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.
42282919
Exploring Local Community Structures in Large Networks
In this paper, we extend the concept of degree from single vertex to sub-graph, and present a formal definition of module/community in a network based on this extension. A new locally optimized algorithm is designed to find the module for a given source vertex in a network. Our analysis shows that the complexity of this algorithm is O(K2d), where K is the number of vertices to be explored in the sub-graph and d is the average degree of the vertices in the sub-graph. Based on this algorithm, we implement a JAVA tool, MoNet, for exploring local community structures in large networks. Using this tool to analyze a co-purchase network from Amazon shows that there are local community structures in this network. Further analyses on these local community structures demonstrate that media items are much easier to form compact local modules than book items do, indicating that recommending digital media items to customers based on co-purchasing information in the online store will be more efficient than recommending books.
7304743
Proxy ecology - cooperative proxies with artificial life
In this paper, we propose a novel P2P cooperative proxy cache system using an individual-based model. We borrow the idea from an ecological system as well as economic systems to manage the cooperative proxies through data and information exchange among individual proxies. The data flow among proxy nodes creates artificial life for the cooperative proxies. The proxy servers with artificial life can automatically configure themselves into a virtual proxy graph. The aggregate effect of caching actions by individual peer proxies automatically distributes the Web document closer to the clients and balances the workload. Our simulation results show that the proposed proxy caching scheme tremendously improves the system performance. In addition, the individual-based design model ensures the simplicity and scalability of the cache system.
9138036
Earthworm: a network memory management technique for large-scale distributed multimedia applications
The two main operating constraints of today's multimedia servers are the I/O bandwidth and communication bandwidth limitations. Both of these problems are addressed in this paper using a novel technique called Earthworm. In this scheme, the network memory is used as a huge cache for buffering multimedia data. Dramatic reduction in the demand on the I/O bandwidth, therefore, can be achieved. This scheme also chains display stations to allow them to forward video streams. This strategy eliminates the congestion at the communication port of the server. Removing this bottleneck allows our technique to operate on the vast aggregate bandwidth of the WAN rather than being constrained by the very limited local bandwidth available to the server. A unique feature of the Earthworm approach is that every display station using the server attempts to make some contribution to the caching space and communication bandwidth. The arrival of a new request, therefore, can be seen as a contributor, rather than just a burden to the server. This characteristic ensures the scalability of our design to support very large multimedia applications.
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.
54104798
Data allocation algorithms for distributed video servers
207558887
Self-adaptive neuro-fuzzy systems for autonomous underwater vehicle control
This paper presents a systematic approach for developing a concise self-adaptive neurofuzzy inference system (SANFIS) with a fast hybrid parameter learning algorithm for on-line learning of the control knowledge for autonomous underwater vehicle (AUV) control. The multi-layered network structure of SANFIS incorporates fuzzy basis functions for better function approximations. We investigate three SANFIS structures with three different types of fuzzy IF-THEN rule-based models and cast the rule formation problem as a clustering problem. A recursive least-squares algorithm and a modified Levenberg-Marquardt algorithm with limited memory are exploited to accelerate the parameter learning process. This hybrid parameter learning algorithm together with an on-line clustering technique and rule examination provide SANFIS with the capability of selforganizing and self-adapting its internal structure (i.e. the fuzzy rules and term sets) for learning the required control knowledge for an AUV to follow desired trajectories. Computer simulations for modeling a control system for an AUV have been conducted to validate the effectiveness of the proposed SANFIS.
2880421
SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size
MOTIVATION
Searches for near exact sequence matches are performed frequently in large-scale sequencing projects and in comparative genomics. The time and cost of performing these large-scale sequence-similarity searches is prohibitive using even the fastest of the extant algorithms. Faster algorithms are desired.


RESULTS
We have developed an algorithm, called SST (Sequence Search Tree), that searches a database of DNA sequences for near-exact matches, in time proportional to the logarithm of the database size n. In SST, we partition each sequence into fragments of fixed length called 'windows' using multiple offsets. Each window is mapped into a vector of dimension 4(k) which contains the frequency of occurrence of its component k-tuples, with k a parameter typically in the range 4-6. Then we create a tree-structured index of the windows in vector space, with tree-structured vector quantization (TSVQ). We identify the nearest neighbors of a query sequence by partitioning the query into windows and searching the tree-structured index for nearest-neighbor windows in the database. When the tree is balanced this yields an O(logn) complexity for the search. This complexity was observed in our computations. SST is most effective for applications in which the target sequences show a high degree of similarity to the query sequence, such as assembling shotgun sequences or matching ESTs to genomic sequence. The algorithm is also an effective filtration method. Specifically, it can be used as a preprocessing step for other search methods to reduce the complexity of searching one large database against another. For the problem of identifying overlapping fragments in the assembly of 120 000 fragments from a 1.5 megabase genomic sequence, SST is 15 times faster than BLAST when we consider both building and searching the tree. For searching alone (i.e. after building the tree index), SST 27 times faster than BLAST.


AVAILABILITY
Request from the authors.
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.
4227250
Content-based image retrieval by clustering
In a typical content-based image retrieval (CBIR) system, query results are a set of images sorted by feature similarities with respect to the query. However, images with high feature similarities to the query may be very different from the query in terms of semantics. This is known as the semantic gap. We introduce a novel image retrieval scheme, CLUster-based rEtrieval of images by unsupervised learning (CLUE), which tackles the semantic gap problem based on a hypothesis: semantically similar images tend to be clustered in some feature space. CLUE attempts to capture semantic concepts by learning the way that images of the same semantics are similar and retrieving image clusters instead of a set of ordered images. Clustering in CLUE is dynamic. In particular, clusters formed depend on which images are retrieved in response to the query. Therefore, the clusters give the algorithm as well as the users semantic relevant clues as to where to navigate. CLUE is a general approach that can be combined with any real-valued symmetric similarity measure (metric or nonmetric). Thus it may be embedded in many current CBIR systems. Experimental results based on a database of about 60, 000 images from COREL demonstrate improved performance.
14697648
An Algorithm for Finding the Largest Approximately Common Substructures of Two Trees
Ordered, labeled trees are trees in which each node has a label and the left-to-right order of its children (if it has any) is fixed. Such trees have many applications in vision, pattern recognition, molecular biology and natural language processing. We consider a substructure of an ordered labeled tree T to be a connected subgraph of T. Given two ordered labeled trees T/sub 1/ and T/sub 2/ and an integer d, the largest approximately common substructure problem is to find a substructure U/sub 1/ of T/sub 1/ and a substructure U/sub 2/ of T/sub 2/ such that U/sub 1/ is within edit distance d of U/sub 2/ and where there does not exist any other substructure V/sub 1/ of T/sub 1/ and V/sub 2/ of T/sub 2/ such that V/sub 1/ and V/sub 2/ satisfy the distance constraint and the sum of the sizes of V/sub 1/ and V/sub 2/ is greater than the sum of the sizes of U/sub 1/ and U/sub 2/. We present a dynamic programming algorithm to solve this problem, which runs as fast as the fastest known algorithm for computing the edit distance of two trees when the distance allowed in the common substructures is a constant independent of the input trees. To demonstrate the utility of our algorithm, we discuss its application to discovering motifs in multiple RNA secondary structures (which are ordered labeled trees).