Geometric optimization methods for the analysis of gene expression data

DNA microarrays provide such a huge amount of data that unsupervised methods are required to reduce the dimension of the data set and to extract meaningful biological information. This work shows that Independent Component Analysis (ICA) is a promising approach for the analysis of genome-wide transcriptomic data. The paper first presents an overview of the most popular algorithms to perform ICA. These algorithms are then applied on a microarray breast-cancer data set. Some issues about the application of ICA and the evaluation of biological relevance of the results are discussed. This study indicates that ICA significantly outperforms Principal Component Analysis (PCA).

Optimization on the orthogonal group for independent component analysis

This paper derives a new algorithm that performs independent component analysis (ICA) by optimizing the contrast function of the RADICAL algorithm. The core idea of the proposed optimization method is to combine the global search of a good initial condition with a gradient-descent algorithm. This new ICA algorithm performs faster than the RADICAL algorithm (based on Jacobi rotations) while still preserving, and even enhancing, the strong robustness properties that result from its contrast. © Springer-Verlag Berlin Heidelberg 2007.

Geometric optimization methods for independent component analysis applied on gene expression data

DNA microarrays provide a huge amount of data and require therefore dimensionality reduction methods to extract meaningful biological information. Independent Component Analysis (ICA) was proposed by several authors as an interesting means. Unfortunately, experimental data are usually of poor quality- because of noise, outliers and lack of samples. Robustness to these hurdles will thus be a key feature for an ICA algorithm. This paper identifies a robust contrast function and proposes a new ICA algorithm. © 2007 IEEE.

Sensitivity analysis and optimization of the nuclear fuel cycle

A sensitivity study has been conducted to assess the robustness of the conclusions presented in the MIT Fuel Cycle Study. The Once Through Cycle (OTC) is considered as the base-line case, while advanced technologies with fuel recycling characterize the alternative fuel cycles. The options include limited recycling in LWRs and full recycling in fast reactors and in high conversion LWRs. Fast reactor technologies studied include both oxide and metal fueled reactors. The analysis allowed optimization of the fast reactor conversion ratio with respect to desired fuel cycle performance characteristics. The following parameters were found to significantly affect the performance of recycling technologies and their penetration over time: Capacity Factors of the fuel cycle facilities, Spent Fuel Cooling Time, Thermal Reprocessing Introduction Date, and incore and Out-of-core TRU Inventory Requirements for recycling technology. An optimization scheme of the nuclear fuel cycle is proposed. Optimization criteria and metrics of interest for different stakeholders in the fuel cycle (economics, waste management, environmental impact, etc.) are utilized for two different optimization techniques (linear and stochastic). Preliminary results covering single and multi-variable and single and multi-objective optimization demonstrate the viability of the optimization scheme.

Robust design optimization of gas turbine compression systems

Gas turbine compression systems are required to perform adequately over a range of operating conditions. Complexity has encouraged the conventional design process for compressors to focus initially on one operating point, usually the most commonor arduous, to draw up an outline design. Generally, only as this initial design is refined is its offdesign performance assessed in detail. Not only does this necessarily introduce a potentially costly and timeconsuming extra loop in the design process, but it also may result in a design whose offdesign behavior is suboptimal. Aversion of nonintrusive polynomial chaos was previously developed in which a set of orthonormal polynomials was generated to facilitate a rapid analysis of robustness in the presence of generic uncertainties with good accuracy. In this paper, this analysis method is incorporated in real time into the design process for the compression system of a three-shaft gas turbine aeroengine. This approach to robust optimization is shown to lead to designs that exhibit consistently improved system performance with reduced sensitivity to offdesign operation.