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.
735304
PARAgrab: a comprehensive architecture for web image management and multimodal querying
We demonstrate PARAgrab - a scalable Web image archival, retrieval, and annotation system that supports multiple querying modalities. The underlying architecture of our large-scale Web image database is described. Querying and visualization techniques used in the system are explained.
7844670
A sparse support vector machine approach to region-based image categorization
Automatic image categorization using low-level features is a challenging research topic in computer vision. In this paper, we formulate the image categorization problem as a multiple-instance learning (MIL) problem by viewing an image as a bag of instances, each corresponding to a region obtained from image segmentation. We propose a new solution to the resulting MIL problem. Unlike many existing MIL approaches that rely on the diverse density framework, our approach performs an effective feature mapping through a chosen metric distance function. Thus the MIL problem becomes solvable by a regular classification algorithm. Sparse SVM is adopted to dramatically reduce the regions that are needed to classify images. The selected regions by a sparse SVM approximate to the target concepts in the traditional diverse density framework. The proposed approach is a lot more efficient in computation and less sensitive to the class label uncertainty. Experimental results are included to demonstrate the effectiveness and robustness of the proposed method.
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.
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.
1269749
Complexity-adaptive search algorithm for block motion estimation
We propose a complexity-adaptive fast block matching algorithm design strategy that allows the user to terminate the algorithm at any target computational complexity. Two complexity-adaptive techniques, frame level complexity allocation and block level complexity allocation, are developed to approach the global complexity-distortion optimization A buffer control strategy is proposed to dynamically adjust the target complexity of one frame. The predictive complexity-distortion benefit list (PCDB list) technique is employed to allocate the target complexity into each block. By these techniques, we modify the full-search block matching, three-step search, new three-step search, and four-step search to the complexity-adaptive algorithms. Experimental results show that the complexity-adaptive algorithms could achieve better performance than traditional fixed algorithms from the viewpoint of complexity-distoftion optimization.
2544976
Generalized 2D principal component analysis for face image representation and recognition
In the tasks of image representation, recognition and retrieval, a 2D image is usually transformed into a 1D long vector and modelled as a point in a high-dimensional vector space. This vector-space model brings up much convenience and many advantages. However, it also leads to some problems such as the Curse of Dimensionality dilemma and Small Sample Size problem, and thus produces us a series of challenges, for example, how to deal with the problem of numerical instability in image recognition, how to improve the accuracy and meantime to lower down the computational complexity and storage requirement in image retrieval, and how to enhance the image quality and meanwhile to reduce the transmission time in image transmission, etc. In this paper, these problems are solved, to some extent, by the proposed Generalized 2D Principal Component Analysis (G2DPCA). G2DPCA overcomes the limitations of the recently proposed 2DPCA (Yang et al., 2004) from the following aspects: (1) the essence of 2DPCA is clarified and the theoretical proof why 2DPCA is better than Principal Component Analysis (PCA) is given; (2) 2DPCA often needs much more coefficients than PCA in representing an image. In this work, a Bilateral-projection-based 2DPCA (B2DPCA) is proposed to remedy this drawback; (3) a Kernel-based 2DPCA (K2DPCA) scheme is developed and the relationship between K2DPCA and KPCA (Scholkopf et al., 1998) is explored. Experimental results in face image representation and recognition show the excellent performance of G2DPCA.
15308504
Efficient and accurate Ethernet simulation
The Internet is increasingly being called upon to provide different levels of service to different applications and users. A practical problem in doing so is that although Ethernet is one of the hops for nearby all communication in the Internet, it does not provide any QoS guarantees. A natural question, therefore, is the effect of offered load on Ethernet throughput and delay. In this paper, we present several techniques for accurately and efficiently modeling the behavior of a heavily loaded Ethernet link. We propose an efficient distributed simulation model, called Fast Ethernet Simulation, that empirically models an Ethernet link to quickly and accurately simulate it. By eliminating the implementation of the CSMA/CD protocol, our approach reduces computational complexity drastically while still maintaining desirable accuracy. Performance results show that our techniques not only add very little overhead (less than 5% in our tests) to the basic cost of simulating an Ethernet link, but also closely match real-world measurements. We also present efficient techniques for compressing cumulative distributions using hyperbolic curves and for monitoring the load on a heavily loaded link. Finally, we show applications to illustrate the potential usage of the Fast Ethernet Simulation.
2380687
Packet classification using multidimensional cutting
This paper introduces a classification algorithm called phHyperCuts. Like the previously best known algorithm, HiCuts, HyperCuts is based on a decision tree structure. Unlike HiCuts, however, in which each node in the decision tree represents a hyperplane, each node in the HyperCuts decision tree represents a k--dimensional hypercube. Using this extra degree of freedom and a new set of heuristics to find optimal hypercubes for a given amount of storage, HyperCuts can provide an order of magnitude improvement over existing classification algorithms. HyperCuts uses 2 to 10 times less memory than HiCuts optimized for memory, while the worst case search time of HyperCuts is 50--500% better than that of HiCuts optimized for speed. Compared with another recent scheme, EGT-PC, HyperCuts uses 1.8--7 times less memory space while the worst case search time is up to 5 times smaller. More importantly, unlike EGT-PC, HyperCuts can be fully pipelined to provide one classification result every packet arrival time, and also allows fast updates.
206571042
An Upper Bound for the Independent Domination Number
Let G be a simple graph of order n and minimum degree ?. The independent domination number i(G) is defined to be the minimum cardinality among all maximal independent sets of vertices of G. In this paper, we show that i(G)?n+2??2n?. Thus a conjecture of Favaron is settled in the affirmative.