CMA – a comprehensive Bioconductor package for supervised classification with high dimensional data

For the last eight years, microarray-based class prediction has been a major topic in statistics, bioinformatics and biomedicine research. Traditional methods often yield unsatisfactory results or may even be inapplicable in the p > n setting where the number of predictors by far exceeds the number of observations, hence the term “ill-posed-problem”. Careful model selection and evaluation satisfying accepted good-practice standards is a very complex task for inexperienced users with limited statistical background or for statisticians without experience in this area. The multiplicity of available methods for class prediction based on high-dimensional data is an additional practical challenge for inexperienced researchers. In this article, we introduce a new Bioconductor package called CMA (standing for “Classification for MicroArrays”) for automatically performing variable selection, parameter tuning, classifier construction, and unbiased evaluation of the constructed classifiers using a large number of usual methods. Without much time and effort, users are provided with an overview of the unbiased accuracy of most top-performing classifiers. Furthermore, the standardized evaluation framework underlying CMA can also be beneficial in statistical research for comparison purposes, for instance if a new classifier has to be compared to existing approaches. CMA is a user-friendly comprehensive package for classifier construction and evaluation implementing most usual approaches. It is freely available from the Bioconductor website at http://bioconductor.org/packages/2.3/bioc/html/CMA.html

CMA – a comprehensive Bioconductor package for supervised classification with high dimensional data

For the last eight years, microarray-based class prediction has been a major topic in statistics, bioinformatics and biomedicine research. Traditional methods often yield unsatisfactory results or may even be inapplicable in the p > n setting where the number of predictors by far exceeds the number of observations, hence the term “ill-posed-problem”. Careful model selection and evaluation satisfying accepted good-practice standards is a very complex task for inexperienced users with limited statistical background or for statisticians without experience in this area. The multiplicity of available methods for class prediction based on high-dimensional data is an additional practical challenge for inexperienced researchers. In this article, we introduce a new Bioconductor package called CMA (standing for “Classification for MicroArrays”) for automatically performing variable selection, parameter tuning, classifier construction, and unbiased evaluation of the constructed classifiers using a large number of usual methods. Without much time and effort, users are provided with an overview of the unbiased accuracy of most top-performing classifiers. Furthermore, the standardized evaluation framework underlying CMA can also be beneficial in statistical research for comparison purposes, for instance if a new classifier has to be compared to existing approaches. CMA is a user-friendly comprehensive package for classifier construction and evaluation implementing most usual approaches. It is freely available from the Bioconductor website at http://bioconductor.org/packages/2.3/bioc/html/CMA.html

A generic face processing framework: technologies, analyses and applications.

Jang Kim-fung.Thesis (M.Phil.)--Chinese University of Hong Kong, 2003.Includes bibliographical references (leaves 108-124).Abstracts in English and Chinese.Abstract --- p.iAcknowledgement --- p.iiiChapter 1 --- Introduction --- p.1Chapter 1.1 --- Background --- p.1Chapter 1.2 --- Introduction about Face Processing Framework --- p.4Chapter 1.2.1 --- Basic architecture --- p.4Chapter 1.2.2 --- Face detection --- p.5Chapter 1.2.3 --- Face tracking --- p.6Chapter 1.2.4 --- Face recognition --- p.6Chapter 1.3 --- The scope and contributions of the thesis --- p.7Chapter 1.4 --- The outline of the thesis --- p.8Chapter 2 --- Facial Feature Representation --- p.10Chapter 2.1 --- Facial feature analysis --- p.10Chapter 2.1.1 --- Pixel information --- p.11Chapter 2.1.2 --- Geometry information --- p.13Chapter 2.2 --- Extracting and coding of facial feature --- p.14Chapter 2.2.1 --- Face recognition --- p.15Chapter 2.2.2 --- Facial expression classification --- p.38Chapter 2.2.3 --- Other related work --- p.44Chapter 2.3 --- Discussion about facial feature --- p.48Chapter 2.3.1 --- Performance evaluation for face recognition --- p.49Chapter 2.3.2 --- Evolution of the face recognition --- p.52Chapter 2.3.3 --- Evaluation of two state-of-the-art face recog- nition methods --- p.53Chapter 2.4 --- Problem for current situation --- p.58Chapter 3 --- Face Detection Algorithms and Committee Ma- chine --- p.61Chapter 3.1 --- Introduction about face detection --- p.62Chapter 3.2 --- Face Detection Committee Machine --- p.64Chapter 3.2.1 --- Review of three approaches for committee machine --- p.65Chapter 3.2.2 --- The approach of FDCM --- p.68Chapter 3.3 --- Evaluation --- p.70Chapter 4 --- Facial Feature Localization --- p.73Chapter 4.1 --- Algorithm for gray-scale image: template match- ing and separability filter --- p.73Chapter 4.1.1 --- Position of face and eye region --- p.74Chapter 4.1.2 --- Position of irises --- p.75Chapter 4.1.3 --- Position of lip --- p.79Chapter 4.2 --- Algorithm for color image: eyemap and separa- bility filter --- p.81Chapter 4.2.1 --- Position of eye candidates --- p.81Chapter 4.2.2 --- Position of mouth candidates --- p.83Chapter 4.2.3 --- Selection of face candidates by cost function --- p.84Chapter 4.3 --- Evaluation --- p.85Chapter 4.3.1 --- Algorithm for gray-scale image --- p.86Chapter 4.3.2 --- Algorithm for color image --- p.88Chapter 5 --- Face Processing System --- p.92Chapter 5.1 --- System architecture and limitations --- p.92Chapter 5.2 --- Pre-processing module --- p.93Chapter 5.2.1 --- Ellipse color model --- p.94Chapter 5.3 --- Face detection module --- p.96Chapter 5.3.1 --- Choosing the classifier --- p.96Chapter 5.3.2 --- Verifying the candidate region --- p.97Chapter 5.4 --- Face tracking module --- p.99Chapter 5.4.1 --- Condensation algorithm --- p.99Chapter 5.4.2 --- Tracking the region using Hue color model --- p.101Chapter 5.5 --- Face recognition module --- p.102Chapter 5.5.1 --- Normalization --- p.102Chapter 5.5.2 --- Recognition --- p.103Chapter 5.6 --- Applications --- p.104Chapter 6 --- Conclusion --- p.106Bibliography --- p.10

Support vector machines to detect physiological patterns for EEG and EMG-based human-computer interaction:a review

Support vector machines (SVMs) are widely used classifiers for detecting physiological patterns in human-computer interaction (HCI). Their success is due to their versatility, robustness and large availability of free dedicated toolboxes. Frequently in the literature, insufficient details about the SVM implementation and/or parameters selection are reported, making it impossible to reproduce study analysis and results. In order to perform an optimized classification and report a proper description of the results, it is necessary to have a comprehensive critical overview of the applications of SVM. The aim of this paper is to provide a review of the usage of SVM in the determination of brain and muscle patterns for HCI, by focusing on electroencephalography (EEG) and electromyography (EMG) techniques. In particular, an overview of the basic principles of SVM theory is outlined, together with a description of several relevant literature implementations. Furthermore, details concerning reviewed papers are listed in tables and statistics of SVM use in the literature are presented. Suitability of SVM for HCI is discussed and critical comparisons with other classifiers are reported

Real-Time Machine Learning Based Open Switch Fault Detection and Isolation for Multilevel Multiphase Drives

Due to the rapid proliferation interest of the multiphase machines and their combination with multilevel inverters technology, the demand for high reliability and resilient in the multiphase multilevel drives is increased. High reliability can be achieved by deploying systematic preventive real-time monitoring, robust control, and efficient fault diagnosis strategies. Fault diagnosis, as an indispensable methodology to preserve the seamless post-fault operation, is carried out in consecutive steps; monitoring the observable signals to generate the residuals, evaluating the observations to make a binary decision if any abnormality has occurred, and identifying the characteristics of the abnormalities to locate and isolate the failed components. It is followed by applying an appropriate reconfiguration strategy to ensure that the system can tolerate the failure. The primary focus of presented dissertation was to address employing computational and machine learning techniques to construct a proficient fault diagnosis scheme in multilevel multiphase drives. First, the data-driven nonlinear model identification/prediction methods are used to form a hybrid fault detection framework, which combines module-level and system-level methods in power converters, to enhance the performance and obtain a rapid real-time detection. Applying suggested nonlinear model predictors along with different systems (conventional two-level inverter and three-level neutral point clamped inverter) result in reducing the detection time to 1% of stator current fundamental period without deploying component-level monitoring equipment. Further, two methods using semi-supervised learning and analytical data mining concepts are presented to isolate the failed component. The semi-supervised fuzzy algorithm is engaged in building the clustering model because the deficient labeled datasets (prior knowledge of the system) leads to degraded performance in supervised clustering. Also, an analytical data mining procedure is presented based on data interpretability that yields two criteria to isolate the failure. A key part of this work also dealt with the discrimination between the post-fault characteristics, which are supposed to carry the data reflecting the fault influence, and the output responses, which are compensated by controllers under closed-loop control strategy. The performance of all designed schemes is evaluated through experiments

Population-level neural coding for higher cognition

Higher cognition encompasses advanced mental processes that enable complex thinking, decision-making, problem-solving, and abstract reasoning. These functions involve integrating information from multiple sensory modalities and organizing action plans based on the abstraction of past information. The neural activity underlying these functions is often complex, and the contribution of single neurons in supporting population-level representations of cognitive variables is not yet clear. In this thesis, I investigated the neural mechanisms underlying higher cognition in higher-order brain regions with single-neuron resolution in human and non-human primates performing working memory tasks. I aimed to understand how representations are arranged and how neurons contribute to the population code. In the first manuscript, I investigated the population-level neural coding for the maintenance of numbers in working memory within the parietal association cortex. By analyzing intra-operative intracranial micro-electrode array recording data, I uncovered distinct representations for numbers in both symbolic and nonsymbolic formats. In the second manuscript, I delved deeper into the neuronal organizing principles of population coding to address the ongoing debate surrounding memory maintenance mechanisms. I unveiled sparse structures in the neuronal implementation of representations and identified biologically meaningful components that can be directly communicated to downstream neurons. These components were linked to subpopulations of neurons with distinct physiological properties and temporal dynamics, enabling the active maintenance of working memory while resisting distraction. Lastly, using an artificial neural network model, I demonstrated that the sparse implementation of temporally modulated working memory representations is preferred in recurrently connected neural populations such as the prefrontal cortex. In summary, this thesis provides a comprehensive investigation of higher cognition in higher-order brain regions, focusing on working memory tasks involving numerical stimuli. By examining neural population coding and unveiling sparse structures in the neuronal implementation of representations, our findings contribute to a deeper understanding of the mechanisms underlying working memory and higher cognitive functions

Machine learning algorithms for cognitive radio wireless networks

In this thesis new methods are presented for achieving spectrum sensing in cognitive radio wireless networks. In particular, supervised, semi-supervised and unsupervised machine learning based spectrum sensing algorithms are developed and various techniques to improve their performance are described. Spectrum sensing problem in multi-antenna cognitive radio networks is considered and a novel eigenvalue based feature is proposed which has the capability to enhance the performance of support vector machines algorithms for signal classification. Furthermore, spectrum sensing under multiple primary users condition is studied and a new re-formulation of the sensing task as a multiple class signal detection problem where each class embeds one or more states is presented. Moreover, the error correcting output codes based multi-class support vector machines algorithms is proposed and investigated for solving the multiple class signal detection problem using two different coding strategies. In addition, the performance of parametric classifiers for spectrum sensing under slow fading channel is studied. To address the attendant performance degradation problem, a Kalman filter based channel estimation technique is proposed for tracking the temporally correlated slow fading channel and updating the decision boundary of the classifiers in real time. Simulation studies are included to assess the performance of the proposed schemes. Finally, techniques for improving the quality of the learning features and improving the detection accuracy of sensing algorithms are studied and a novel beamforming based pre-processing technique is presented for feature realization in multi-antenna cognitive radio systems. Furthermore, using the beamformer derived features, new algorithms are developed for multiple hypothesis testing facilitating joint spatio-temporal spectrum sensing. The key performance metrics of the classifiers are evaluated to demonstrate the superiority of the proposed methods in comparison with previously proposed alternatives