Genomic data integration is a key goal to be achieved towards large-scale genomic data analysis. This process is very challenging due to the diverse sources of information resulting from genomics experiments. In this work, we review methods designed to combine genomic data recorded from microarray gene expression (MAGE) experiments. It has been acknowledged that the main source of variation between different MAGE datasets is due to the so-called 'batch effects'. The methods reviewed here perform data integration by removing (or more precisely attempting to remove) the unwanted variation associated with batch effects. They are presented in a unified framework together with a wide range of evaluation tools, which are mandatory in assessing the efficiency and the quality of the data integration process. We provide a systematic description of the MAGE data integration methodology together with some basic recommendation to help the users in choosing the appropriate tools to integrate MAGE data for large-scale analysis; and also how to evaluate them from different perspectives in order to quantify their efficiency. All genomic data used in this study for illustration purposes were retrieved from InSilicoDB http://insilico.ulb.ac.be.

A plenitude of feature selection (FS) methods is available in the literature, most of them rising as a need to analyze data of very high dimension, usually hundreds or thousands of variables. Such data sets are now available in various application areas like combinatorial chemistry, text mining, multivariate imaging, or bioinformatics. As a general accepted rule, these methods are grouped in filters, wrappers, and embedded methods. More recently, a new group of methods has been added in the general framework of FS: ensemble techniques. The focus in this survey is on filter feature selection methods for informative feature discovery in gene expression microarray (GEM) analysis, which is also known as differentially expressed genes (DEGs) discovery, gene prioritization, or biomarker discovery. We present them in a unified framework, using standardized notations in order to reveal their technical details and to highlight their common characteristics as well as their particularities.

BackgroundWith an abundant amount of microarray gene expression data sets available through public repositories, new possibilities lie in combining multiple existing data sets. In this new context, analysis itself is no longer the problem, but retrieving and consistently integrating all this data before delivering it to the wide variety of existing analysis tools becomes the new bottleneck.ResultsWe present the newly released R/Bioconductor package which, together with the earlier released R/Bioconductor package, allows consistent retrieval, integration and analysis of publicly available microarray gene expression data sets. Inside the package a set of five visual and six quantitative validation measures are available as well.ConclusionsBy providing (i) access to uniformly curated and preprocessed data, (ii) a collection of techniques to remove the batch effects between data sets from different sources, and (iii) several validation tools enabling the inspection of the integration process, these packages enable researchers to fully explore the potential of combining gene expression data for downstream analysis. The power of using both packages is demonstrated by programmatically retrieving and integrating gene expression studies from the InSilico DB repository [https://insilicodb.org/app/].

In this paper we introduce a new decentralized digital currency, called NRGcoin. Prosumers in the smart grid trade locally produced renewable energy using NRGcoins, the value of which is determined on an open currency exchange market. Similar to Bitcoins, this currency offers numerous advantages over fiat currency, but unlike Bitcoins it is generated by injecting energy into the grid, rather than spending energy on computational power. In addition, we propose a novel trading paradigm for buying and selling green energy in the smart grid. Our mechanism achieves demand response by providing incentives to prosumers to balance their production and consumption out of their own self-interest. We study the advantages of our proposed currency over traditional money and environmental instruments, and explore its benefits for all parties in the smart grid.

In multi-objective problems, it is key to find compromising solutions that balance different objectives. The linear scalarization function is often utilized to translate the multiobjective nature of a problem into a standard, single-objective problem. Generally, it is noted that such as linear combination can only find solutions in convex areas of the Pareto front, therefore making the method inapplicable in situations where the shape of the front is not known beforehand, as is often the case. We propose a non-linear scalarization function, called the Chebyshev scalarization function, as a basis for action selection strategies in multi-objective reinforcement learning. The Chebyshev scalarization method overcomes the flaws of the linear scalarization function as it can (i) discover Pareto optimal solutions regardless of the shape of the front, i.e. convex as well as non-convex , (ii) obtain a better spread amongst the set of Pareto optimal solutions and (iii) is not particularly dependent on the actual weights used.

Notwithstanding important advances in the context of single-variant pathogenicity identification, novel breakthroughs in discerning the origins of many rare diseases require methods able to identify more complex genetic models. We present here the Variant Combinations Pathogenicity Predictor (VarCoPP), a machine-learning approach that identifies pathogenic variant combinations in gene pairs (called digenic or bilocus variant combinations). We show that the results produced by this method are highly accurate and precise, an efficacy that is endorsed when validating the method on recently published independent disease-causing data. Confidence labels of 95% and 99% are identified, representing the probability of a bilocus combination being a true pathogenic result, providing geneticists with rational markers to evaluate the most relevant pathogenic combinations and limit the search space and time. Finally, the VarCoPP has been designed to act as an interpretable method that can provide explanations on why a bilocus combination is predicted as pathogenic and which biological information is important for that prediction. This work provides an important step toward the genetic understanding of rare diseases, paving the way to clinical knowledge and improved patient care.

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In multi-objective multi-agent systems (MOMASs), agents explicitly consider the possible trade-offs between conflicting objective functions. We argue that compromises between competing objectives in MOMAS should be analyzed on the basis of the utility that these compromises have for the users of a system, where an agent’s utility function maps their payoff vectors to scalar utility values. This utility-based approach naturally leads to two different optimization criteria for agents in a MOMAS: expected scalarized returns (ESRs) and scalarized expected returns (SERs). In this article, we explore the differences between these two criteria using the framework of multi-objective normal-form games (MONFGs). We demonstrate that the choice of optimization criterion (ESR or SER) can radically alter the set of equilibria in a MONFG when nonlinear utility functions are used.