positions ESQNs in the global Machine Learning area, and provides examples of their use and performances. We show on largely used benchmarks that ESQNs are very accurate tools, and we illustrate how they compare with standard ESNs.

A market of potato commodity for industry scale usage is engaging several types of actors. They are farmers, middlemen, and industries. A multi-agent system has been built to simulate these actors into agent entities, based on manually given parameters within a simulation scenario file. Each type of agents has its own fuzzy logic representing actual actors' knowledge, to be used to interpreting values and take appropriated decision of it while on simulation. The system will simulate market activities with programmed behaviors then produce the results as spreadsheet and chart graph files. These results consist of each agent's yearly finance and commodity data. The system will also predict each of next value from these outputs.

Locality-sensitive hashing converts high-dimensional feature vectors, such as image and speech, into bit arrays and allows high-speed similarity calculation with the Hamming distance. There is a hashing scheme that maps feature vectors to bit arrays depending on the signs of the inner products between feature vectors and the normal vectors of hyperplanes placed in the feature space. This hashing can be seen as a discretization of the feature space by hyperplanes. If labels for data are given, one can determine the hyperplanes by using learning algorithms. However, many proposed learning methods do not consider the hyperplanes' offsets. Not doing so decreases the number of partitioned regions, and the correlation between Hamming distances and Euclidean distances becomes small. In this paper, we propose a lift map that converts learning algorithms without the offsets to the ones that take into account the offsets. With this method, the learning methods without the offsets give the discretizations of spaces as if it takes into account the offsets. For the proposed method, we input several high-dimensional feature data sets and studied the relationship between the statistical characteristics of data, the number of hyperplanes, and the effect of the proposed method.

In science and engineering, intelligent processing of complex signals such as images, sound or language is often performed by a parameterized hierarchy of nonlinear processing layers, sometimes biologically inspired. Hierarchical systems (or, more generally, nested systems) offer a way to generate complex mappings using simple stages. Each layer performs a different operation and achieves an ever more sophisticated representation of the input, as, for example, in an deep artificial neural network, an object recognition cascade in computer vision or a speech front-end processing. Joint estimation of the parameters of all the layers and selection of an optimal architecture is widely considered to be a difficult numerical nonconvex optimization problem, difficult to parallelize for execution in a distributed computation environment, and requiring significant human expert effort, which leads to suboptimal systems in practice. We describe a general mathematical strategy to learn the parameters and, to some extent, the architecture of nested systems, called the method of auxiliary coordinates (MAC). This replaces the original problem involving a deeply nested function with a constrained problem involving a different function in an augmented space without nesting. The constrained problem may be solved with penalty-based methods using alternating optimization over the parameters and the auxiliary coordinates. MAC has provable convergence, is easy to implement reusing existing algorithms for single layers, can be parallelized trivially and massively, applies even when parameter derivatives are not available or not desirable, and is competitive with state-of-the-art nonlinear optimizers even in the serial computation setting, often providing reasonable models within a few iterations.

The results in this paper add useful tools to the theory of sets of desirable gambles, a growing toolbox for reasoning with partial probability assessments. We investigate how to combine a number of marginal coherent sets of desirable gambles into a joint set using the properties of epistemic irrelevance and independence. We provide formulas for the smallest such joint, called their independent natural extension, and study its main properties. The independent natural extension of maximal coherent sets of desirable gambles allows us to define the strong product of sets of desirable gambles. Finally, we explore an easy way to generalise these results to also apply for the conditional versions of epistemic irrelevance and independence. Having such a set of tools that are easily implemented in computer programs is clearly beneficial to fields, like AI, with a clear interest in coherent reasoning under uncertainty using general and robust uncertainty models that require no full specification.

A fundamental question in systems biology is the construction and training to data of mathematical models. Logic formalisms have become very popular to model signaling networks because their simplicity allows us to model large systems encompassing hundreds of proteins. An approach to train (Boolean) logic models to high-throughput phospho-proteomics data was recently introduced and solved using optimization heuristics based on stochastic methods. Here we demonstrate how this problem can be solved using Answer Set Programming (ASP), a declarative problem solving paradigm, in which a problem is encoded as a logical program such that its answer sets represent solutions to the problem. ASP has significant improvements over heuristic methods in terms of efficiency and scalability, it guarantees global optimality of solutions as well as provides a complete set of solutions. We illustrate the application of ASP with in silico cases based on realistic networks and data.