9586691
A New Approach for Alignment of Multiple Proteins
We introduce a new graph-based multiple sequence alignment method for protein sequences. We name our method HSA (Horizontal Sequence Alignment) for it horizontally slides a window on the protein sequences simultaneously. Current progressive alignment tools build up final alignment by adding sequences one by one to existing alignment. Thus, they have the shortcoming of order-dependent alignment. In contrast, HSA considers all the proteins at once. It obtains final alignment by concatenating cliques of graph. In order to find a biologically relevant alignment, HSA takes secondary structure information as well as amino acid sequences into account. The experimental results show that HSA achieves higher accuracy compared to existing tools on BAliBASE benchmarks. The improvement is more significant for proteins with low similarity.
41716369
Learning Object Models, Languages, Authoring Tools and Registry Service for Achieving Dynamic and Collaborative E-Learning
5541899
Automatic identification of digital video based on shot-level sequence matching
To locate a video clip in large collections is very important for retrieval applications, especially for digital rights management. In this paper, we present a novel technique for automatic identification of digital video. This new algorithm is based on dynamic programming that fully uses the temporal dimension to measure the similarity between two video sequences. A normalized chromaticity histogram is used as a feature which is illumination-invariant. Dynamic programming is applied on shot-level to find the optimal nonlinear mapping between video sequences. Two new normalized distance measures are presented for video sequence matching. One measure is based on the normalization of the optimal path found by dynamic programming. The other measure combines both the visual features and the temporal information. Experimental results show that the shot-level approach is robust to frame rate conversion, color correction, and compressions. The proposed distance measures are suitable for variable-length comparisons.
12113641
Neighbor number, valley seeking and clustering
This paper proposes a novel nonparametric clustering algorithm capable of identifying shape-free clusters. This algorithm is based on a nonparametric estimation of the normalized density derivative (NDD) and the local convexity of the density distribution function, both of which are represented in a very concise form in terms of neighbor numbers. We use NDD to measure the dissimilarity between each pair of observations in a local neighborhood and to build a connectivity graph. Combined with the local convexity, this similarity measure can detect observations in local minima (valleys) of the density function, which separate observations in different major clusters. We demonstrate that this algorithm has a close relationship with the single-linkage hierarchical clustering and can be viewed as its extension. The performance of the algorithm is tested with both synthetic and real datasets. An example of color image segmentation is also given. Comparisons with several representative existing algorithms show that the proposed method can robustly identify major clusters even when there are complex configurations and/or large overlaps.
194152
A class of nonlinear stochastic volatility models and its implications for pricing currency options
A class of stochastic volatility (SV) models is proposed by applying the Box-Cox transformation to the volatility equation. This class of nonlinear SV (N-SV) models encompasses all standard SV models, including the well-known lognormal (LN) SV model. It allows to empirically compare and test all standard specifications in a very convenient way and provides a measure of the degree of departure from the classical models. A likelihood-based technique is developed for analyzing the model. Daily dollar/pound exchange rate data provide some evidence against LN model and strong evidence against all the other classical specifications. An efficient algorithm is proposed to study the economic importance of the proposed model on pricing currency options.
13613044
Low-Cost and Reliable Mutual Anonymity Protocols in Peer-to-Peer Networks
We present several protocols to achieve mutual communication anonymity between an information requester and a provider in a P2P information-sharing environment, such that neither the requester nor the provider can identify each other, and no other peers can identify the two communicating parties with certainty. Most existing solutions achieve mutual anonymity in pure P2P systems without any trusted central controls. Compared with two such representative ones, our protocols improve efficiency in two different ways. First, utilizing trusted third parties and aiming at both reliability and low-cost, we propose a group of mutual anonymity protocols. We show that with some limited central support, our protocols can accomplish the goals of anonymity, efficiency, and reliability. Second, we propose a mutual anonymity protocol which relies solely on self-organizations among peers without any trusted central controls. In this protocol, the returning path can be shorter than the requesting path. This protocol does not need to broadcast the requested file back to the requester so that the bandwidth is saved and efficiency is improved. In addition, this protocol does not need special nodes to keep indices of sharing files, thus eliminating the index maintenance overhead and the potential for inconsistency between index records and peer file contents. We have evaluated our techniques in a browser-sharing environment. We show that the average increase in response time caused by our protocols is negligible, and these protocols show advantages over existing protocols in a P2P system.
28741459
Learning Layouts of Biological Datasets Semi-automatically
A key challenge associated with the existing approaches for data integration and workflow creation for bioinformatics is the effort required to integrate a new data source. As new data sources emerge, and data formats and contents of existing data sources evolve, wrapper programs need to be written or modified. This can be extremely time consuming, tedious, and error-prone. 
 
This paper describes our semi-automatic approach for learning the layout of a flat-file bioinformatics dataset. Our approach involves three key steps. The first step is to use a number of heuristics to infer the delimiters used in the program. Specifically, we have developed a metric that uses information on the frequency and starting position of sequences. Based on this metric, we are able to find a superset of delimiters, and then we can seek user input to eliminate the incorrect ones. Our second step involves generating a layout descriptor based on the relative order in which the delimiters occur. Our final step is to generate a parser based on the layout descriptor. Our heuristics for finding the delimiters has been evaluated using three popular flat-file biological datasets.