Statistical analysis and meta-analysis of microarray data

The microarray technology provides a high-throughput technique to study gene expression. Microarrays can help us diagnose different types of cancers, understand biological processes, assess host responses to drugs and pathogens, find markers for specific diseases, and much more. Microarray experiments generate large amounts of data. Thus, effective data processing and analysis are critical for making reliable inferences from the data. ^ The first part of dissertation addresses the problem of finding an optimal set of genes (biomarkers) to classify a set of samples as diseased or normal. Three statistical gene selection methods (GS, GS-NR, and GS-PCA) were developed to identify a set of genes that best differentiate between samples. A comparative study on different classification tools was performed and the best combinations of gene selection and classifiers for multi-class cancer classification were identified. For most of the benchmarking cancer data sets, the gene selection method proposed in this dissertation, GS, outperformed other gene selection methods. The classifiers based on Random Forests, neural network ensembles, and K-nearest neighbor (KNN) showed consistently god performance. A striking commonality among these classifiers is that they all use a committee-based approach, suggesting that ensemble classification methods are superior. ^ The same biological problem may be studied at different research labs and/or performed using different lab protocols or samples. In such situations, it is important to combine results from these efforts. The second part of the dissertation addresses the problem of pooling the results from different independent experiments to obtain improved results. Four statistical pooling techniques (Fisher inverse chi-square method, Logit method. Stouffer's Z transform method, and Liptak-Stouffer weighted Z-method) were investigated in this dissertation. These pooling techniques were applied to the problem of identifying cell cycle-regulated genes in two different yeast species. As a result, improved sets of cell cycle-regulated genes were identified. The last part of dissertation explores the effectiveness of wavelet data transforms for the task of clustering. Discrete wavelet transforms, with an appropriate choice of wavelet bases, were shown to be effective in producing clusters that were biologically more meaningful. ^

Quality of experience evaluation of voice communication: an affect-based approach

Voice communication systems such as Voice-over IP (VoIP), Public Switched Telephone Networks, and Mobile Telephone Networks, are an integral means of human tele-interaction. These systems pose distinctive challenges due to their unique characteristics such as low volume, burstiness and stringent delay/loss requirements across heterogeneous underlying network technologies. Effective quality evaluation methodologies are important for system development and refinement, particularly by adopting user feedback based measurement. Presently, most of the evaluation models are system-centric (Quality of Service or QoS-based), which questioned us to explore a user-centric (Quality of Experience or QoE-based) approach as a step towards the human-centric paradigm of system design. We research an affect-based QoE evaluation framework which attempts to capture users' perception while they are engaged in voice communication. Our modular approach consists of feature extraction from multiple information sources including various affective cues and different classification procedures such as Support Vector Machines (SVM) and k-Nearest Neighbor (kNN). The experimental study is illustrated in depth with detailed analysis of results. The evidences collected provide the potential feasibility of our approach for QoE evaluation and suggest the consideration of human affective attributes in modeling user experience.