5763734
Finding approximate patterns in undirected acyclic graphs
Abstract We consider an approximate pattern matching problem for undirected acyclic graphs. Specifically, let P be a pattern graph, D a data graph and t an integer. We present an algorithm to locate a subgraph in D whose distance from P is at most t . The distance measure used here is the degree-2 metric published previously. The time complexity of our algorithm is O(N P N D d d log d) where N P and N D are the number of nodes in P and D , respectively; d =min{ d P , d D }; d P and d D are the maximum degree of P and D , respectively. Central to our algorithm is a procedure for finding approximate patterns in rooted unordered trees and freely allowing cuts. We discuss two applications of the algorithms in chemical information search and website management on the Internet.
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).
46369194
Mining Frequent Agreement Subtrees in Phylogenetic Databases
32133517
Information Extraction from the Structured Part of Office Documents
The contents of office documents can be divided into structured and unstructured parts. In this paper, we present a sample-based approach to analyzing a document to form its layout and conceptual structures, and then extracting information from the structured part of the office documents. We represent a document's layout structure as an ordered labeled tree structure using nested segmentation, and its conceptual structure as a set of attribute type pairs. The layout similarities between the document to be processed and samples are identified by employing an approximate tree matching method. The conceptual similarities are identified by analyzing document and sample contents, and by measuring the degree of conceptual closeness. Finally, the information is extracted by instantiating the attributes specified in the conceptual structure based on the result of document structure analysis.
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.
17604851
Efficient point coverage in wireless sensor networks
We study minimum-cost sensor placement on a bounded 3D sensing field, R, which comprises a number of discrete points that may or may not be grid points. Suppose we have ℓ types of sensors available with different sensing ranges and different costs. We want to find, given an integer σ ≥ 1, a selection of sensors and a subset of points to place these sensors such that every point in R is covered by at least σ sensors and the total cost of the sensors is minimum. This problem is known to be NP-hard. Let ki denote the maximum number of points that can be covered by a sensor of the ith type. We present in this paper a polynomial-time approximation algorithm for this problem with a proven approximation ratio $${\gamma = \sum_{i=1}^{\ell} k_{i} -\sigma+1}$$. In applications where the distance of any two points has a fixed positive lower bound, each ki is a constant, and so we have a polynomial-time approximation algorithms with a constant guarantee. While γ may be large, we note that it is only a worst-case upper bound. In practice the actual approximation ratio is small, even on randomly generated points that do not have a fixed positive minimum distance between them. We provide a number of numerical results for comparing approximation solutions and optimal solutions, and show that the actual approximation ratios in these examples are all less than 3, even though γ is substantially larger.
31977888
Polynomial Time Productivity, Approximations, and Levelability
This paper studies polynomial-time approximations to intractable sets using the concept of p-productivity. It is shown that every (deterministic and nondeterministic) superpolynomial-time computable p-productive set is p-levelable. All $ \leq _m^p $-complete sets for any deterministic superpolynomial time class are shown to be p-productive. It is then shown that the complement of any honest k-creative set in NP is p-levelable. This settles an open problem in Homer [Theoret. Comput. Sci., 47 (1986), pp. 169–180].
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.
14581620
Network cache model for wireless proxy caching
We propose a wireless network cache model to facilitate the cooperative proxy caching in wireless base stations. A self-configured and adaptive virtual proxy graph (VPG) is used to achieve efficient data search, data cache and data replication. Based on demand, the aggregate effect of data caching, searching and replicating actions by individual proxies automatically distributes cached Web documents closer to the interested mobile clients. Our performance study demonstrates that the proposed individual-based wireless proxy caching scheme outperforms existing caching schemes in terms of different performance metrics.
15454128
An Approach for Modeling and Analysis of Security System Architectures
Security system architecture governs the composition of components in security systems and interactions between them. It plays a central role in the design of software security systems that ensure secure access to distributed resources in networked environment. In particular, the composition of the systems must consistently assure security policies that it is supposed to enforce. However, there is currently no rigorous and systematic way to predict and assure such critical properties in security system design. A systematic approach is introduced to address the problem. We present a methodology for modeling security system architecture and for verifying whether required security constraints are assured by the composition of the components. We introduce the concept of security constraint patterns, which formally specify the generic form of security policies that all implementations of the system architecture must enforce. The analysis of the architecture is driven by the propagation of the global security constraints onto the components in an incremental process. We show that our methodology is both flexible and scalable. It is argued that such a methodology not only ensures the integrity of critical early design decisions, but also provides a framework to guide correct implementations of the design. We demonstrate the methodology through a case study in which we model and analyze the architecture of the Resource Access Decision (RAD) Facility, an OMG standard for application-level authorization service.