Independent component analysis of microarray data in the study of endometrial cancer.

Gene microarray technology is highly effective in screening for differential gene expression and has hence become a popular tool in the molecular investigation of cancer. When applied to tumours, molecular characteristics may be correlated with clinical features such as response to chemotherapy. Exploitation of the huge amount of data generated by microarrays is difficult, however, and constitutes a major challenge in the advancement of this methodology. Independent component analysis (ICA), a modern statistical method, allows us to better understand data in such complex and noisy measurement environments. The technique has the potential to significantly increase the quality of the resulting data and improve the biological validity of subsequent analysis. We performed microarray experiments on 31 postmenopausal endometrial biopsies, comprising 11 benign and 20 malignant samples. We compared ICA to the established methods of principal component analysis (PCA), Cyber-T, and SAM. We show that ICA generated patterns that clearly characterized the malignant samples studied, in contrast to PCA. Moreover, ICA improved the biological validity of the genes identified as differentially expressed in endometrial carcinoma, compared to those found by Cyber-T and SAM. In particular, several genes involved in lipid metabolism that are differentially expressed in endometrial carcinoma were only found using this method. This report highlights the potential of ICA in the analysis of microarray data.

Closing the gap: Improved bounds on optimal POMDP solutions

POMDP algorithms have made significant progress in recent years by allowing practitioners to find good solutions to increasingly large problems. Most approaches (including point-based and policy iteration techniques) operate by refining a lower bound of the optimal value function. Several approaches (e.g., HSVI2, SARSOP, grid-based approaches and online forward search) also refine an upper bound. However, approximating the optimal value function by an upper bound is computationally expensive and therefore tightness is often sacrificed to improve efficiency (e.g., sawtooth approximation). In this paper, we describe a new approach to efficiently compute tighter bounds by i) conducting a prioritized breadth first search over the reachable beliefs, ii) propagating upper bound improvements with an augmented POMDP and iii) using exact linear programming (instead of the sawtooth approximation) for upper bound interpolation. As a result, we can represent the bounds more compactly and significantly reduce the gap between upper and lower bounds on several benchmark problems. Copyright © 2011, Association for the Advancement of Artificial Intelligence. All rights reserved.

Automatic construction and natural-language description of nonparametric regression models

Copyright © 2014, Association for the Advancement of Artificial Intelligence (www.aaai.org). All rights reserved. This paper presents the beginnings of an automatic statistician, focusing on regression problems. Our system explores an open-ended space of statistical models to discover a good explanation of a data set, and then produces a detailed report with figures and natural- language text. Our approach treats unknown regression functions non- parametrically using Gaussian processes, which has two important consequences. First, Gaussian processes can model functions in terms of high-level properties (e.g. smoothness, trends, periodicity, changepoints). Taken together with the compositional structure of our language of models this allows us to automatically describe functions in simple terms. Second, the use of flexible nonparametric models and a rich language for composing them in an open-ended manner also results in state- of-the-art extrapolation performance evaluated over 13 real time series data sets from various domains.