9642703
Discovering typical structures of documents: a road map approach
The structure of a document refers to the role and hierarchy of subdocument references. Many online documents are similarly structured, though not identically structured. We study the problem of discovering “typical” structures of a collection of such documents, where the user specifies the minimum frequency of a typical structure. We will consider structural features of subdocument references such as labeling, nesting, ordering, cyclicity, and wild-card references, like those found on the Web and digital libraries. Typical structures can be used to serve the following purposes. (a) The “table-ofcontent” for gaining the general information of a source. (b) A road map for browsing and querying a source. (c) A basis for clustering documents. (d) Partial schemas for building structured layers to provide standard database access methods. (e) User/customer’s interests and browsing patterns. We present a solution to the discovery problem.
36964410
A Knowledge Object Oriented System for High Throughput Collection and Analysis of Data
11034725
Data Mining Tools for Biological Sequences
We describe a methodology, as well as some related data mining tools, for analyzing sequence data. The methodology comprises three steps: (a) generating candidate features from the sequences, (b) selecting relevant features from the candidates, and (c) integrating the selected features to build a system to recognize specific properties in sequence data. We also give relevant techniques for each of these three steps. For generating candidate features, we present various types of features based on the idea of k-grams. For selecting relevant features, we discuss signal-to-noise, t-statistics, and entropy measures, as well as a correlation-based feature selection method. For integrating selected features, we use machine learning methods, including C4.5, SVM, and Naive Bayes. We illustrate this methodology on the problem of recognizing translation initiation sites. We discuss how to generate and select features that are useful for understanding the distinction between ATG sites that are translation initiation sites and those that are not. We also discuss how to use such features to build reliable systems for recognizing translation initiation sites in DNA sequences.
13995613
DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences
UNLABELLED
DNAFSMiner (DNA Functional Sites Miner) is a web-based software toolbox to recognize functional sites in nucleic acid sequences. Currently in this toolbox, we provide two software: TIS Miner and Poly(A) Signal Miner. The TIS Miner can be used to predict translation initiation sites in vertebrate DNA/mRNA/cDNA sequences, and the Poly(A) Signal Miner can be used to predict polyadenylation [poly(A)] signals in human DNA sequences. The prediction results are better than those by literature methods on two benchmark applications. This good performance is mainly attributable to our unique learning method. DNAFSMiner is available free of charge for academic and non-profit organizations.


AVAILABILITY
http://research.i2r.a-star.edu.sg/DNAFSMiner/


CONTACT
huiqing@i2r.a-star.edu.sg.
10722883
Use of extreme patient samples for outcome prediction from gene expression data
MOTIVATION
Patient outcome prediction using microarray technologies is an important application in bioinformatics. Based on patients' genotypic microarray data, predictions are made to estimate patients' survival time and their risk of tumor metastasis or recurrence. So, accurate prediction can potentially help to provide better treatment for patients.


RESULTS
We present a new computational method for patient outcome prediction. In the training phase of this method, we make use of two types of extreme patient samples: short-term survivors who got an unfavorable outcome within a short period and long-term survivors who were maintaining a favorable outcome after a long follow-up time. These extreme training samples yield a clear platform for us to identify relevant genes whose expression is closely related to the outcome. The selected extreme samples and the relevant genes are then integrated by a support vector machine to build a prediction model, by which each validation sample is assigned a risk score that falls into one of the special pre-defined risk groups. We apply this method to several public datasets. In most cases, patients in high and low risk groups stratified by our method have clearly distinguishable outcome status as seen in their Kaplan-Meier curves. We also show that the idea of selecting only extreme patient samples for training is effective for improving the prediction accuracy when different gene selection methods are used.
15390292
Selection of patient samples and genes for outcome prediction
Gene expression profiles with clinical outcome data enable monitoring of disease progression and prediction of patient survival at the molecular level. We present a new computational method for outcome prediction. Our idea is to use an informative subset of original training samples. This subset consists of only short-term survivors who died within a short period and long-term survivors who were still alive after a long follow-up time. These extreme training samples yield a clear platform to identify genes whose expression is related to survival. To find relevant genes, we combine two feature selection methods - entropy measure and Wilcoxon rank sum test - so that a set of sharp discriminating features are identified. The selected training samples and genes are then integrated by a support vector machine to build a prediction model, by which each validation sample is assigned a survival/relapse risk score for drawing Kaplan-Meier survival curves. We apply this method to two data sets: diffuse large-B-cell lymphoma (DLBCL) and primary lung adenocarcinoma. In both cases, patients in high and low risk groups stratified by our risk scores are clearly distinguishable. We also compare our risk scores to some clinical factors, such as International Prognostic Index score for DLBCL analysis and tumor stage information for lung adenocarcinoma. Our results indicate that gene expression profiles combined with carefully chosen learning algorithms can predict patient survival for certain diseases.
5884956
Query Selection Techniques for Efficient Crawling of Structured Web Sources
The high quality, structured data from Web structured sources is invaluable for many applications. Hidden Web databases are not directly crawlable by Web search engines and are only accessible through Web query forms or via Web service interfaces. Recent research efforts have been focusing on understanding these Web query forms. A critical but still largely unresolved question is: how to efficiently acquire the structured information inside Web databases through iteratively issuing meaningful queries? In this paper we focus on the central issue of enabling efficient Web database crawling through query selection, i.e. how to select good queries to rapidly harvest data records from Web databases. We model each structured Web database as a distinct attribute-value graph. Under this theoretical framework, the database crawling problem is transformed into a graph traversal one that follows "relational" links. We show that finding an optimal query selection plan is equivalent to finding a Minimum Weighted Dominating Set of the corresponding database graph, a well-known NP-Complete problem. We propose a suite of query selection techniques aiming at optimizing the query harvest rate. Extensive experimental evaluations over real Web sources and simulations over controlled database servers validate the effectiveness of our techniques and provide insights for future efforts in this
17890414
Identifying significant genes from microarray data
Microarray technology is a recent development in experimental molecular biology which can produce quantitative expression measurements for thousands of genes in a single, cellular mRNA sample. These many gene expression measurements form a composite profile of the sample, which can be used to differentiate samples from different classes such as tissue types or treatments. However, for the gene expression profile data obtained in a specific comparison, most likely only some of the genes will, be differentially expressed between the classes, while many other genes have similar expression levels. Selecting a list of informative differential genes from these data is important for microarray data analysis. In this paper, we describe a framework for selecting informative genes, called ranking and combination analysis (RAC), which combines various existing informative gene selection methods. We conducted experiments using three data sets and six existing feature selection methods. The results show that the RAC framework is a robust and efficient approach to identify informative gene for microarray data. The combination approach on two selecting methods almost always performed better than the less efficient individual, and in many cases, better than both. More significantly, when considering all three data sets together, the combination approach, on average, outperforms each individual feature selection method. All of these indicate that RCA might be a viable and feasible approach for the microarray gene expression analysis.
17436749
Feature Transformation and Multivariate Decision Tree Induction
Univariate decision trees (UDT's) have inherent problems of replication, repetition, and fragmentation. Multivariate decision trees (MDT's) have been proposed to overcome some of the problems. Close examination of the conventional ways of building MDT's, however, reveals that the fragmentation problem still persists. A novel approach is suggested to minimize the fragmentation problem by separating hyperplane search from decision tree building. This is achieved by feature transformation. Let the initial feature vector be x, the new feature vector after feature transformation T is y, i.e., y = T(x). We can obtain an MDTb y (1) building a UDT on y; and (2) replacing new features y at each node with the combinations of initial features x. We elaborate on the advantages of this approach, the details of T, and why it is expected to perform well. Experiments are conducted in order to confirm the analysis, and results are compared to those of C4.5, OC1, and CART.
18200538
Mining "Hidden Phrase" Definitions from the Web
Keyword searching is the most common form of document search on the Web. Many Web publishers manually annotate the META tags and titles of their pages with frequently queried phrases in order to improve their placement and ranking. A "hidden phrase" is defined as a phrase that occurs in the META tag of a Web page but not in its body. In this paper we present an algorithm that mines the definitions of hidden phrases from the Web documents. Phrase definitions allow (i) publishers to find relevant phrases with high query frequency, and, (ii) search engines to test if the content of the body of a document matches the phrases. We use co-occurrence clustering and association rule mining algorithms to learn phrase definitions from high-dimensional data sets. We also provide experimental results.
653966
Fan-Type Theorem for Long Cycles Containing a Specified Edge
In this paper, we prove that if G is 3-connected noncomplete graph of order n satisfying min{max{d(u),d(v)}:d(u,v)=2}=μ, then for each edge e, G has a cycle containing e of length at least min{n,2μ}, unless G is a spanning subgraph of Kμ + Kcn−μ or K3+(lKμ−2∪Ks), where n=l(μ−2)+s+3,1≤s≤μ−2.