17699044
Automated Discovery of Active Motifs in Multiple RNA Secondary Structures
In this paper we present a method for discovering approximately common motifs (also known as active motifs) in multiple RNA secondary structures. The secondary structures can be represented as ordered trees (i.e., the order among siblings matters). Motifs in these trees are connected subgraphs that can differ in both substitutions and deletions/insertions. The proposed method consists of two steps: (1) find candidate motifs in a small sample of the secondary structures; (2) search all of the secondary structures to determine how frequently these motifs occur (within the allowed approximation) in the secondary structures. To reduce the running time, we develop two optimization heuristics based on sampling and pattern matching techniques. Experimental results obtained by running these algorithms on both generated data and RNA secondary structures show the good performance of the algorithms. To demonstrate the utility of our algorithms, we discuss their applications to conducting the phylogenetic study of RNA sequences obtained from GenBank.
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).
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.
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.
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.
7340804
Cooperative proxy caching for wireless base stations
This paper proposes a mobile cache model to facilitate the cooperative proxy caching in wireless base stations. This mobile cache model uses a network cache line to record the caching state information about a web document for effective data search and cache space management. Based on the proposed mobile cache model, a P2P cooperative proxy caching scheme is proposed to use a self-configured and self-managed virtual proxy graph (VPG), independent of the underlying wireless network structure and adaptive to the network and geographic environment changes, to achieve efficient data search, data cache and date replication. Based on demand, the aggregate effect of data caching, searching and replicating actions by individual proxy servers automatically migrates the cached web documents closer to the interested clients. In addition, a cache line migration (CLM) strategy is proposed to flow and replicate the heads of network cache lines of web documents associated with a moving mobile host to the new base station during the mobile host handoff. These replicated cache line heads provide direct links to the cached web documents accessed by the moving mobile hosts in the previous base station, thus improving the mobile web caching performance. Performance studies have shown that the proposed P2P cooperative proxy caching schemes significantly outperform existing caching schemes.
9478197
A support vector machine with a hybrid kernel and minimal Vapnik-Chervonenkis dimension
We present a mechanism to train support vector machines (SVMs) with a hybrid kernel and minimal Vapnik-Chervonenkis (VC) dimension. After describing the VC dimension of sets of separating hyperplanes in a high-dimensional feature space produced by a mapping related to kernels from the input space, we proposed an optimization criterion to design SVMs by minimizing the upper bound of the VC dimension. This method realizes a structural risk minimization and utilizes a flexible kernel function such that a superior generalization over test data can be obtained. In order to obtain a flexible kernel function, we develop a hybrid kernel function and a sufficient condition to be an admissible Mercer kernel based on common Mercer kernels (polynomial, radial basis function, two-layer neural network, etc.). The nonnegative combination coefficients and parameters of the hybrid kernel are determined subject to the minimal upper bound of the VC dimension of the learning machine. The use of the hybrid kernel results in a better performance than those with a single common kernel. Experimental results are discussed to illustrate the proposed method and show that the SVM with the hybrid kernel outperforms that with a single common kernel in terms of generalization power.
19723482
A learning process to the identification of feature points on Chinese characters
The paper describes a new stroke extraction approach to identify the feature points of a character, using line-filtering and learning-based techniques. The line-filtering technique based on the convolution operations with a set of 1-D Gabor templates is efficient in extracting the stroke segments of the character and robust in noise tolerance. Furthermore, unlike conventional feature-point detection techniques where decision rules and thresholds have to be specified, our learning-based technique for feature-point identification implicitly represents the rules and thresholds without further parameter adjustments. Experimental results show that the learning-based technique is capable of generalizing the learning knowledge to identify feature points and can get an average identification rate of 95.27% for hand-printed test characters and 96.78% for machine-printed test characters.
3235521
Towards an accurate AS-level traceroute tool
Traceroute is widely used to detect routing problems, characterize end-to-end paths, and discover the Internet topology. Providing an accurate list of the Autonomous Systems (ASes) along the forwarding path would make traceroute even more valuable to researchers and network operators. However, conventional approaches to mapping traceroute hops to AS numbers are not accurate enough. Address registries are often incomplete and out-of-date. BGP routing tables provide a better IP-to-AS mapping, though this approach has significant limitations as well. Based on our extensive measurements, about 10% of the traceroute paths have one or more hops that do not map to a unique AS number, and around 15% of the traceroute AS paths have an AS loop. In addition, some traceroute AS paths have extra or missing AS hops due to Internet eXchange Points, sibling ASes managed by the same institution, and ASes that do not advertise routes to their infrastructure. Using the BGP tables as a starting point, we propose techniques for improving the IP-to-AS mapping as an important step toward an AS-level traceroute tool. Our algorithms draw on analysis of traceroute probes, reverse DNS lookups, BGP routing tables, and BGP update messages collected from multiple locations. We also discuss how the improved IP-to-AS mapping allows us to home in on cases where the BGP and traceroute AS paths differ for legitimate reasons.
21940463
A hybrid method for unconstrained handwritten numeral recognition by combining structural and neural "gas" classifiers
Abstract This paper presents a hybrid method for handwritten numeral recognition that combines two compensatory recognition algorithms by analysing their performance for several aspects. The skeleton-based structural recognition algorithm employed in this method is robust under distortion but sensitive to noise and flaws. On the other hand, the neural network classifier, which uses scaled binary images as features and the neural “gas” model for classification, is relatively immune to noise and flaws but sensitive to distortion. The different performances of the two algorithms for broken, connected or slanted numerals, and the measurement-level decision provided by the neural network are detected and combined with different strategies to develop matching rules for each recognition method. Five combination methods based on performance analysis are developed to meet different requirements. As the two algorithms have fairly compensatory properties, the proposed method improves the recognition rate and reliability by exploiting the advantages and avoiding the weaknesses of each classifier. The experimental results from a large set of data show the efficiency and robustness of the proposed method.