17750098
Lineage Path Integration for Phylogenetic Resources
With the increase of genome and proteome data, phylogenetic information and phylogenetic analysis tools are increasing greatly in current biological repositories. First, many repositories allow users to browse information about species through taxonomic tools. These tools present the species with its lineage path and links to the various types of information the repository provides about the species. Second, some multiple sequence alignment tools offer users basic phylogenetic data through applying basic reconstruction algorithms to the alignment. With the availability of this information in multiple locations, integrated tools are needed to allow the user to compare this data. This paper presents data integration research on lineage paths using the BIO-AJAX framework. It introduces BIO-AJAX for Lineage Paths, a tool that integrates lineage path information for NCBI Taxonomy Database [1] and the Integrated Taxonomic Information System (ITIS)[6].
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.
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.
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.
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).
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.
14219803
A new method to measure the semantic similarity of GO terms
MOTIVATION
Although controlled biochemical or biological vocabularies, such as Gene Ontology (GO) (http://www.geneontology.org), address the need for consistent descriptions of genes in different data sources, there is still no effective method to determine the functional similarities of genes based on gene annotation information from heterogeneous data sources.


RESULTS
To address this critical need, we proposed a novel method to encode a GO term's semantics (biological meanings) into a numeric value by aggregating the semantic contributions of their ancestor terms (including this specific term) in the GO graph and, in turn, designed an algorithm to measure the semantic similarity of GO terms. Based on the semantic similarities of GO terms used for gene annotation, we designed a new algorithm to measure the functional similarity of genes. The results of using our algorithm to measure the functional similarities of genes in pathways retrieved from the saccharomyces genome database (SGD), and the outcomes of clustering these genes based on the similarity values obtained by our algorithm are shown to be consistent with human perspectives. Furthermore, we developed a set of online tools for gene similarity measurement and knowledge discovery.


AVAILABILITY
The online tools are available at: http://bioinformatics.clemson.edu/G-SESAME.


SUPPLEMENTARY INFORMATION
http://bioinformatics.clemson.edu/Publication/Supplement/gsp.htm.
16538539
Optimal jumper insertion for antenna avoidance under ratio upper-bound
Antenna effect may damage gate oxides during plasma-based fabrication process. The antenna ratio of total exposed antenna area to total gate oxide area is directly related to the amount of damage. Jumper insertion is a common technique applied at routing and post-layout stages to avoid and to fix the problems caused by the antenna effect. This paper presents an optimal algorithm for jumper insertion under the ratio upper-bound. It handles Steiner trees with obstacles. The algorithm us based on dynamic programming while works on free trees. The time complexity is O(alpha|V|2 ) and the space complexity is O(|V|2), where |V| is the number of nodes in the routing tree and a is a factor depending on how to find a non-blocked position on a wire for a jumper
789503
Exploiting the Web as the multilingual corpus for unknown query translation
target languages. To facilitate a cross-language information retrieval (CLIR) service in digital library systems, it is important to develop a powerful query translation engine. This must be able to automatically translate users’ queries from multiple source languages to the target languages that the systems accept. Conventional approaches to CLIR can be divided into two groups: dictionary-based and corpora-based. A dictionarybased approach (Ballesteros & Croft, 1997) utilizes a simple translation dictionary in which each query term is looked up and translated into its corresponding terms in the target language. However, terms may have multiple ambiguous meanings and many new unknown terms that are not covered in the dictionary cannot be translated. Corpora-based approach (Nie, Isabelle, Simard & Durand, 1999) incorporates multilingual corpus where texts in different languages are collected for translation purpose. Either comparable texts (Fung & Yee, 1998) or parallel texts (Nie et al., 1999) can be used as the multilingual corpus. Parallel texts contain bilingual sentences, from which word or phrase translations can be extracted by appropriate sentence alignment methods (Gale & Church, 1993). Comparable texts share similar concepts in content, but do not necessarily show alignment correspondence for translation. Because there is a fundamental word mismatch problem that queries and documents might not share the same words, the basic assumption of such approaches is that as queries get longer, the severity of the problem tends to decrease. Query expansion techniques (Ballesteros & Croft, 1997) can therefore be used to enrich query terms not covered in documents. However, these approaches present some fundamental difficulties for digital libraries that wish to support practical CLIR services. First, most of existing digital libraries contain only monolingual text collections; hence, there is no bilingual corpus for cross-lingual training. Second, real Exploiting the Web as the Multilingual Corpus for Unknown Query Translation
14843520
Deriving knowledge from figures for digital libraries
Figures in digital documents contain important information. Current digital libraries do not summarize and index information available within figures for document retrieval. We present our system on automatic categorization of figures and extraction of data from 2-D plots. A machine-learning based method is used to categorize figures into a set of predefined types based on image features. An automated algorithm is designed to extract data values from solid line curves in 2-D plots. The semantic type of figures and extracted data values from 2-D plots can be integrated with textual information within documents to provide more effective document retrieval services for digital library users. Experimental evaluation has demonstrated that our system can produce results suitable for real-world use.
6283537
A bandwidth management technique for hierarchical storage in large-scale multimedia servers
Using magnetic disks as a cache for tertiary storage has been shown to be an effective way to address the high storage coats of large-scale multimedia servers. The authors investigate a technique for managing the bandwidth of such a hierarchical storage design. In existing schemes, all data items are treated equally; and the same I/O rate is used to load data from tertiary storage when they are requested. In their approach, different loading rates are used for data items with different characteristics. For frequently used items, one keeps a large percentage of data in the disk buffer and needs to use only a small I/O rate to load the missing portions on demand. On the contrary, a larger portion of less frequently used items is kept in the tertiary storage. To minimize their access latencies, larger I/O rates are used to load the missing parts when these items are needed. They formally prove that this approach is better than using the same loading rate for all data items. They also show simulation results to quantitatively demonstrate the benefits of the technique. They confirm that the scheme is able to provide higher system throughput while ensuring very short latencies (i.e., several seconds) for essentially all accesses. Such good performance is achieved using surprisingly small disk space (i.e., about 5% or less of the database size).