Evolutionary approaches for the reverse-engineering of gene regulatory networks: A study on a biologically realistic dataset

<p>Abstract</p> <p>Background</p> <p>Inferring gene regulatory networks from data requires the development of algorithms devoted to structure extraction. When only static data are available, gene interactions may be modelled by a Bayesian Network (BN) that represents the presence of direct interactions from regulators to regulees by conditional probability distributions. We used enhanced evolutionary algorithms to stochastically evolve a set of candidate BN structures and found the model that best fits data without prior knowledge.</p> <p>Results</p> <p>We proposed various evolutionary strategies suitable for the task and tested our choices using simulated data drawn from a given bio-realistic network of 35 nodes, the so-called insulin network, which has been used in the literature for benchmarking. We assessed the inferred models against this reference to obtain statistical performance results. We then compared performances of evolutionary algorithms using two kinds of recombination operators that operate at different scales in the graphs. We introduced a niching strategy that reinforces diversity through the population and avoided trapping of the algorithm in one local minimum in the early steps of learning. We show the limited effect of the mutation operator when niching is applied. Finally, we compared our best evolutionary approach with various well known learning algorithms (MCMC, K2, greedy search, TPDA, MMHC) devoted to BN structure learning.</p> <p>Conclusion</p> <p>We studied the behaviour of an evolutionary approach enhanced by niching for the learning of gene regulatory networks with BN. We show that this approach outperforms classical structure learning methods in elucidating the original model. These results were obtained for the learning of a bio-realistic network and, more importantly, on various small datasets. This is a suitable approach for learning transcriptional regulatory networks from real datasets without prior knowledge.</p

An on-line Pittsburgh LCS for the Three-Cornered Coevolution Framework

The Three-Cornered Coevolution Framework describes a method that is capable of addressing classification tasks through coevolution (coadaptive evolution) where three different agents (i.e. a generation agent and two classification agents) learn and adapt to the changes of the problems without human involvement. Here, artificial problems can be generated in concert with classification agents in order to provide insight into their relationships. Previous work on the Two-Cornered Coevolution Framework provided foundation for implementing the system that was able to set-up the problem’s difficulty appropriately while triggering the coevolutionary process. However, the triggering process was set manually without utilising the third agent as proposed in the original framework to perform this task. Previous work on the Three-Cornered Coevolution introduced the third agent (a new classification agent) to trigger the coevolutionary process within the system, where its functionality and effect on the system requires investigation. This paper details the implementation for this case; two classification agents that use different styles of learning techniques (e.g. supervised versus reinforcement learning techniques) is adapted in the classification agents to learn the various classification problems. Ultimately, Learning Classifier System (LCS) is chosen to be implemented in the participating agents. LCS has several potential characteristics, such as interpretability, generalization capability and variations in representation, that are suitable for the system. Experiments show that the Pittsburgh-style LCS with the adaptation of Tabu Search technique in S capable to autonomously adjust the problem’s difficulty and generate a wide range of problems for classification. The adaptation of A-PLUS to an ‘on-line’ system is successful implemented. Further, the classification agents (i.e. R and I) are able to solve the classification tasks where the classification performance are varied. The Three-Cornered Coevolution Framework offers a great potential for autonomous learning and provides useful insight into coevolution learning over the standard studies of pattern recognition. The system is capable of autonomously generating various problems, learning and providing insight into each learning system’s ability by determining the problem domains where they perform relatively well. This is in contrast to humans having to determine the problem domains.</p

Search for supersymmetry in events with large missing transverse momentum, jets, and at least one tau lepton in 20 fb−1 of √s= 8 TeV proton-proton collision data with the ATLAS detector

© 2014, The Author(s). A search for supersymmetry (SUSY) in events with large missing transverse momentum, jets, at least one hadronically decaying tau lepton and zero or one additional light leptons (electron/muon), has been performed using 20.3fb−1of proton-proton collision data at √ s= 8 TeV recorded with the ATLAS detector at the Large Hadron Collider. No excess above the Standard Model background expectation is observed in the various signal regions and 95% confidence level upper limits on the visible cross section for new phenomena are set. The results of the analysis are interpreted in several SUSY scenarios, significantly extending previous limits obtained in the same final states. In the framework of minimal gauge-mediated SUSY breaking models, values of the SUSY breaking scale Λ below 63 TeV are excluded, independently of tan β. Exclusion limits are also derived for an mSUGRA/CMSSM model, in both the R-parity-conserving and R-parity-violating case. A further interpretation is presented in a framework of natural gauge mediation, in which the gluino is assumed to be the only light coloured sparticle and gluino masses below 1090 GeV are excluded