1365809
New techniques for extracting features from protein sequences
In this paper we propose new techniques to extract features from protein sequences. We then use the features as inputs for a Bayesian neural network (BNN) and apply the BNN to classifying protein sequences obtained from the PIR (Protein Information Resource) database maintained at the National Biomedical Research Foundation. To evaluate the performance of the proposed approach, we compare it with other protein classifiers built based on sequence alignment and machine learning methods. Experimental results show the high precision of the proposed classifier and the complementarity of the bioinformatics tools studied in the paper.
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.
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).
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.
54104798
Data allocation algorithms for distributed video servers
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.
9192804
Efficient and robust streaming provisioning in VPNs
Today, most large companies maintain virtual private networks (VPNs) to connect their remote locations into a single secure network. VPNs can be quite large covering more than 1000 locations and in most cases use standard Internet protocols and services. Such VPNs are implemented using a diverse set of technologies such as Frame Relay, MPLS, or IPSEC to achieve the goal of privacy and performance isolation from the public Internet.Using VPNs to distribute live content has recently received tremendous interest. For example, a VPN could be used to broadcast a CEO-employee town hall meeting. To distribute this type of content economically without overloading the network, the deployment of streaming caches or splitters is most likely required.In this paper, we address the problem of optimally placing such streaming splitters or caches to broadcast to a given set of VPN endpoints under the constraints typically found within a VPN. In particular, we introduce an efficient algorithm with complexity O(V), V being the number of routers in the VPN. This guarantees the optimal cache placement if interception is used for redirection. We prove that the general problem is NP-hard and introduce multiple heuristics for efficient and robust cache placement suitable under different constraints. At the expense of increased implementation complexity, each heuristic solution provides additional saving in the number of caches required. We evaluate proposed solutions using extensive simulations. In particular, we show our flow-based solution is very close to the optimal.
5646579
Comparing User-assisted and Automatic Query Translation
For the 2002 Cross-Language Evaluation Forum Interactive Track, the University of Maryland team focused on query formulation and reformulation. Twelve people performed a total of forty eight searches in the German document collection using English queries. Half of the searches were with user-assisted query translation, and half with fully automatic query translation. For the user-assisted query translation condition, participants were provided two types of cues about the meaning of each translation: a list of other terms with the same translation (potential synonyms), and a sentence in which the word was used in a translation-appropriate context. Four searchers performed the official iCLEF task, the other eight searched a smaller collection. Searchers performing the official task were able to make more accurate relevance judgments with user-assisted query translation for three of the four topics. We observed that the number of query iterations seems to vary systematically with topic, system, and collection, and we are analyzing query content and ranked retrieval measures to obtain further insight into these variations in search behavior.
11808205
Mending broken handwriting with a macrostructure analysis method to improve recognition
Abstract Broken characters always create problems in handwriting recognition systems, especially those using boundary and/or skeleton information. This paper presents a macrostructure analysis (MSA) mending method based on skeleton and boundary information and an MSA that investigates the stroke tending direction and other properties of handwritings. A new skeleton end extension algorithm is introduced, which compensates the defectiveness of the skeletonization algorithm and obtains a satisfactory skeleton. When combined with suitable parameters, improved performance from a handwriting classifier is achieved. The experimental results from over 13 000 numerals show the efficiency and robustness of the proposed method, raising recognition rates by over 10% for broken handwritten digits, from 74.8% to 86.4%.