Development and evaluation of machine learning algorithms for biomedical applications

Gene network inference and drug response prediction are two important problems in computational biomedicine. The former helps scientists better understand the functional elements and regulatory circuits of cells. The latter helps a physician gain full understanding of the effective treatment on patients. Both problems have been widely studied, though current solutions are far from perfect. More research is needed to improve the accuracy of existing approaches. This dissertation develops machine learning and data mining algorithms, and applies these algorithms to solve the two important biomedical problems. Specifically, to tackle the gene network inference problem, the dissertation proposes (i) new techniques for selecting topological features suitable for link prediction in gene networks; a graph sparsification method for network sampling; (iii) combined supervised and unsupervised methods to infer gene networks; and (iv) sampling and boosting techniques for reverse engineering gene networks. For drug sensitivity prediction problem, the dissertation presents (i) an instance selection technique and hybrid method for drug sensitivity prediction; (ii) a link prediction approach to drug sensitivity prediction; a noise-filtering method for drug sensitivity prediction; and (iv) transfer learning approaches for enhancing the performance of drug sensitivity prediction. Substantial experiments are conducted to evaluate the effectiveness and efficiency of the proposed algorithms. Experimental results demonstrate the feasibility of the algorithms and their superiority over the existing approaches

Statistical learning methods for mining marketing and biological data

Nowadays, the value of data has been broadly recognized and emphasized. More and more decisions are made based on data and analysis rather than solely on experience and intuition. With the fast development of networking, data storage, and data collection capacity, data have increased dramatically in industry, science and engineering domains, which brings both great opportunities and challenges. To take advantage of the data flood, new computational methods are in demand to process, analyze and understand these datasets. This dissertation focuses on the development of statistical learning methods for online advertising and bioinformatics to model real world data with temporal or spatial changes. First, a collaborated online change-point detection method is proposed to identify the change-points in sparse time series. It leverages the signals from the auxiliary time series such as engagement metrics to compensate the sparse revenue data and improve detection efficiency and accuracy through smart collaboration. Second, a task-specific multi-task learning algorithm is developed to model the ever-changing video viewing behaviors. With the 1-regularized task-specific features and jointly estimated shared features, it allows different models to seek common ground while reserving differences. Third, an empirical Bayes method is proposed to identify 3\u27 and 5\u27 alternative splicing in RNA-seq data. It formulates alternative 3\u27 and 5\u27 splicing site selection as a change-point problem and provides for the first time a systematic framework to pool information across genes and integrate various information when available, in particular the useful junction read information, in order to obtain better performance