Evolving artificial datasets to improve interpretable classifiers

Differential Evolution can be used to construct effective and compact artificial training datasets for machine learning algorithms. In this paper, a series of comparative experiments are performed in which two simple interpretable supervised classifiers (specifically, Naive Bayes and linear Support Vector Machines) are trained (i) directly on “real” data, as would be the normal case, and (ii) indirectly, using special artificial datasets derived from real data via evolutionary optimization. The results across several challenging test problems show that supervised classifiers trained indirectly using our novel evolution-based approach produce models with superior predictive classification performance. Besides presenting the accuracy of the learned models, we also analyze the sensitivity of our artificial data optimization process to Differential Evolution's parameters, and then we examine the statistical characteristics of the artificial data that is evolved

Network estimation in State Space Model with L1-regularization constraint

Biological networks have arisen as an attractive paradigm of genomic science ever since the introduction of large scale genomic technologies which carried the promise of elucidating the relationship in functional genomics. Microarray technologies coupled with appropriate mathematical or statistical models have made it possible to identify dynamic regulatory networks or to measure time course of the expression level of many genes simultaneously. However one of the few limitations fall on the high-dimensional nature of such data coupled with the fact that these gene expression data are known to include some hidden process. In that regards, we are concerned with deriving a method for inferring a sparse dynamic network in a high dimensional data setting. We assume that the observations are noisy measurements of gene expression in the form of mRNAs, whose dynamics can be described by some unknown or hidden process. We build an input-dependent linear state space model from these hidden states and demonstrate how an incorporated $L_{1}$ regularization constraint in an Expectation-Maximization (EM) algorithm can be used to reverse engineer transcriptional networks from gene expression profiling data. This corresponds to estimating the model interaction parameters. The proposed method is illustrated on time-course microarray data obtained from a well established T-cell data. At the optimum tuning parameters we found genes TRAF5, JUND, CDK4, CASP4, CD69, and C3X1 to have higher number of inwards directed connections and FYB, CCNA2, AKT1 and CASP8 to be genes with higher number of outwards directed connections. We recommend these genes to be object for further investigation. Caspase 4 is also found to activate the expression of JunD which in turn represses the cell cycle regulator CDC2.Comment: arXiv admin note: substantial text overlap with arXiv:1308.359