A hybrid direct search and model-based derivative-free optimization method with dynamic decision processing

A derivative-free optimization (DFO) method is an optimization method that does not make use of derivative information in order to find the optimal solution. It is advantageous for solving real-world problems in which the only information available about the objective function is the output for a specific input. In this thesis, we develop the framework for a DFO method, referred to as the DQL method. It is designed to be a versatile hybrid method capable of performing direct search, quadratic-model search, and line search all in the same method. We develop a series of different direct search, quadratic-model search, and line search strategies within this framework. The benchmark results indicate that each of these strategies has distinct advantages in different scenarios and that there is no clear winner. We develop the Smart DQL method by allowing the method to determine the optimal search strategies in various circumstances. The Smart DQL method is applied to the problem of solid tank design for 3D radiation dosimetry. We show that, given the same evaluation budget, the Smart DQL method produces a higher-quality solution than the Grid Search method that was originally employed by the UBCO 3D Radiation Dosimetry Research Group.Science, Irving K. Barber Faculty of (Okanagan)Computer Science, Mathematics, Physics and Statistics, Department of (Okanagan)Graduat

A Hybrid Direct Search and Model-Based Derivative-Free Optimization Method with Dynamic Decision Processing and Application in Solid-Tank Design

A derivative-free optimization (DFO) method is an optimization method that does not make use of derivative information in order to find the optimal solution. It is advantageous for solving real-world problems in which the only information available about the objective function is the output for a specific input. In this paper, we develop the framework for a DFO method called the DQL method. It is designed to be a versatile hybrid method capable of performing direct search, quadratic-model search, and line search all in the same method. We develop and test a series of different strategies within this framework. The benchmark results indicate that each of these strategies has distinct advantages and that there is no clear winner in the overall performance among efficiency and robustness. We develop the Smart DQL method by allowing the method to determine the optimal search strategies in various circumstances. The Smart DQL method is applied to a problem of solid-tank design for 3D radiation dosimetry provided by the UBCO (University of British Columbia—Okanagan) 3D Radiation Dosimetry Research Group. Given the limited evaluation budget, the Smart DQL method produces high-quality solutions

Ion Fusion of High-Resolution LC MS-Based Metabolomics Data to Discover More Reliable Biomarkers

A systematic approach for the fusion of associated ions from a common molecule was developed to generate "one feature for one peak" metabolomics data. This approach guarantees that each molecule is equally selected as a potential biomarker and may largely enhance the chance to obtain reliable findings without employing redundant ion information. The ion fusion is based on low mass variation in contrast to the theoretical calculation measured by a high-resolution mass spectrometer, such as LTQ orbitrap, and a high correlation of ion pairs from the same molecule. The mass characteristics of isotopic distribution, neutral loss, and adduct ions were simultaneously applied to inspect each extracted ion in the range of a predefined retention time window. The correlation coefficient was computed with the corresponding intensities of each ion pair among all experimental samples. Serum metabolomics data for the investigation of hepatocellular carcinoma (HCC) and healthy controls were utilized as an example to demonstrate this strategy. In total, 609 and 1084 ion pairs were respectively found meeting one or more criteria for fusion, and therefore fused to 106 and 169 metabolite features of the datasets in the positive and negative modes, respectively. The important metabolite features were separately discovered and compared to distinguish the HCC from the healthy controls using the two datasets with and without ion fusion. The results show that the developed method can be an effective tool to process high-resolution mass spectrometry data in "omics" studies

A Novel Strategy for Large-Scale Metabolomics Study by Calibrating Gross and Systematic Errors in Gas Chromatography-Mass Spectrometry

Metabolomics is increasingly applied to discover and validate metabolite biomarkers and illuminate biological variations. Combination of multiple analytical batches in large-scale and long-term metabolomics is commonly utilized to generate robust metabolomics data, but gross and systematic errors are often observed. The appropriate calibration methods are required before statistical analyses. Here, we develop a novel correction strategy for large-scale and long-term metabolomics study, which could integrate metabolomics data from multiple batches and different instruments by calibrating gross and systematic errors. The gross error calibration method applied various statistical and fitting models of the feature ratios between two adjacent quality control (QC) samples to screen and calibrate outlier variables. Virtual QC of each sample was produced by a linear fitting model of the feature intensities between two neighboring QCs to obtain a correction factor and remove the systematic bias. The suggested method was applied to handle metabolic profiling data of 1197 plant samples in nine batches analyzed by two gas chromatography mass spectrometry instruments. The method was evaluated by the relative standard deviations of all the detected peaks, the average Pearson correlation coefficients, and Euclidean distance of QCs and non-QC replicates. The results showed the established approach outperforms the commonly used internal standard correction and total intensity signal correction methods, it could be used to integrate the metabolomics data from multiple analytical batches and instruments, and it allows the frequency of QC to one injection of every 20 real samples. The suggested method makes a large amount of metabolomics analysis practicable

Ion Fusion of High-Resolution LC–MS-Based Metabolomics Data to Discover More Reliable Biomarkers

A systematic approach for the fusion of associated ions from a common molecule was developed to generate “one feature for one peak” metabolomics data. This approach guarantees that each molecule is equally selected as a potential biomarker and may largely enhance the chance to obtain reliable findings without employing redundant ion information. The ion fusion is based on low mass variation in contrast to the theoretical calculation measured by a high-resolution mass spectrometer, such as LTQ orbitrap, and a high correlation of ion pairs from the same molecule. The mass characteristics of isotopic distribution, neutral loss, and adduct ions were simultaneously applied to inspect each extracted ion in the range of a predefined retention time window. The correlation coefficient was computed with the corresponding intensities of each ion pair among all experimental samples. Serum metabolomics data for the investigation of hepatocellular carcinoma (HCC) and healthy controls were utilized as an example to demonstrate this strategy. In total, 609 and 1084 ion pairs were respectively found meeting one or more criteria for fusion, and therefore fused to 106 and 169 metabolite features of the datasets in the positive and negative modes, respectively. The important metabolite features were separately discovered and compared to distinguish the HCC from the healthy controls using the two datasets with and without ion fusion. The results show that the developed method can be an effective tool to process high-resolution mass spectrometry data in “omics” studies

Highly Breathable and Stretchable Strain Sensors with Insensitive Response to Pressure and Bending

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