19014339
Biological Data Mining Using Bayesian Neural Networks: A Case Study
Biological data mining is the activity of finding significant information in biomolecular data. The significant information may refer to motifs, clusters, genes, and protein signatures. This paper presents an example of biological data mining: the recognition of promoters in DNA. We propose a two-level ensemble of classifiers to recognize E. Coli promoter sequences. The first-level classifiers include three Bayesian neural networks that learn from three different feature sets. The outputs of the first-level classifiers are combined in the second-level to give the final result. Empirical study shows that a precision rate of 92.2% is achieved, indicating an excellent performance of the proposed approach.
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.
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).
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.
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.
2016479
Shape-Based Curve Growing Model and Adaptive Regularization for Pulmonary Fissure Segmentation in CT
This paper presents a shape-based curve-growing algorithm for object recognition in the field of medical imaging. The proposed curve growing process, modeled by a Bayesian network, is influenced by both image data and prior knowledge of the shape of the curve. A maximum a posteriori (MAP) solution is derived using an energy-minimizing mechanism. It is implemented in an adaptive regularization framework that balances the influence of image data and shape prior in estimating the curve, and reflects the causal dependencies in the Bayesian network. The method effectively alleviates over-smoothing, an effect that can occur with other regularization methods. Moreover, the proposed framework also addresses initialization and local minima problems. Robustness and performance of the proposed method are demonstrated by segmentation of pulmonary fissures in computed tomography (CT) images.
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.
26197775
Using Neural Networks to Determine Sugeno Measures by Statistics
Abstract To replace the traditional weighted average method, Choquet integrals or Sugeno integrals with respect to fuzzy measures are used to obtain a synthetic evaluation of a given object (or its quality, function, etc. respectively) with multi-attribute. Generally, it is not easy to determine fuzzy measures in real problems due to the subjectivity of human thinking. It is even much more difficult than determining weights in the weighted average method, because of the nonadditivity of fuzzy measures. This paper uses a neural network algorithm to optimize the inverse problem of synthetic evaluation, and thus to determine Sugeno measures by the Choquet integral and statistics of given data. Since the Choquet integral is a generalization of the weighted average method, this technology has a broad applicability in areas of multivariate analysis, decision making, pattern recognition, image and speech processing and expert systems. Copyright © 1996 Elsevier Science Ltd.
15454128
An Approach for Modeling and Analysis of Security System Architectures
Security system architecture governs the composition of components in security systems and interactions between them. It plays a central role in the design of software security systems that ensure secure access to distributed resources in networked environment. In particular, the composition of the systems must consistently assure security policies that it is supposed to enforce. However, there is currently no rigorous and systematic way to predict and assure such critical properties in security system design. A systematic approach is introduced to address the problem. We present a methodology for modeling security system architecture and for verifying whether required security constraints are assured by the composition of the components. We introduce the concept of security constraint patterns, which formally specify the generic form of security policies that all implementations of the system architecture must enforce. The analysis of the architecture is driven by the propagation of the global security constraints onto the components in an incremental process. We show that our methodology is both flexible and scalable. It is argued that such a methodology not only ensures the integrity of critical early design decisions, but also provides a framework to guide correct implementations of the design. We demonstrate the methodology through a case study in which we model and analyze the architecture of the Resource Access Decision (RAD) Facility, an OMG standard for application-level authorization service.
39858986
On the Connectivity of (4;g)-Cages