37775039
An approximate search engine for structural databases
When a person interested in a topic enters a keyword into a Web search engine, the response is nearly instantaneous (and sometimes overwhelming). The impressive speed is due to clever inverted index structures, caching, and a domain-independent knowledge of strings. Our project seeks to construct algorithms, data structures, and software that approach the speed of keyword-based search engines for queries on structural databases.
A structural database is one whose data objects include trees, graphs, or a set of interrelated labeled points in two, three, or higher dimensional space. Examples include databases holding (i) protein secondary and tertiary structure, (ii) phylogenetic trees, (iii) neuroanatomical networks, (iv) parse trees, (v) molecular diagrams, and (vi) XML documents. Comparison queries on such databases require solving variants of the graph isomorphism or subisomorphism problems (for which all known algorithms are exponential), so we have explored a large heuristic space.
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.
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).
12107864
Kernel Trick Embedded Gaussian Mixture Model
In this paper, we present a kernel trick embedded Gaussian Mixture Model (GMM), called kernel GMM. The basic idea is to embed kernel trick into EM algorithm and deduce a parameter estimation algorithm for GMM in feature space. Kernel GMM could be viewed as a Bayesian Kernel Method. Compared with most classical kernel methods, the proposed method can solve problems in probabilistic framework. Moreover, it can tackle nonlinear problems better than the traditional GMM. To avoid great computational cost problem existing in most kernel methods upon large scale data set, we also employ a Monte Carlo sampling technique to speed up kernel GMM so that it is more practical and efficient. Experimental results on synthetic and real-world data set demonstrate that the proposed approach has satisfing performance.
9700223
Discovering Frequent Closed Partial Orders from Strings
Mining knowledge about ordering from sequence data is an important problem with many applications, such as bioinformatics, Web mining, network management, and intrusion detection. For example, if many customers follow a partial order in their purchases of a series of products, the partial order can be used to predict other related customers' future purchases and develop marketing campaigns. Moreover, some biological sequences (e.g., microarray data) can be clustered based on the partial orders shared by the sequences. Given a set of items, a total order of a subset of items can be represented as a string. A string database is a multiset of strings. In this paper, we identify a novel problem of mining frequent closed partial orders from strings. Frequent closed partial orders capture the nonredundant and interesting ordering information from string databases. Importantly, mining frequent closed partial orders can discover meaningful knowledge that cannot be disclosed by previous data mining techniques. However, the problem of mining frequent closed partial orders is challenging. To tackle the problem, we develop Frecpo (for frequent closed partial order), a practically efficient algorithm for mining the complete set of frequent closed partial orders from large string databases. Several interesting pruning techniques are devised to speed up the search. We report an extensive performance study on both real data sets and synthetic data sets to illustrate the effectiveness and the efficiency of our approach
54104798
Data allocation algorithms for distributed video servers
35286842
On the NP-Isomorphism Problem with Respect to Random Instances
This paper takes a new approach to studying the NP-isomorphism problem initiated by Berman and Hartmanis. We consider polynomial-time computable and invertible bijections among NP-complete sets that preserve the underlying natural distributions on random instances. We show that there are natural NP-complete problems which are not polynomially isomorphic when instances are chosen at random because no polynomial-time isomorphisms can preserve the underlying natural distributions on instances of these problems, On the other hand, we show that all the known average-case NP-complete problems under many-one reductions are polynomially isomorphic with respect to their distributions on random instances. Simple and accessible proofs to the known average-case NP-complete problems are presented when establishing the isomorphism result. New average-case NP-complete problems are also presented.
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.