5724385
An iterative relaxation technique for the NMR backbone assignment problem
NMR spectroscopy is one of the popular experiments to determine protein structures. An important stage of protein structure determination by using NMR is protein backbone resonance assignment (or backbone assignment for short). Due to the messiness and disorder of NMR spectral data, backbone assignment is usually a tedious and time-consuming manual work. This raises a great interest in developing an efficient and automatic method to perform backbone assignment. An iterative algorithm is proposed that is equipped with two operations: grouping and linking. Grouping is responsible for peak picking and part of connectivity determination. Ideally, those peaks with the same H/sup N/ and N chemical shifts can be grouped together; peaks belonging to the same group can be used to determine the order of two consecutive spin systems. However, in real situation, grouping is a difficult task due to false positives and false negatives. We sometimes add hypothetic peaks to tackle false negatives and use linking operation to remove false positives. Linking is responsible for part of connectivity determination and backbone assignment. Given a protein sequence and partial connectivity information, we try to link connected spin systems as much as possible. False positive spin systems may create conflicts in the linking stage. To find a good assignment on a noisy dataset, the backbone assignment problem is modeled as a maximum independent set problem. Although the problem is NP-complete, there are heuristic methods that obtain pretty good results.
6185076
Text categorization using automatically acquired domain ontology
In this paper, we describe ontology-based text categorization in which the domain ontologies are automatically acquired through morphological rules and statistical methods. The ontology-based approach is a promising way for general information retrieval applications such as knowledge management or knowledge discovery. As a way to evaluate the quality of domain ontologies, we test our method through several experiments. Automatically acquired domain ontologies, with or without manual editing, have been used for text categorization. The results are quite satisfactory. Furthermore, we have developed an automatic method to evaluate the quality of our domain ontology.
4516498
Using Instant Messaging to Provide an Intelligent Learning Environment
Instant Messaging enables learners and educators to interact in an on-line environment. In this paper, we propose an intelligent ChatBot system, based on instant messaging, for student on-line coaching in an English learning environment. The proposed ChatBot facilitates synchronous communication with students by using ready reference materials including, dictionaries, authorized conversation material with speaking, and a question-answering function. The agent records and analyzes conversations so that the teacher can assess students' progress. Our contribution in this paper is that we integrate the NLP Tool and AIML into an instant messaging-based ChatBot for English as a Second Language programs.
1251407
Reference metadata extraction using a hierarchical knowledge representation framework
The integration of bibliographical information on scholarly publications available on the Internet is an important task in the academic community. Accurate reference metadata extraction from such publications is essential for the integration of metadata from heterogeneous reference sources. In this paper, we propose a hierarchical template-based reference metadata extraction method for scholarly publications. We adopt a hierarchical knowledge representation framework called INFOMAP, which automatically extracts metadata. The experimental results show that, by using INFOMAP, we can extract author, title, journal, volume, number (issue), year, and page information from different kinds of reference styles with a high degree of precision. The overall average accuracy is 92.39% for the six major reference styles compared in this study.
2987495
Independent Sets in Circular-Arc Graphs
This paper presents a linear time algorithm for the independent set problem on circular-arc graphs. previous algorithms for this problem have assumed that the input is a set of circular-arcs and solve the problem in O(n) time. However, the fastest known algorithm for constructing the circular-are representation from a set of adjacency lists takes O(n2) time. We show that we can solve the problem in O(n + m) time, when we are given the circular-arc graph as a set of adjacency lists.
2578042
Trustworthy keyword search for regulatory-compliant records retention
Recent litigation and intense regulatory focus on secure retention of electronic records have spurred a rush to introduce Write-Once-Read-Many (WORM) storage devices for retaining business records such as electronic mail. However, simply storing records in WORM storage is insuffcient to ensure that the records are trustworthy, i.e., able to provide irrefutable proof and accurate details of past events. Specifically, some form of index is needed for timely access to the records, but unless the index is maintained securely, the records can in effect be hidden or altered, even if stored in WORM storage. In this paper, we systematically analyze the requirements for establishing a trustworthy inverted index to enable keyword-based search queries. We propose a novel scheme for effcient creation of such an index and demonstrate, through extensive simulations and experiments with an enterprise keyword search engine, that the scheme can achieve online update speeds while maintaining good query performance. In addition, we present a secure index structure for multi-keyword queries that supports insert, lookup and range queries in time logarithmic in the number of documents.
6232755
Algorithms for minimum covering by cliques and maximum clique in claw-free perfect graphs
An algorithm is given for determining a minimum cardinality clique cover ongraphs that do not contain claws, odd holes or odd anti-holes. These graphs are also shown to be perfect so that we obtain a new proof of the strong perfect graph theorem for claw-free graphs. A by-product of our analysis is an algorithm for determining a maximum cardinality clique on claw-free perfect graphs.
16227528
Fast image retrieval using color-spatial information
Abstract. In this paper, we present an image retrieval system that employs both the color and spatial information of images to facilitate the retrieval process. The basic unit used in our technique is a single-colored cluster, which bounds a homogeneous region of that color in an image. Two clusters from two images are similar if they are of the same color and overlap in the image space. The number of clusters that can be extracted from an image can be very large, and it affects the accuracy of retrieval. We study the effect of the number of clusters on retrieval effectiveness to determine an appropriate value for “optimal'' performance. To facilitate efficient retrieval, we also propose a multi-tier indexing mechanism called the Sequenced Multi-Attribute Tree (SMAT). We implemented a two-tier SMAT, where the first layer is used to prune away clusters that are of different colors, while the second layer discriminates clusters of different spatial locality. We conducted an experimental study on an image database consisting of 12,000 images. Our results show the effectiveness of the proposed color-spatial approach, and the efficiency of the proposed indexing mechanism.
11584462
The automatic improvement of locality in storage systems
Disk I/O is increasingly the performance bottleneck in computer systems despite rapidly increasing disk data transfer rates. In this article, we propose Automatic Locality-Improving Storage (ALIS), an introspective storage system that automatically reorganizes selected disk blocks based on the dynamic reference stream to increase effective storage performance. ALIS is based on the observations that sequential data fetch is far more efficient than random access, that improving seek distances produces only marginal performance improvements, and that the increasingly powerful processors and large memories in storage systems have ample capacity to reorganize the data layout and redirect the accesses so as to take advantage of rapid sequential data transfer. Using trace-driven simulation with a large set of real workloads, we demonstrate that ALIS considerably outperforms prior techniques, improving the average read performance by up to 50% for server workloads and by about 15% for personal computer workloads. We also show that the performance improvement persists as disk technology evolves. Since disk performance in practice is increasing by only about 8% per year, the benefit of ALIS may correspond to as much as several years of technological progress.