11677932
Fast Similarity Search in Three-Dimensional Structure Databases
Given a database D of three-dimensional (3D) molecular structures and a target molecule Q, the similarity search problem is to find the molecules O in D that match Q after allowing for an arbitrary number of whole-structure rotations and translations as well as a certain number of edit operations. The edit operations include relabeling an atom, deleting an atom, and inserting an atom. This search operation arises in many biochemical applications. In this paper we study the similarity search problem and a class of related queries. We present a computer vision based technique, called geometric hashing, for processing these queries. Experimental results on a database of 3D molecular structures obtained from the National Cancer Institute indicate the good performance of the presented technique.
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.
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.
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.
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.
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.
61565821
Modelling and stability of FAST TCP
We introduce a discrete-time model of FAST TCP that fully captures the effect of self-clocking and compare it with the traditional continuous-time model. While the continuous-time model predicts instability for homogeneous sources sharing a single link when feedback delay is large, experiments suggest otherwise. Using the discrete-time model, we prove that FAST TCP is locally asymptotically stable in general networks when all sources have a common round-trip feedback delay, no matter how large the delay is. We also prove global stability for a single bottleneck link in the absence of feedback delay. The techniques developed here are new and applicable to other protocols.
45865876
Graph theoretic characterization and reliability of the generalized Boolean n-cube network
In this paper, a general class of Boolean n-cube structures is investigated. The interconnection is based on a mixed radix number system which results in a variety of generalized Boolean n-cube structures for a given number of processors N = x·2y, where x and y are positive integers. A number of interesting properties of the network are revealed. By a constructive method, the node connectivity of this network is found. Finally, we show that the graph is super-λ and is an optimal reliable structure for interconnection networks.
31564513
Packing of Unequal Spheres and Automated Radiosurgical Treatment Planning
We study an optimization problem of packing unequal spheres into a three-dimensional (3D) bounded region in connection with radiosurgical treatment planning. Given an input (R, V, S, L), where R is a 3D bounded region, V a positive integer, S a multiset of spheres, and L a location constraint on spheres, we want to find a packing of R using the minimum number of spheres in S such that the covered volume is at least V; the location constraint L is satisfied; and the number of points on the boundary of R that are touched by spheres is maximized. Such a packing arrangement corresponds to an optimal radiosurgical treatment planning. Finding an optimal solution to the problem, however, is computationally intractable. In particular, we show that this optimization problem and several related problems are NP-hard. Hence, some form of approximations is needed. One approach is to consider a simplified problem under the assumption that spheres of arbitrary (integral) diameters are available with unlimited supply, and there are no location constraints. This approach has met with certain success in medical applications using a dynamic programming algorithm (Bourland and Wu, 1996; Wu, 1996). We propose in this paper an improvement to the algorithm that can greatly reduce its computation cost.
6163740
SEP: a space efficient pipelining technique for managing disk buffers in multimedia servers
We present techniques for managing disks as a buffer for the tertiary storage of multimedia servers. A unified disk space is used to not only cache frequently referenced objects, but also to provide staging buffers for playing back objects. A new staging technique and three buffer replacement policies are investigated. The simulation results indicate that the staging method is very efficient, and each of the replacement policies offers significant additional improvement. Some of the performance issues are also analyzed analytically. The mathematical model provides guidelines for good multimedia systems design using the proposed techniques.