12113641
Neighbor number, valley seeking and clustering
This paper proposes a novel nonparametric clustering algorithm capable of identifying shape-free clusters. This algorithm is based on a nonparametric estimation of the normalized density derivative (NDD) and the local convexity of the density distribution function, both of which are represented in a very concise form in terms of neighbor numbers. We use NDD to measure the dissimilarity between each pair of observations in a local neighborhood and to build a connectivity graph. Combined with the local convexity, this similarity measure can detect observations in local minima (valleys) of the density function, which separate observations in different major clusters. We demonstrate that this algorithm has a close relationship with the single-linkage hierarchical clustering and can be viewed as its extension. The performance of the algorithm is tested with both synthetic and real datasets. An example of color image segmentation is also given. Comparisons with several representative existing algorithms show that the proposed method can robustly identify major clusters even when there are complex configurations and/or large overlaps.
14773046
Predicting methylation status of CpG islands in the human brain
MOTIVATION
Over 50% of human genes contain CpG islands in their 5'-regions. Methylation patterns of CpG islands are involved in tissue-specific gene expression and regulation. Mis-epigenetic silencing associated with aberrant CpG island methylation is one mechanism leading to the loss of tumor suppressor functions in cancer cells. Large-scale experimental detection of DNA methylation is still both labor-intensive and time-consuming. Therefore, it is necessary to develop in silico approaches for predicting methylation status of CpG islands.


RESULTS
Based on a recent genome-scale dataset of DNA methylation in human brain tissues, we developed a classifier called MethCGI for predicting methylation status of CpG islands using a support vector machine (SVM). Nucleotide sequence contents as well as transcription factor binding sites (TFBSs) are used as features for the classification. The method achieves specificity of 84.65% and sensitivity of 84.32% on the brain data, and can also correctly predict about two-third of the data from other tissues reported in the MethDB database.


AVAILABILITY
An online predictor based on MethCGI is available at http://166.111.201.7/MethCGI.html


CONTACT
mzhang@cshl.edu


SUPPLEMENTARY INFORMATION
Supplementary data available at Bioinformatics online and http://166.111.201.7/help.html.
17528755
Significance of Gene Ranking for Classification of Microarray Samples
Many methods for classification and gene selection with microarray data have been developed. These methods usually give a ranking of genes. Evaluating the statistical significance of the gene ranking is important for understanding the results and for further biological investigations, but this question has not been well addressed for machine learning methods in existing works. Here, we address this problem by formulating it in the framework of hypothesis testing and propose a solution based on resampling. The proposed r-test methods convert gene ranking results into position p-values to evaluate the significance of genes. The methods are tested on three real microarray data sets and three simulation data sets with support vector machines as the method of classification and gene selection. The obtained position p-values help to determine the number of genes to be selected and enable scientists to analyze selection results by sophisticated multivariate methods under the same statistical inference paradigm as for simple hypothesis testing methods
207738295
Kernel Nearest-Neighbor Algorithm
The ‘kernel approach’ has attracted great attention with the development of support vector machine (SVM) and has been studied in a general way. It offers an alternative solution to increase the computational power of linear learning machines by mapping data into a high dimensional feature space. This ‘approach’ is extended to the well-known nearest-neighbor algorithm in this paper. It can be realized by substitution of a kernel distance metric for the original one in Hilbert space, and the corresponding algorithm is called kernel nearest-neighbor algorithm. Three data sets, an artificial data set, BUPA liver disorders database and USPS database, were used for testing. Kernel nearest-neighbor algorithm was compared with conventional nearest-neighbor algorithm and SVM Experiments show that kernel nearest-neighbor algorithm is more powerful than conventional nearest-neighbor algorithm, and it can compete with SVM.
3568899
Whole Execution Traces
Different types of program profiles (control flow, value, address, and dependence) have been collected and extensively studied by researchers to identify program characteristics that can then be exploited to develop more effective compilers and architectures. Due to the large amounts of profile data produced by realistic program runs, most work has focused on separately collecting and compressing different types of profiles. In this paper we present a unified representation of profiles called Whole Execution Trace (WET) which includes the complete information contained in each of the above types of traces. Thus WETs provide a basis for a next generation software tool that will enable mining of program profiles to identify program characteristics that require understanding of relationships among various types of profiles. The key features of our WET representation are: WET is constructed by labeling a static program representation with profile information such that relavent and related profile information can be directly accessed by analysis algorithms as they traverse the representation; a highly effective two tier strategy is used to significantly compress the WET; and compression techniques are designed such that they do not adversely affect the ability to rapidly traverse WET for extracting subsets of information corresponding to individual profile types as well as a combination of profile types (e.g., in form of dynamic slices of WETs). Our experimentation shows that on an average execution traces resulting from execution of 647 Million statements can be stored in 331 Megabytes of storage after compression. The compression factors range from 16 to 83. Moreover the rates at which different types of profiles can be individually or simultaneously extracted are high.
18569940
Segmentation of bright targets using wavelets and adaptive thresholding
A general systematic method for the detection and segmentation of bright targets is developed. We use the term "bright target" to mean a connected, cohesive object which has an average intensity distribution above that of the rest of the image. We develop an analytic model for the segmentation of targets, which uses a novel multiresolution analysis in concert with a Bayes classifier to identify the possible target areas. A method is developed which adaptively chooses thresholds to segment targets from background, by using a multiscale analysis of the image probability density function (PDF). A performance analysis based on a Gaussian distribution model is used to show that the obtained adaptive threshold is often close to the Bayes threshold. The method has proven robust even when the image distribution is unknown. Examples are presented to demonstrate the efficiency of the technique on a variety of targets.
14024342
A Semantic Approach for Mining Hidden Links from Complementary and Non-interactive Biomedical Literature
Two complementary and non-interactive literature sets of articles, when they are considered together, can reveal useful information of scientific interest not apparent in either of the two sets alone. Swanson called the existence of such hidden links as undiscovered public knowledge (UPK). The novel connection between Raynaud disease and fish oils was uncovered from complementary and non-interactive biomedical literature by Swanson in 1986. Since then, there have been many approaches to uncover UPK by mining the biomedical literature. These earlier works, however, required substantial manual intervention to reduce the number of possible connections. This paper proposes a semantic-based mining model for undiscovered public knowledge using the biomedical literature. Our method replaces manual ad-hoc pruning by using semantic knowledge from the biomedical ontologies. Using the semantic types and semantic relationships of the biomedical concepts, our prototype system can identify the relevant concepts collected from Medline and generate the novel hypothesis between these concepts. The system successfully replicates Swanson’s two famous discoveries: Raynaud disease/fish oils and migraine/magnesium. Compared with previous approaches such as LSI-based and traditional association rule-based methods, our method generates much fewer but more relevant novel hypotheses, and requires much less human intervention in the discovery procedure
9689230
Doubly stochastic matrices of trees
Abstract In this paper, we obtain sharp upper and lower bounds for the smallest entries of doubly stochastic matrices of trees and characterize all extreme graphs which attain the bounds. We also present a counterexample to Merris’ conjecture on relations between the smallest entry of the doubly stochastic matrix and the algebraic connectivity of a graph in [R. Merris, Doubly stochastic graph matrices II, Linear Multilinear Algebr. 45 (1998) 275–285].
6359793
Integration of cluster ensemble and EM based text mining for microarray gene cluster identification and annotation
In this paper, we design and develop a unified system GE-Miner (Gene Expression Miner) to integrate cluster ensemble, text clustering and multi document summarization and provide an environment for comprehensive gene expression data analysis. We present a novel cluster ensemble approach to generate high quality gene cluster. In our text summarization module, given a gene cluster, our Expectation Maximization (EM) based algorithm can automatically identify subtopics and extract most probable terms for each topic. Then, the extracted top k topical terms from each subtopic are combined to form the biological explanation of each gene cluster. Experimental results demonstrate that our system can obtain high quality clusters and provide informative key terms for the gene clusters.