14960694
Comparative analysis of gene sets in the gene ontology space under the multiple hypothesis testing framework
The gene ontology (GO) resource can be used as a powerful tool to uncover the properties shared among, and specific to, a list of genes produced by high-throughput functional genomics studies, such as microarray studies. In the comparative analysis of several gene lists, researchers maybe interested in knowing which GO terms are enriched in one list of genes but relatively depleted in another. Statistical tests such as Fisher's exact test or Chi-square test can be performed to search for such GO terms. However, because multiple GO terms are tested simultaneously, individual p-values from individual tests do not serve as good indicators for picking GO terms. Furthermore, these multiple tests are highly correlated, usual multiple testing procedures that work under an independence assumption are not applicable. In this paper we introduce a procedure, based on false discovery rate (FDR), to treat this correlated multiple testing problem. This procedure calculates a moderately conserved estimator of q-value for every GO term. We identify the GO terms with q-values that satisfy a desired level as the significant GO terms. This procedure has been implemented into the GoSurfer software. GoSurfer is a windows based graphical data mining tool. It is freely available at http://www.gosurfer.org.
10820274
Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: application to mass spec data
MOTIVATION
Analysis of high-throughput proteomic/genomic data, in particular, surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) data and microarray data, has led to a multitude of techniques aimed at identifying potential biomarkers. Most of the statistical techniques for comparing two groups are based on qualitative measures such as P-value. A quantitative way such as interval estimation for the contrasts of two groups is more appealing.


RESULTS
We have devised a simultaneous confidence bands method capable of detecting potential biomarkers, while controlling for overall confidence coverage level, in high-dimensional datasets that discriminate two treatment groups using a permutation scheme. For example, for the SELDI-TOF MS data, we deal with the entire spectrum simultaneously and construct (1 - alpha) confidence bands for the mean differences between groups. Furthermore, peaks were identified based on the maximal differences between the groups as determined by the confidence bands. The analysis method herein described gives both qualitative (P-value) and quantitative data (magnitude of difference). The Clinical Proteomics Programs Databank's ovarian cancer dataset and data from in-house samples containing known spiked-in proteins were analyzed. We were able to identify potential biomarkers similar to those described in previous analysis of the ovarian cancer data, however, while these markers are highly significant between cancer and normal groups, our analysis indicated the absolute difference between the two groups was minimal. In addition, we found additional markers than those previously described with greater differences in average intensities. The proposed confidence bands method successfully detected the spiked-in peaks, as well as, secondary peaks generated by adducts and double-charged species. We also illustrate our method utilizing paired gene expression data from a prostate cancer microarray experiment by constructing confidence bands for the fold changes between cancer and normal samples.


AVAILABILITY
R-package, 'seie.zip' (license: GNU GPL), is publiclly available at http://research2.dfci.harvard.edu/dfci/MS_spike-in_data/
22347603
Two supervised learning approaches for name disambiguation in author citations
81526
Capability based mediation in TSIMMIS
Conventional mediators focus their attention on the contents of the sources and their relationship to the integrated views provided to the users. They do not take into account the capabilities of sources to answer queries. This may lead them to generate plans involving source queries that cannot be answered by the sources. In the TSIMMIS system, we have developed a source capability sensitive plan generation module that constructs feasible plans for user queries in the presence of limited source capabilities
15590248
A Class of Discrete Multiresolution Random Fields and Its Application to Image Segmentation
In this paper, a class of Random Field model, defined on a multiresolution array is used in the segmentation of gray level and textured images. The novel feature of one form of the model is that it is able to segment images containing unknown numbers of regions, where there may be significant variation of properties within each region. The estimation algorithms used are stochastic, but because of the multiresolution representation, are fast computationally, requiring only a few iterations per pixel to converge to accurate results, with error rates of 1-2 percent across a range of image structures and textures. The addition of a simple boundary process gives accurate results even at low resolutions, and consequently at very low computational cost.
17199559
Data Mining for Direct Marketing: Problems and Solutions
Direct marketing is a process of identifying likely buyers of certain products and promoting the products accordingly. It is increasingly used by banks, insurance companies, and the retail industry. Data mining can provide an effective tool for direct marketing. During data mining, several specific problems arise. For example, the class distribution is extremely unbalanced (the response rate is about 1%), the predictive accuracy is no longer suitable for evaluating learning methods, and the number of examples can be too large. In this paper, we discuss methods of coping with these problems based on our experience on direct-marketing projects using data mining.
3194322
Efficient record linkage in large data sets
This paper describes an efficient approach to record linkage. Given two lists of records, the record-linkage problem consists of determining all pairs that are similar to each other where the overall similarity between two records is defined based on domain-specific similarities over individual attributes constituting the record. The record-linkage problem arises naturally in the context of data cleansing that usually precedes data analysis and mining. We explore a novel approach to this problem. For each attribute of records, we first map values to a multidimensional Euclidean space that preserves domain-specific similarity. Many mapping algorithms can be applied, and we use the FastMap approach as an example. Given the merging rule that defines when two records are Similar a set of attributes are chosen along which the merge will proceed A multidimensional similarity join over the chosen attributes is used to determine similar pairs of records. Our extensive experiments using real data sets show that our solution has very good efficiency and accuracy.
17330404
A supervised visual wrapper generator for Web-data extraction
Extracting data from Web pages using wrappers is a fundamental problem arising in a large variety of applications of vast practical interest. In this paper, we propose a novel schema-guided approach to wrapper generation. We provide a user-friendly interface that allows users to define the schema of the data to be extracted, and specifies mappings from a HTML page to the target schema. Based on the mappings, the system can automatically generate an extraction rule to extract data from the page. Our approach to wrapper generation can significantly reduce the work of human beings in this process. And the user never has to deal with the internal extraction rule, or even familiarity with the details of HTML.