Bayesian methodology for genetics of complex diseases

Genetic research of complex diseases is a challenging, but exciting, area of research. The early development of the research was limited, however, until the completion of the Human Genome and HapMap projects, along with the reduction in the cost of genotyping, which paves the way for understanding the genetic composition of complex diseases. In this thesis, we focus on the statistical methods for two aspects of genetic research: phenotype definition for diseases with complex etiology and methods for identifying potentially associated Single Nucleotide Polymorphisms (SNPs) and SNP-SNP interactions. With regard to phenotype definition for diseases with complex etiology, we firstly investigated the effects of different statistical phenotyping approaches on the subsequent analysis. In light of the findings, and the difficulties in validating the estimated phenotype, we proposed two different methods for reconciling phenotypes of different models using Bayesian model averaging as a coherent mechanism for accounting for model uncertainty. In the second part of the thesis, the focus is turned to the methods for identifying associated SNPs and SNP interactions. We review the use of Bayesian logistic regression with variable selection for SNP identification and extended the model for detecting the interaction effects for population based case-control studies. In this part of study, we also develop a machine learning algorithm to cope with the large scale data analysis, namely modified Logic Regression with Genetic Program (MLR-GEP), which is then compared with the Bayesian model, Random Forests and other variants of logic regression.

Optimal online prediction in adversarial environments

In many prediction problems, including those that arise in computer security and computational finance, the process generating the data is best modelled as an adversary with whom the predictor competes. Even decision problems that are not inherently adversarial can be usefully modeled in this way, since the assumptions are sufficiently weak that effective prediction strategies for adversarial settings are very widely applicable.

Optimal online prediction in adversarial environments

In many prediction problems, including those that arise in computer security and computational finance, the process generating the data is best modelled as an adversary with whom the predictor competes. Even decision problems that are not inherently adversarial can be usefully modeled in this way, since the assumptions are sufficiently weak that effective prediction strategies for adversarial settings are very widely applicable.

Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

Background The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. Results In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. Conclusion A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

A comparison of alternative bankruptcy prediction models

Early models of bankruptcy prediction employed financial ratios drawn from pre-bankruptcy financial statements and performed well both in-sample and out-of-sample. Since then there has been an ongoing effort in the literature to develop models with even greater predictive performance. A significant innovation in the literature was the introduction into bankruptcy prediction models of capital market data such as excess stock returns and stock return volatility, along with the application of the Black–Scholes–Merton option-pricing model. In this note, we test five key bankruptcy models from the literature using an upto- date data set and find that they each contain unique information regarding the probability of bankruptcy but that their performance varies over time. We build a new model comprising key variables from each of the five models and add a new variable that proxies for the degree of diversification within the firm. The degree of diversification is shown to be negatively associated with the risk of bankruptcy. This more general model outperforms the existing models in a variety of in-sample and out-of-sample tests.

Aerial object following using visual fuzzy servoing

This article presents a visual servoing system to follow a 3D moving object by a Micro Unmanned Aerial Vehicle (MUAV). The presented control strategy is based only on the visual information given by an adaptive tracking method based on the colour information. A visual fuzzy system has been developed for servoing the camera situated on a rotary wing MAUV, that also considers its own dynamics. This system is focused on continuously following of an aerial moving target object, maintaining it with a fixed safe distance and centred on the image plane. The algorithm is validated on real flights on outdoors scenarios, showing the robustness of the proposed systems against winds perturbations, illumination and weather changes among others. The obtained results indicate that the proposed algorithms is suitable for complex controls task, such object following and pursuit, flying in formation, as well as their use for indoor navigation

Triangular Linguistic Fuzzy based performance measurement model for supply chain to assess leanness attributes

Increasing global competitiveness worldwide has forced manufacturing organizations to produce high-quality products more quickly and at a competitive cost. In order to reach these goals, they need good quality components from suppliers at optimum price and lead time. This actually forced all the companies to adapt different improvement practices such as lean manufacturing, Just in Time (JIT) and effective supply chain management. Applying new improvement techniques and tools cause higher establishment costs and more Information Delay (ID). On the contrary, these new techniques may reduce the risk of stock outs and affect supply chain flexibility to give a better overall performance. But industry people are unable to measure the overall affects of those improvement techniques with a standard evaluation model .So an effective overall supply chain performance evaluation model is essential for suppliers as well as manufacturers to assess their companies under different supply chain strategies. However, literature on lean supply chain performance evaluation is comparatively limited. Moreover, most of the models assumed random values for performance variables. The purpose of this paper is to propose an effective supply chain performance evaluation model using triangular linguistic fuzzy numbers and to recommend optimum ranges for performance variables for lean implementation. The model initially considers all the supply chain performance criteria (input, output and flexibility), converts the values to triangular linguistic fuzzy numbers and evaluates overall supply chain performance under different situations. Results show that with the proposed performance measurement model, improvement area for each variable can be accurately identified.