15077137
Modeling nonlinearity in dilution design microarray data
MOTIVATION
Dilution design (Mixed tissue RNA) has been utilized by some researchers to evaluate and assess the performance of multiple microarray platforms. Current microarray data analysis approaches assume that the quantified signal intensities are linearly related to the expression of the corresponding genes in the sample. However, there are sources of nonlinearity in microarray expression measurements. Such nonlinearity study in the expressions of the RNA mixtures provides a new way to analyze gene expression data, and we argue that the nonlinearity can reveal novel information for microarray data analysis. Therefore, we proposed a statistical model, called proportion model, which is based on the linear regression analysis. To approximately quantify the nonlinearity in the dilution design, a new calibration, beta ratio (BR) was derived from the proportion model. Furthermore, a new adjusted fold change (adj-FC) was proposed to predict the true FC without nonlinearity, in particular for large FC.


RESULTS
We applied our method to one microarray dilution dataset. The experimental results indicated that, to some extent, there are global biases comparing with the linear assumption for the significant genes. Further analysis of those highly expressed genes with significant nonlinearity revealed some promising results, e.g. 'poison' effect was discovered for some genes in RNA mixtures. The adj-FCs of those genes with 'poison' effect, indicate that the nonlinearity can be also caused by the inherent feature of the genes besides signal noise and technical variation. Moreover, when percentage of overlapping genes (POG) was used as a cross-platform consistency measure, adj-FC outperformed simple fold change to show that Affymetrix and Illumina platforms are consistent.


AVAILABILITY
The R codes which implements all described methods, and some Supplementary material, are freely available from http://www.utdallas.edu/~ying.liu/BetaRatio.htm
41398857
BIRD: Biomedical Information Integration and Discovery with Semantic Web Services
Biomedical research is now information intensive; the volume and diversity of new data sources challenges current database technologies. The development and tuning of database technologies for biology and medicine will maintain and accelerate the current pace for innovation and discovery. New promising application fields such as the Semantic Web and Semantic Web Services can leverage the potential of biomedical information integration and discovery, facing the problem of semantic heterogeneity of biomedical information sources in a variety of storage and data formats widely distributed both across the Internet and within individual organizations. In this paper, we present BIRD, a fully-fledged biomedical information integration solution that combines natural language analysis and semantically-empowered techniques to ascertain how the user needs can be best fit. Our approach is backed with a proof-of-concept implementation where the breakthrough and efficiency of integrating the biomedical publications database PubMed, the Database of Interacting Proteins (DIP) and the Munich Information Center for Protein Sequences (MIPS) has been tested.
44495329
Enumeration on Nonseparable Planar Maps
Abstract This paper provides some functional equations satisfied by the generating functions for nonseparable rooted planar maps with the valency of root-vertex, the number of edges and the valency of root-faces of the maps as three parameters. But the solutions of these equations can only be obtained indirectly by considering some relations between nonseparable and general rooted planar maps. One of them is an answer to the open problem 6.1 in Liu (1983, Comb. Optim. CORR83-26, University of Waterloo).
206025536
Enumerating near-4-regular maps on the sphere and the torus
In this paper rooted near-4-regular maps on the plane and the torus are counted with formulae with respect to four parameters: the root valency, the number of edges, the inner faces, and nonroot-vertex loops. In particular, the number of rooted near-4-regular maps on those surfaces with exactly k nonroot-vertex loops is investigated.
9387669
Multiclass discovery in array data
BackgroundA routine goal in the analysis of microarray data is to identify genes with expression levels that correlate with known classes of experiments. In a growing number of array data sets, it has been shown that there is an over-abundance of genes that discriminate between known classes as compared to expectations for random classes. Therefore, one can search for novel classes in array data by looking for partitions of experiments for which there are an over-abundance of discriminatory genes. We have previously used such an approach in a breast cancer study.ResultsWe describe the implementation of an unsupervised classification method for class discovery in microarray data. The method allows for discovery of more than two classes. We applied our method on two published microarray data sets: small round blue cell tumors and breast tumors. The method predicts relevant classes in the data sets with high success rates.ConclusionsWe conclude that the proposed method is accurate and efficient in finding biologically relevant classes in microarray data. Additionally, the method is useful for quality control of microarray experiments. We have made the method available as a computer program.
258700
Cervical Cancer Detection Using SVM Based Feature Screening
We present a novel feature screening algorithm by deriving relevance measures from the decision boundary of Support Vector Ma- chines. It alleviates the "independence" assumption of traditional screen- ing methods, e.g. those based on Information Gain and Augmented Vari- ance Ratio, without sacrificing computational efficiency. We applied the proposed method to a bottom-up approach for automatic cervical cancer detection in multispectral microscopic thin PAP smear images. An initial set of around 4,000 multispectral texture features is effectively reduced to a computationally manageable size. The experimental results show significant improvements in pixel-level classification accuracy compared to traditional screening methods.
10184967
Tree-to-String Alignment Template for Statistical Machine Translation
We present a novel translation model based on tree-to-string alignment template (TAT) which describes the alignment between a source parse tree and a target string. A TAT is capable of generating both terminals and non-terminals and performing reordering at both low and high levels. The model is linguistically syntax-based because TATs are extracted automatically from word-aligned, source side parsed parallel texts. To translate a source sentence, we first employ a parser to produce a source parse tree and then apply TATs to transform the tree into a target string. Our experiments show that the TAT-based model significantly outperforms Pharaoh, a state-of-the-art decoder for phrase-based models.