Classification of gene functions using support vector machine for time-course gene expression data

Since most biological systems are developmental and dynamic, time-course gene expression profiles provide an important characterization of gene functions. Assigning functions for genes with unknown functions based on time-course gene expressions is an important task in functional genomics. Recently, various methods have been proposed for the classification of gene functions based on time-course gene expression data. In this paper, we consider the classification of gene functions from functional data analysis viewpoint, where a functional support vector machine is adopted. The functional support vector machine can model temporal effects of time-course gene expression data by incorporating the coefficients as well as the basis matrix obtained from a finite expansion of gene expressions on a set of basis functions. We apply the functional support vector machine to both real microarray and simulated data. Our results indicate that the functional support vector machine is effective in discriminating gene functions of time-course gene expressions with predefined functions. The method also provides valuable functional information about interactions between genes and allows the assignment of new functions to genes with unknown functions.     

Utilization of virtual samples to facilitate cancer identification for DNA microarray data in the early stages of an investigation

DNA microarray datasets are generally small in size, high dimensional with many non-discriminative genes, and non-linear with outliers. Their size/dimension ratio suggests that DNA microarray datasets are identified as small-sample problems. Recently, researchers have developed various gene selection algorithms to discover genes that are most relevant to a specific disease, and thus to reduce computation. Most gene selection algorithms improve learning performance and efficiency, but still suffer from the limitation of insufficient training samples in the datasets. Moreover, in the early stage of diagnosing a new disease, very limited data can be obtained. Therefore, the derived diagnostic model is usually unreliable to identify the new disease. Consequently, the diagnostic performance cannot always be robust, even with the gene selection algorithms.To solve the problem of very limited training dataset with non-linear data or outliers, we propose the method GVSG (Group Virtual Sample Generation), which is a non-linear Virtual Sample Generation algorithm. This non-linear method detects the characteristics in the very limited data, forms discrete groups of each discriminative gene, and systematically generates virtual samples for each of these to accelerate and stabilize the modeling process. The results show that this method significantly improves the learning accuracy in the early stage of DNA microarray data.     

Theoretical and practical aspects of the quadratic error in the local linear estimation of the conditional density for functional data

The problem of the nonparametric local linear estimation of the conditional density of a scalar response variable given a random variable taking values in a semi-metric space is considered. Some theoretical and practical asymptotic properties of this estimator are established. The usefulness of the estimator is highlighted through the exact expression involved in the leading terms of the quadratic error, and by conducting a computational investigation to show the superiority of this estimation method for the conditional density and then for the conditional mode. Moreover, in order to verify the pertinence of the technique, from a practical point of view, it is applied to a real dataset.     

Nonlinear aircraft sensor fault reconstruction in the presence of disturbances validated by real flight data

This paper proposes an approach for Inertial Measurement Unit sensor fault reconstruction by exploiting a ground speed-based kinematic model of the aircraft flying in a rotating earth reference system. Two strategies for the validation of sensor fault reconstruction are presented: closed-loop validation and open-loop validation. Both strategies use the same kinematic model and a newly-developed Adaptive Two-Stage Extended Kalman Filter to estimate the states and faults of the aircraft. Simulation results demonstrate the effectiveness of the proposed approach compared to an approach using an airspeed-based kinematic model. Furthermore, the major contribution is that the proposed approach is validated using real flight test data including the presence of external disturbances such as turbulence. Three flight scenarios are selected to test the performance of the proposed approach. It is shown that the proposed approach is robust to model uncertainties, unmodeled dynamics and disturbances such as time-varying wind and turbulence. Therefore, the proposed approach can be incorporated into aircraft Fault Detection and Isolation systems to enhance the performance of the aircraft.