5981810
An efficient ontology comparison tool for semantic Web applications
With the growing access to heterogeneous and independent data repositories, determining the semantic difference of two ontologies is critical in information retrieval, information integration and semantic web applications. In this paper, we propose an ontology comparison tool based on a novel senses refinement algorithm, which builds a senses set to accurately represent the semantics of the input ontology. The senses refinement algorithm automatically extracts senses from the electronic lexical database WordNet (locally installed or online), removes unnecessary senses based on the relationship among the entity classes of the ontology, and specifies relations and constraints of the concepts in the refined senses set. The senses refinement converts the measurement of ontology difference into simple set operations based on set theory, thus ensures the efficiency and accuracy of the ontology comparison. Our experimental studies show that the proposed senses refinement algorithm outperforms the naive senses set construction algorithm in terms of efficiency and accuracy.
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).
54104798
Data allocation algorithms for distributed video servers
1925100
Self-configuration protocols for P2P networks
This paper proposes and evaluates different protocols for individual peers to self-configure the P2P overlay networks in various network environments. For small-scale homogeneous networks, an optimizer peer selection protocol is proposed and found to be superior to other peer selection protocols, including random, egoist, altruist and greedy protocols, in terms of network diameter and node eccentricity. For large-scale heterogeneous P2P systems, peer-power based peer selection protocols are proposed to self-configure semi-structured overlay networks for heterogeneous P2P systems. An index-based query mechanism is also proposed for peers to search documents in the P2P network. Performance studies demonstrate that the proposed self-configuration protocols and search scheme are efficient and viable, and the self-configured P2P network has a significantly lower query cost than traditional Gnutella-like P2P systems. In addition, a caching-assisted query mechanism is proposed to exploit the surplus storage power of the peers, improving further the query efficiency. Caching-assisted query permits a quicker response to subsequent queries for popular data without incurring the excessive overhead of globally replicated directory information.
14997765
2PSM: an efficient framework for searching video information in a limited-bandwidth environment
Abstract. We present a novel technique, called 2-Phase Service Model, for streaming videos to home users in a limited-bandwidth environment. This scheme first delivers some number of non-adjacent data fragments to the client in Phase 1. The missing fragments are then transmitted in Phase 2 as the client is playing back the video. This approach offers many benefits. The isochronous bandwidth required for Phase 2 can be controlled within the capability of the transport medium. The data fragments received during Phase 1 can be used to provide an excellent preview of the video. They can also be used to facilitate VCR-style operations such as fast-forward and fast-reverse. Systems designed based on this method are less expensive because the fast-forward and fast-reverse versions of the video files are no longer needed. Eliminating these files also improves system performance because mapping between the regular files and their fast-forward and fast-reverse versions is no longer part of the VCR operations. Furthermore, since each client machine handles its own VCR-style interaction, this technique is very scalable. We provide simulation results to show that 2-Phase Service Model is able to handle VCR functions efficiently. We also implement a video player called {\em FRVplayer}. With this prototype, we are able to judge that the visual quality of the previews and VCR-style operations is excellent. These features are essential to many important applications. We discuss the application of FRVplayer in the design of a video management system, called VideoCenter. This system is intended for Internet applications such as digital video libraries.
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.
266135
Accuracy improvement for identifying translation initiation sites in microbial genomes
MOTIVATION
At present the computational gene identification methods in microbial genomes have a high prediction accuracy of verified translation termination site (3' end), but a much lower accuracy of the translation initiation site (TIS, 5' end). The latter is important to the analysis and the understanding of the putative protein of a gene and the regulatory machinery of the translation. Improving the accuracy of prediction of TIS is one of the remaining open problems.


RESULTS
In this paper, we develop a four-component statistical model to describe the TIS of prokaryotic genes. The model incorporates several features with biological meanings, including the correlation between translation termination site and TIS of genes, the sequence content around the start codon; the sequence content of the consensus signal related to ribosomal binding sites (RBSs), and the correlation between TIS and the upstream consensus signal. An entirely non-supervised training system is constructed, which takes as input a set of annotated coding open reading frames (ORFs) by any gene finder, and gives as output a set of organism-specific parameters (without any prior knowledge or empirical constants and formulas). The novel algorithm is tested on a set of reliable datasets of genes from Escherichia coli and Bacillus subtillis. MED-Start may correctly predict 95.4% of the start sites of 195 experimentally confirmed E.coli genes, 96.6% of 58 reliable B.subtillis genes. Moreover, the test results indicate that the algorithm gives higher accuracy for more reliable datasets, and is robust to the variation of gene length. MED-Start may be used as a postprocessor for a gene finder. After processing by our program, the improvement of gene start prediction of gene finder system is remarkable, e.g. the accuracy of TIS predicted by MED 1.0 increases from 61.7 to 91.5% for 854 E.coli verified genes, while that by GLIMMER 2.02 increases from 63.2 to 92.0% for the same dataset. These results show that our algorithm is one of the most accurate methods to identify TIS of prokaryotic genomes.


AVAILABILITY
The program MED-Start can be accessed through the website of CTB at Peking University: http://ctb.pku.edu.cn/main/SheGroup/MED_Start.htm.
17726002
Average-case completeness of a word problem for groups
This paper presents a bounded word problem for groups whose random instances are hard on average. The problem is to decide, when given a finitely presented group G, words ~, y, z, and an integer k, whether (Z–lyZ)Z can be obtained from Z(x–l yz) in G using elementary Tietze transformations for at most k times. We show that the problem is average-case NP-complete when instances are chosen at random under a uniform distribution. NP-completeness of more general bounded word problems for groups is shown as well.
17608350
End-user place annotation on mobile devices: a comparative study
Advances in Location-Based Services (LBS) are opening opportunities for using the location of people, places, and things to augment or streamline interaction. While computers work with physical locations like latitude and longitude directly, people usually think and speak in terms of places, which adds personal, environmental and social meaning to a location. To address this conceptual mismatch, location-aware applications must incorporate the notion of place to achieve their full potential. In this paper, we investigate four techniques for collecting end-user place annotations interactively using cell phones. The results from a usability study suggest that while all the four methods receive similar preference ratings in understandability, the "photo memo plus offline editing" method is the most favorite approach in ease of use. In addition, users indicated their desire to adopt more than one place annotation method in location-aware applications.
30210949
Exact and approximate algorithms for unordered tree matching
We consider the problem of comparison between unordered trees, i.e., trees for which the order among siblings is unimportant. The criterion for comparison is the distance as measured by a weighted sum of the costs of deletion, insertion and relabel operations on tree nodes. Such comparisons may contribute to pattern recognition efforts in any field (e.g., genetics) where data can naturally be characterized by unordered trees. In companion work, we have shown this problem to be NP-complete. This paper presents an efficient enumerative algorithm and several heuristics leading to approximate solutions. The algorithms are based on probabilistic hill climbing and bipartite matching techniques. The paper evaluates the accuracy and time efficiency of the heuristics by applying them to a set of trees transformed from industrial parts based on a previously proposed morphological model. >
14765514
Information Discovery, Extraction and Integration for the Hidden Web
In this paper, we report our initial investigations on the problems of automatically extracting data objects from a given hidden-web source (i.e., the web site with an HTML search form) and automatically assigning semantics to the extracted data. We also propose some future work to address the problem of information discovery and integration for hidden-web sources.