46369194
Mining Frequent Agreement Subtrees in Phylogenetic Databases
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.
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.
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.
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.
16584684
Diagonal Flips in Labelled Planar Triangulations
Abstract. A classical result of Wagner states that any two (unlabelled) planar triangulations with the same number of vertices can be transformed into each other by a finite sequence of diagonal flips. Recently Komuro gives a linear bound on the maximum number of diagonal flips needed for such a transformation. In this paper we show that any two labelled triangulations can be transformed into each other using at most O(nlogn) diagonal flips. We will also show that any planar triangulation with n>4 vertices has at least n− 2 flippable edges. Finally, we prove that if the minimum degree of a triangulation is at least 4, then it contains at least 2n + 3 flippable edges. These bounds can be achieved by an infinite class of triangulations.
414995
Combining bidirectional translation and synonymy for cross-language information retrieval
This paper introduces a general framework for the use of translation probabilities in cross-language information retrieval based on the notion that information retrieval fundamentally requires matching what the searcher means with what the author of a document meant. That perspective yields a computational formulation that provides a natural way of combining what have been known as query and document translation. Two well-recognized techniques are shown to be a special case of this model under restrictive assumptions. Cross-language search results are reported that are statistically indistinguishable from strong monolingual baselines for both French and Chinese documents.
5934543
Data Distortion for Privacy Protection in a Terrorist Analysis System
Data distortion is a critical component to preserve privacy in security-related data mining applications, such as in data mining-based terrorist analysis systems. We propose a sparsified Singular Value Decomposition (SVD) method for data distortion. We also put forth a few metrics to measure the difference between the distorted dataset and the original dataset. Our experimental results using synthetic and real world datasets show that the sparsified SVD method works well in preserving privacy as well as maintaining utility of the datasets.
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.
10726926
A scalable integrated region-based image retrieval system
We present a scalable algorithm for indexing and retrieving images based on region segmentation. The method uses statistical clustering on region features and IRM (integrated region matching), a measure developed to evaluate overall similarity between images. It incorporates properties of all the regions in the images by a region-matching scheme. The algorithm has been implemented as a part of our experimental SIMPLIcity (Semantics-sensitive Integrated Matching for Picture LIbraries) image retrieval system and tested on large-scale image databases of both general-purpose images and pathology slides. Experiments have demonstrated that this technique maintains the accuracy of the original system while reducing the matching time significantly.