Statistical modeling of protein lysate array data

The protein lysate array is an emerging technology for quantifying the protein concentration ratios in multiple biological samples. It is gaining popularity, and has the potential to answer questions about post-translational modifications and protein pathway relationships. Statistical inference for a parametric quantification procedure has been inadequately addressed in the literature, mainly due to two challenges: the increasing dimension of the parameter space and the need to account for dependence in the data. Each chapter of this thesis addresses one of these issues. In Chapter 1, an introduction to the protein lysate array quantification is presented, followed by the motivations and goals for this thesis work. In Chapter 2, we develop a multi-step procedure for the Sigmoidal models, ensuring consistent estimation of the concentration level with full asymptotic efficiency. The results obtained in this chapter justify inferential procedures based on large-sample approximations. Simulation studies and real data analysis are used to illustrate the performance of the proposed method in finite-samples. The multi-step procedure is simpler in both theory and computation than the single-step least squares method that has been used in current practice. In Chapter 3, we introduce a new model to account for the dependence structure of the errors by a nonlinear mixed effects model. We consider a method to approximate the maximum likelihood estimator of all the parameters. Using the simulation studies on various error structures, we show that for data with non-i.i.d. errors the proposed method leads to more accurate estimates and better confidence intervals than the existing single-step least squares method.

Recomendr-entity recommendation based on ad-hoc dimensions

The growing availability and popularity of opinion rich resources on the online web resources, such as review sites and personal blogs, has made it convenient to find out about the opinions and experiences of layman people. But, simultaneously, this huge eruption of data has made it difficult to reach to a conclusion. In this thesis, I develop a novel recommendation system, Recomendr that can help users digest all the reviews about an entity and compare candidate entities based on ad-hoc dimensions specified by keywords. It expects keyword specified ad-hoc dimensions/features as input from the user and based on those features; it compares the selected range of entities using reviews provided on the related User Generated Contents (UGC) e.g. online reviews. It then rates the textual stream of data using a scoring function and returns the decision based on an aggregate opinion to the user. Evaluation of Recomendr using a data set in the laptop domain shows that it can effectively recommend the best laptop as per user-specified dimensions such as price. Recomendr is a general system that can potentially work for any entities on which online reviews or opinionated text is available.