Ann Nowé

A Survey on Filter Techniques for Feature Selection in Gene Expression Microarray Analysis

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.

Evolutionary game theory and multi-agent reinforcement learning

In this paper we survey the basics of reinforcement learning and (evolutionary) game theory, applied to the field of multi-agent systems. This paper contains three parts. We start with an overview on the fundamentals of reinforcement learning. Next we summarize the most important aspects of evolutionary game theory. Finally, we discuss the state-of-the-art of multi-agent reinforcement learning and the mathematical connection with evolutionary game theory.

Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages

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 inSilicoMerging R/Bioconductor package which, together with the earlier released inSilicoDb R/Bioconductor package, allows consistent retrieval, integration and analysis of publicly available microarray gene expression data sets. Inside the inSilicoMerging 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/].

Exploring selfish reinforcement learning in repeated games with stochastic rewards

In this paper we introduce a new multi-agent reinforcement learning algorithm, called exploring selfish reinforcement learning (ESRL). ESRL allows agents to reach optimal solutions in repeated non-zero sum games with stochastic rewards, by using coordinated exploration. First, two ESRL algorithms for respectively common interest and conflicting interest games are presented. Both ESRL algorithms are based on the same idea, i.e. an agent explores by temporarily excluding some of the local actions from its private action space, to give the team of agents the opportunity to look for better solutions in a reduced joint action space. In a latter stage these two algorithms are transformed into one generic algorithm which does not assume that the type of the game is known in advance. ESRL is able to find the Pareto optimal solution in common interest games without communication. In conflicting interest games ESRL only needs limited communication to learn a fair periodical policy, resulting in a good overall policy. Important to know is that ESRL agents are independent in the sense that they only use their own action choices and rewards to base their decisions on, that ESRL agents are flexible in learning different solution concepts and they can handle both stochastic, possible delayed rewards and asynchronous action selection. A real-life experiment, i.e. adaptive load-balancing of parallel applications is added.

InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor

Genomics datasets are increasingly useful for gaining biomedical insights, with adoption in the clinic underway. However, multiple hurdles related to data management stand in the way of their efficient large-scale utilization. The solution proposed is a web-based data storage hub. Having clear focus, flexibility and adaptability, InSilico DB seamlessly connects genomics dataset repositories to state-of-the-art and free GUI and command-line data analysis tools. The InSilico DB platform is a powerful collaborative environment, with advanced capabilities for biocuration, dataset sharing, and dataset subsetting and combination. InSilico DB is available from https://insilicodb.org.

inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO

Microarray technology has become an integral part of biomedical research and increasing amounts of datasets become available through public repositories. However, re-use of these datasets is severely hindered by unstructured, missing or incorrect biological samples information; as well as the wide variety of preprocessing methods in use. The inSilicoDb R/Bioconductor package is a command-line front-end to the InSilico DB, a web-based database currently containing 86 104 expert-curated human Affymetrix expression profiles compiled from 1937 GEO repository series. The use of this package builds on the Bioconductor projects focus on reproducibility by enabling a clear workflow in which not only analysis, but also the retrieval of verified data is supported.

Bee Behaviour in Multi-agent Systems

In this paper we present a new, non-pheromone-based algorithm inspired by the behaviour of bees. The algorithm combines both recruitment and navigation strategies. We investigate whether this new algorithm outperforms pheromone-based algorithms, inspired by the behaviour of ants, in the task of foraging. From our experiments, we conclude that (i) the bee-inspired algorithm is significantly more efficient when finding and collecting food, i.e., it uses fewer iterations to complete the task; (ii) the bee-inspired algorithm is more scalable, i.e., it requires less computation time to complete the task, even though in small worlds, the ant-inspired algorithm is faster on a time-per-iteration measure; and finally, (iii) our current bee-inspired algorithm is less adaptive than ant-inspired algorithms.

Scalarized multi-objective reinforcement learning: Novel design techniques

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 multi-objective 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.

Designing multi-objective multi-armed bandits algorithms: A study

We propose an algorithmic framework for multi-objective multi-armed bandits with multiple rewards. Different partial order relationships from multi-objective optimization can be considered for a set of reward vectors, such as scalarization functions and Pareto search. A scalarization function transforms the multi-objective environment into a single objective environment and are a popular choice in multi-objective reinforcement learning. Scalarization techniques can be straightforwardly implemented into the current multi-armed bandit framework, but the efficiency of these algorithms depends very much on their type, linear or non-linear (e.g. Chebyshev), and their parameters. Using Pareto dominance order relationship allows to explore the multi-objective environment directly, however this can result in large sets of Pareto optimal solutions. In this paper we propose and evaluate the performance of multi-objective MABs using three regret metric criteria. The standard UCB1 is extended to scalarized multi-objective UCB1 and we propose a Pareto UCB1 algorithm. Both algorithms are proven to have a logarithmic upper bound for their expected regret. We also introduce a variant of the scalarized multi-objective UCB1 that removes online inefficient scalarizations in order to improve the algorithms efficiency. These algorithms are experimentally compared on multi-objective Bernoulli distributions, Pareto UCB1 being the algorithm with the best empirical performance.

Two-Step Particle Swarm Optimization to Solve the Feature Selection Problem

In this paper we propose a new model of particle swarm optimization called two-step PSO. The basic idea is to split the heuristic search performed by particles into two stages. We have studied the performance of this new algorithm for the feature selection problem by using the reduct concept of the rough set theory. Experimental results obtained show that the two-step approach improves over the PSO model in calculating reducts, with the same computational cost.