28415004
Scientific Data Mining: A Case Study
Scientific data mining is the activity of finding significant information in scientific data. This paper presents an example of scientific data mining: the discovery of approximately common patterns in RNA secondary structures. We represent an RNA secondary structure by an ordered labeled tree based on a previously proposed scheme. The patterns in the trees are substructures that can differ in both substitutions and deletions/insertions of nodes of the trees. Our techniques incorporate approximate tree matching algorithms and novel heuristics for discovery and optimization. Experimental results obtained by running these algorithms on both generated data and RNA secondary structures show the good performance of the algorithms. It is shown that the optimization heuristics speed up the discovery algorithm by a factor of 10. Moreover, our optimized approach is 100,000 times faster than the brute force method.
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.
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.
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).
14138215
Multiresolution object-of-interest detection for images with low depth of field
This paper describes a novel multiresolution image segmentation algorithm for separating sharply focused objects-of-interest from other foreground or background objects in low depth-of-field (DOF) images, such as sports, telephoto, macro, and microscopic images. The algorithm takes a multiscale context-dependent approach to segment images based on features extracted from wavelet coefficients in high-frequency bands. The algorithm is fully automatic in that all parameters are image-independent. Experiments with the algorithm on more than 100 low DOF images have shown results close to the human segmentation of these images. Besides high accuracy, the algorithm also provides high speed. A 768/spl times/512 pixel image can be segmented within two seconds on a Pentium Pro 300 MHz PC.
16538539
Optimal jumper insertion for antenna avoidance under ratio upper-bound
Antenna effect may damage gate oxides during plasma-based fabrication process. The antenna ratio of total exposed antenna area to total gate oxide area is directly related to the amount of damage. Jumper insertion is a common technique applied at routing and post-layout stages to avoid and to fix the problems caused by the antenna effect. This paper presents an optimal algorithm for jumper insertion under the ratio upper-bound. It handles Steiner trees with obstacles. The algorithm us based on dynamic programming while works on free trees. The time complexity is O(alpha|V|2 ) and the space complexity is O(|V|2), where |V| is the number of nodes in the routing tree and a is a factor depending on how to find a non-blocked position on a wire for a jumper
16046090
Nonlinear blind source separation using higher order statistics and a genetic algorithm
This paper presents a novel method for blindly separating unobservable independent source signals from their nonlinear mixtures. The demixing system is modeled using a parameterized neural network whose parameters can be determined under the criterion of independence of its outputs. Two cost functions based on higher order statistics are established to measure the statistical dependence of the outputs of the demixing system. The proposed method utilizes a genetic algorithm (GA) to minimize the highly nonlinear and nonconvex cost functions. The GA-based global optimization technique is able to obtain superior separation solutions to the nonlinear blind separation problem from any random initial values. Compared to conventional gradient-based approaches, the GA-based approach for blind source separation is characterized by high accuracy, robustness, and convergence rate. In particular, it is very suitable for the case of limited available data. Simulation results are discussed to demonstrate that the proposed GA-based approach is capable of separating independent sources from their nonlinear mixtures generated by a parametric separation model.
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.
19646455
The upper bound of essential cyclomatic numbers of hypergraphs
Abstract The essential cyclomatic number of a hypergraph is the maximum number of independent essential cycles of the hypergraph. In this paper, we first prove a general upper bound for the cyclomatic number in terms of the size, order and edge-size of a hypergraph. Then we give a sharp upper bound for ( n −2)-uniform hypergraphs of order n by solving an extremal problem of graphs. It is remarkable that this sharp upper bound is not generally achieved by the complete ( n −2)-uniform hypergraphs.