1311296
A structure-based search engine for phylogenetic databases
Phylogenetic trees are essential for understanding the relationships among organisms or taxa. Many of the current techniques for searching phylogenetic repositories allow the user to perform a keyword-type search or an aligned sequence data search, or to browse a hierarchical list of taxa. Here we describe a new search engine that allows the user to present an example phylogeny, or a query tree, and then searches a phylogenetic database for trees that contain the query structure. The presented search engine is fully operational and is available on the World Wide Web.
14900181
Unordered tree mining with applications to phylogeny
Frequent structure mining (FSM) aims to discover and extract patterns frequently occurring in structural data, such as trees and graphs. FSM finds many applications in bioinformatics, XML processing, Web log analysis, and so on. We present a new FSM technique for finding patterns in rooted unordered labeled trees. The patterns of interest are cousin pairs in these trees. A cousin pair is a pair of nodes sharing the same parent, the same grandparent, or the same great-grandparent, etc. Given a tree T, our algorithm finds all interesting cousin pairs of T in O(|T|/sup 2/) time where |T| is the number of nodes in T. Experimental results on synthetic data and phylogenies show the scalability and effectiveness of the proposed technique. To demonstrate the usefulness of our approach, we discuss its applications to locating co-occurring patterns in multiple evolutionary trees, evaluating the consensus of equally parsimonious trees, and finding kernel trees of groups of phylogenies. We also describe extensions of our algorithms for undirected acyclic graphs (or free trees).
236203
New Techniques for DNA Sequence Classification
DNA sequence classification is the activity of determining whether or not an unlabeled sequence S belongs to an existing class C. This paper proposes two new techniques for DNA sequence classification. The first technique works by comparing the unlabeled sequence S with a group of active motifs discovered from the elements of C and by distinction with elements outside of C. The second technique generates and matches gapped fingerprints of S with elements of C. Experimental results obtained by running these algorithms on long and well conserved Alu sequences demonstrate the good performance of the presented methods compared with FASTA. When applied to less conserved and relatively short functional sites such as splice-junctions, a variation of the second technique combining fingerprinting with consensus sequence analysis gives better results than the current classifiers employing text compression and machine learning algorithms.
11616193
Automatic Hierarchical Classification of Structured Deep Web Databases
We present a method that automatically classifies structured deep Web databases according to a pre-defined topic hierarchy. We assume that there are some manually classified databases, i.e., training databases, in every node of the topic hierarchy. Each training database is probed using queries constructed from the node titles of the topic hierarchy and the query result counts reported by the database are used to represent the content of the database. Hence, when adding a new database it can be probed by the same set of queries and classified to a node whose training databases are most similar to the new one. Specifically, a support vector machine classifier is trained on each internal node of the topic hierarchy with these training databases and the new database can be classified into the hierarchy top-down level by level. A feature extension method is proposed to create discriminant features. Experiments run on real structured Web databases collected from the Internet show that this classification method is quite accurate.
2286283
Query result ranking over e-commerce web databases
To deal with the problem of too many results returned from an E-commerce Web database in response to a user query, this paper proposes a novel approach to rank the query results. Based on the user query, we speculate how much the user cares about each attribute and assign a corresponding weight to it. Then, for each tuple in the query result, each attribute value is assigned a score according to its "desirableness" to the user. These attribute value scores are combined according to the attribute weights to get a final ranking score for each tuple. Tuples with the top ranking scores are presented to the user first. Our ranking method is domain independent and requires no user feedback. Experimental results demonstrate that this ranking method can effectively capture a user's preferences.
12680145
Finding Patterns in Three-Dimensional Graphs: Algorithms and Applications to Scientific Data Mining
Presents a method for finding patterns in 3D graphs. Each node in a graph is an undecomposable or atomic unit and has a label. Edges are links between the atomic units. Patterns are rigid substructures that may occur in a graph after allowing for an arbitrary number of whole-structure rotations and translations as well as a small number (specified by the user) of edit operations in the patterns or in the graph. (When a pattern appears in a graph only after the graph has been modified, we call that appearance "approximate occurrence.") The edit operations include relabeling a node, deleting a node and inserting a node. The proposed method is based on the geometric hashing technique, which hashes node-triplets of the graphs into a 3D table and compresses the label-triplets in the table. To demonstrate the utility of our algorithms, we discuss two applications of them in scientific data mining. First, we apply the method to locating frequently occurring motifs in two families of proteins pertaining to RNA-directed DNA polymerase and thymidylate synthase and use the motifs to classify the proteins. Then, we apply the method to clustering chemical compounds pertaining to aromatic compounds, bicyclicalkanes and photosynthesis. Experimental results indicate the good performance of our algorithms and high recall and precision rates for both classification and clustering.
14753351
Making MIRACLEs: Interactive translingual search for Cebuano and Hindi
Searching is inherently a user-centered process; people pose the questions for which machines seek answers, and ultimately people judge the degree to which retrieved documents meet their needs. Rapid development of interactive systems that use queries expressed in one language to search documents written in another poses five key challenges: (1) interaction design, (2) query formulation, (3) cross-language search, (4) construction of translated summaries, and (5) machine translation. This article describes the design of MIRACLE, an easily extensible system based on English queries that has previously been used to search French, German, and Spanish documents, and explains how the capabilities of MIRACLE were rapidly extended to accommodate Cebuano and Hindi. Evaluation results for the cross-language search component are presented for both languages, along with results from a brief full-system interactive experiment with Hindi. The article concludes with some observations on directions for further research on interactive cross-language information retrieval.
2808817
BGP routing stability of popular destinations
The Border Gateway Protocol (BGP) plays a crucial role in the delivery of traffic in the Internet. Fluctuations in BGP routes cause degradation in user performance, increased processing load on routers, and changes in the distribution of traffic load over the network. Although earlier studies have raised concern that BGP routes change quite often, previous work has not considered whether these routing fluctuations affect a significant portion of the traffic. This paper shows that the small number of popular destinations responsible for the bulk of Internet traffic have remarkably stable BGP routes. The vast majority of BGP instability stems from a small number of unpopular destinations. We draw these conclusions from a joint analysis of BGP update messages and flow-level traffic measurements from AT&T's IP backbone. In addition, we analyze the routing stability of destination prefixes corresponding to the NetRating's list of popular Web sites using the update messages collected by the RouteViews and RIPE-NCC servers. Our results suggest that operators can engineer their networks under the assumption that the BGP advertisements associated with most of the traffic are reasonably stable.
1791876
A Region-Based Fuzzy Feature Matching Approach to Content-Based Image Retrieval
This paper proposes a fuzzy logic approach, UFM (unified feature matching), for region-based image retrieval. In our retrieval system, an image is represented by a set of segmented regions, each of which is characterized by a fuzzy feature (fuzzy set) reflecting color, texture, and shape properties. As a result, an image is associated with a family of fuzzy features corresponding to regions. Fuzzy features naturally characterize the gradual transition between regions (blurry boundaries) within an image and incorporate the segmentation-related uncertainties into the retrieval algorithm. The resemblance of two images is then defined as the overall similarity between two families of fuzzy features and quantified by a similarity measure, UFM measure, which integrates properties of all the regions in the images. Compared with similarity measures based on individual regions and on all regions with crisp-valued feature representations, the UFM measure greatly reduces the influence of inaccurate segmentation and provides a very intuitive quantification. The UFM has been implemented as a part of our experimental SIMPLIcity image retrieval system. The performance of the system is illustrated using examples from an image database of about 60,000 general-purpose images.
6695976
Precise Environmental Searches: Integrating Hierarchical Information Search with EnviroDaemon
Information retrieval has evolved from searches of references, to abstracts, to documents. Search on the Web involves search engines that promise to parse full-text and other files: audio, video, and multimedia. With the indexable Web at 320 million pages and growing, difficulties with locating relevant information have become apparent. The most prevalent means for information retrieval relies on syntax-based methods: keywords or strings of characters are presented to a search engine, and it returns all the matches in the available documents. This method is satisfactory and easy to implement, but it has some inherent limitations that make it unsuitable for many tasks. Instead of looking for syntactical patterns, the user often is interested in keyword meaning or the location of a particular word in a title or header. This paper describes some precise search approaches in the environmental domain that locate information according to syntactic criteria, augmented by the utilization of information in a certain context. The main emphasis of this paper lies in the treatment of structured knowledge, where essential aspects about the topic of interest are encoded not only by the individual items, but also by their relationships among each other. Examples for such structured knowledge are hypertext documents, diagrams, logical and chemical formulae. Benefits of this approach are enhanced precision and approximate search in an already focused, context-specific search engine for the environment: EnviroDaemon.
38052408
Towards a practical, secure, and very large scale online election
We propose a practical and secure electronic voting protocol for large-scale online elections. Our protocol satisfies a large set of important criteria that has never been put together in a single protocol before. Among all electronic voting schemes in the literature, Sensus, a security-conscious electronic voting protocol proposed by Cranor and Cytron (1997), satisfies most of our criteria. Sensus has been implemented and used in mock elections. However, Sensus suffers from several major drawbacks. For instance, we show that even if all voters follow the Sensus protocol honestly, some voters' votes may still be replaced with different votes without being detected. Our protocol overcomes these drawbacks.