206452274
A System for Approximate Tree Matching
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, programming compilation, and natural language processing. Many of the applications involve comparing trees or retrieving/extracting information from a repository of trees. Examples include classification of unknown patterns, analysis of newly sequenced RNA structures, semantic taxonomy for dictionary definitions, generation of interpreters for nonprocedural programming languages, and automatic error recovery and correction for programming languages. Previous systems use exact matching (or generalized regular expression matching) for tree comparison. This paper presents a system, called approximate-tree-by-example (ATBE), which allows inexact matching of trees. The ATBE system interacts with the user through a simple but powerful query language; graphical devices are provided to facilitate inputing the queries. The paper describes the architecture of ATBE, illustrates its use and describes some aspects of ATBE implementation. We also discuss the underlying algorithms and provide some sample applications. >
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).
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.
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.
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.
28468806
Space-code bloom filter for efficient per-flow traffic measurement
Per-flow traffic measurement is critical for usage accounting, traffic engineering, and anomaly detection. Previous methodologies are either based on random sampling (e.g., Cisco's NetFlow), which is inaccurate, or only account for the "elephants". We introduce a novel technique for measuring per-flow traffic approximately, for all flows regardless of their sizes, at very high-speed (say, OC768). The core of this technique is a novel data structure called space code bloom filter (SCBF). A SCBF is an approximate representation of a multiset; each element in this multiset is a traffic flow and its multiplicity is the number of packets in the flow. The multiplicity of an element in the multiset represented by SCBF can be estimated through either of two mechanisms-maximum likelihood estimation (MLE) or mean value estimation (MVE). Through parameter tuning, SCBF allows for graceful tradeoff between measurement accuracy and computational and storage complexity. SCBF also contributes to the foundation of data streaming by introducing a new paradigm called blind streaming. We evaluate the performance of SCBF through mathematical analysis and through experiments on packet traces gathered from a tier-1 ISP backbone. Our results demonstrate that SCBF achieves reasonable measurement accuracy with very low storage and computational complexity
1715921
Medium access control in mobile ad hoc networks: challenges and solutions
Summary Mobile ad hoc networks (MANETs) are useful in environment where fixed network infrastructure is unavailable. To function normally, MANETs demand an efficient and distributed medium access control (MAC) protocol. However, characteristics of MANETs such as radio link vulnerability, mobility, limited power pose great challenges on MAC design. This paper surveys the recent advances in MAC design for MANETs. We first identify the challenges that are facing MAC in MANETs. Then we discuss the proposed MAC schemes according to their design goals, focusing on some critical design issues, and tradeoffs. Finally, we point out some future research directions. Copyright # 2006 John Wiley & Sons, Ltd.
1305119
Minimizing roundoff errors of prefix sums via dynamic construction of Huffman trees
The prefix-sum operation, which returns all prefix sums on a sequence of numbers, plays an important role in many applications. We study how to efficiently evaluate prefix sums on positive floating-point numbers such that the worst-case roundoff error of each sum is minimized. A direct approach to this problem builds a Huffman tree for each prefix subsequence from scratch, requiring exactly quadratic time for every input X. We can do better by taking advantage of the current Huffman tree to build the next Huffman tree, using dynamic insertions and deletions on Huffman trees. Consequently, subquadratic time suffices for various input patterns. We also provide experimental comparisons of all the algorithms studied in this paper on inputs that are randomly and uniformly generated.
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.
8736717
Skew detection and reconstruction based on maximization of variance of transition-counts
Abstract The input document images with skew can be a serious problem in the optical character recognition system. A robust method is proposed in this paper for skew detection and reconstruction in document images which can contain less text areas, high noises, tables, figures, flow-chart, and photos. The basic idea of our approach is the maximization of variance of transition counts for the skew detection and text-orientation determination. Once the skew angle is determined, the scanning-line model is applied to reconstruct the skew images. 103 documents with great varieties have been tested and successfully processed. The average detection time of A4 size image is 4.86 s and the reconstruction time is 5.52 s. The proposed approach is also compared with the existing algorithms published in the literature and our method gets some significant improvements in skew detection and reconstruction.