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.
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).
32133517
Information Extraction from the Structured Part of Office Documents
The contents of office documents can be divided into structured and unstructured parts. In this paper, we present a sample-based approach to analyzing a document to form its layout and conceptual structures, and then extracting information from the structured part of the office documents. We represent a document's layout structure as an ordered labeled tree structure using nested segmentation, and its conceptual structure as a set of attribute type pairs. The layout similarities between the document to be processed and samples are identified by employing an approximate tree matching method. The conceptual similarities are identified by analyzing document and sample contents, and by measuring the degree of conceptual closeness. Finally, the information is extracted by instantiating the attributes specified in the conceptual structure based on the result of document structure analysis.
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.
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.
18182406
Recurrent neural networks for minimum infinity-norm kinematic control of redundant manipulators
This paper presents two neural network approaches to minimum infinity-norm solution of the velocity inverse kinematics problem for redundant robots. Three recurrent neural networks are applied for determining a joint velocity vector with its maximum absolute value component being minimal among all possible joint velocity vectors corresponding to the desired end-effector velocity. In each proposed neural network approach, two cooperating recurrent neural networks are used. The first approach employs two Tank-Hopfield networks for linear programming. The second approach employs two two-layer recurrent neural networks for quadratic programming and linear programming, respectively. Both the minimal 2-norm and infinity-norm of joint velocity vector can be obtained from the output of the recurrent neural networks. Simulation results demonstrate that the proposed approaches are effective with the second approach being better in terms of accuracy and optimality.
94229
Translating unknown queries with web corpora for cross-language information retrieval
It is crucial for cross-language information retrieval (CLIR) systems to deal with the translation of unknown queries due to that real queries might be short. The purpose of this paper is to investigate the feasibility of exploiting the Web as the corpus source to translate unknown queries for CLIR. We propose an online translation approach to determine effective translations for unknown query terms via mining of bilingual search-result pages obtained from Web search engines. This approach can alleviate the problem of the lack of large bilingual corpora, translate many unknown query terms, provide flexible query specifications, and extract semantically-close translations to benefit CLIR tasks -- especially for cross-language Web search.
5570863
Solving the small sample size problem in face recognition using generalized discriminant analysis
The goal of face recognition is to distinguish persons via their facial images. Each person's images form a cluster, and a new image is recognized by assigning it to the correct cluster. Since the images are very high-dimensional, it is necessary to reduce their dimension. Linear discriminant analysis (LDA) has been shown to be effective at dimension reduction while preserving the cluster structure of the data. It is classically defined as an optimization problem involving covariance matrices that represent the scatter within and between clusters. The requirement that one of these matrices be nonsingular restricts its application to datasets in which the dimension of the data does not exceed the sample size. For face recognition, however, the dimension typically exceeds the number of images in the database, resulting in what is referred to as the small sample size problem. Recently, the applicability of LDA has been extended by using the generalized singular value decomposition (GSVD) to circumvent the nonsingularity requirement, thus making LDA directly applicable to face recognition data. Our experiments confirm that LDA/GSVD solves the small sample size problem very effectively as compared with other current methods.
5318094
Fast approximation of centrality
Social studies researchers use graphs to model group activities in social networks. An important property in this context is the centrality of a vertex: the inverse of the average distance to each other vertex. We describe a randomized approximation algorithm for centrality in weighted graphs. For graphs exhibiting the small world phenomenon, our method estimates the centrality of all vertices with high probability within a (1 + ∈) factor in near-linear time.
7844670
A sparse support vector machine approach to region-based image categorization
Automatic image categorization using low-level features is a challenging research topic in computer vision. In this paper, we formulate the image categorization problem as a multiple-instance learning (MIL) problem by viewing an image as a bag of instances, each corresponding to a region obtained from image segmentation. We propose a new solution to the resulting MIL problem. Unlike many existing MIL approaches that rely on the diverse density framework, our approach performs an effective feature mapping through a chosen metric distance function. Thus the MIL problem becomes solvable by a regular classification algorithm. Sparse SVM is adopted to dramatically reduce the regions that are needed to classify images. The selected regions by a sparse SVM approximate to the target concepts in the traditional diverse density framework. The proposed approach is a lot more efficient in computation and less sensitive to the class label uncertainty. Experimental results are included to demonstrate the effectiveness and robustness of the proposed method.