7215055
An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors
Positional DNA sequencing by hybridization (PSBH) is a recently proposed enhancement of DNA sequencing by hybridization (SBH, potentially a powerful alternative to the DNA sequencing by gel electrophoresis). It has been discussed in many papers and applied to large scale sequencing by hybridization. However, the computational part of PSBH reconstruction is a difficult problem, especially for the occurrence of hybridization errors. So far the problem has not been solved well. Taking PSBH as a combinatorial optimization problem, a novel reconstruction approach to PSBH is presented in this paper. The proposed approach accepts both the negative and positive errors and can greatly reduce ambiguities in the reconstruction of PSBH. The computational experiment shows that our algorithm works satisfactorily and correctly on the test data, especially for the positive errors and k-tuple repetitions.
14218778
Reconstruction of DNA sequencing by hybridization
MOTIVATION
It is widely recognized that the hybridization process is prone to errors and that the future of DNA sequencing by hybridization is predicated on the ability to successfully cope with such errors. However, the occurrence of hybridization errors results in the computational difficulty of the reconstruction of DNA sequencing by hybridization. The reconstruction problem of DNA sequencing by hybridization with errors is a strongly NP-hard problem. So far the problem has not been solved well.


RESULTS
In this paper, a new approach is presented to solve the reconstruction problem of DNA sequencing by hybridization, which realizes the computational part of the SBH experiment. The proposed algorithm accepts both the negative and positive errors. The computational experiments show that the algorithm behaves satisfactorily, especially for the case with k-tuple repetitions and positive errors.
12946822
Partial parallel factorization in soft-decision Reed-Solomon decoding
Reed-Solomon (RS) codes have very broad applications in communications and data storage systems. The recently developed Koetter-Vardy (KV) soft-decision decoding algorithm of RS codes can achieve substantial coding gain, while has a complexity polynomial with respect to the codeword length. One of the major steps of the KV algorithm is the factorization step. A prediction-based architecture is developed in prior efforts to reduce the latency and silicon area of this step. However, the speedup can be achieved by this approach is limited by the serial nature of the factorization algorithm. The computations involved in multiple iteration levels can not be carried out simultaneously. In this work, a novel partial parallel architecture is proposed for the factorization step. The partial 2-parallel architecture can achieve a speedup of 19% over prior works.
1464666
Feedforward neural networks with multilevel hidden neurons for remotely sensed image classification
Artificial neural network has been, used as a powerful tool for pattern classification. However, it is difficult to train when the data exhibit non-sparse or overlapping pattern classes which is often the case in practical applications. In this paper, we introduce the feedforward neural network with the hidden layer consisting of multilevel neurons. The convergence property of one-layer neural network with multilevel neurons is proved. The new feedforward model is inherently capable of fuzzy pattern classification of non-sparse or overlapping pattern classes. As an application, we apply the network for the classification of LANDSAT TM data. The results show that this approach produces better results compared with conventional neural networks.
3393161
BIG: An agent for resource-bounded information gathering and decision making
Abstract The World Wide Web has become an invaluable information resource but the explosion of available information has made Web search a time consuming and complex process. The large number of information sources and their different levels of accessibility, reliability and associated costs present a complex information gathering control problem. This paper describes the rationale, architecture, and implementation of a next generation information gathering system—a system that integrates several areas of Artificial Intelligence research under a single umbrella. Our solution to the information explosion is an information gathering agent, BIG, that plans to gather information to support a decision process, reasons about the resource trade-offs of different possible gathering approaches, extracts information from both unstructured and structured documents, and uses the extracted information to refine its search and processing activities.
3575990
Pruning dynamic slices with confidence
Given an incorrect value produced during a failed program run (e.g., a wrong output value or a value that causes the program to crash), the backward dynamic slice of the value very frequently captures the faulty code responsible for producing the incorrect value. Although the dynamic slice often contains only a small percentage of the statements executed during the failed program run, the dynamic slice can still be large and thus considerable effort may be required by the programmer to locate the faulty code.In this paper we develop a strategy for pruning the dynamic slice to identify a subset of statements in the dynamic slice that are likely responsible for producing the incorrect value. We observe that some of the statements used in computing the incorrect value may also have been involved in computing correct values (e.g., a value produced by a statement in the dynamic slice of the incorrect value may also have been used in computing a correct output value prior to the incorrect value). For each such executed statement in the dynamic slice, using the value profiles of the executed statements, we compute a confidence value ranging from 0 to 1 - a higher confidence value corresponds to greater likelihood that the execution of the statement produced a correct value. Given a failed run involving execution of a single error, we demonstrate that the pruning of a dynamic slice by excluding only the statements with the confidence value of 1 is highly effective in reducing the size of the dynamic slice while retaining the faulty code in the slice. Our experiments show that the number of distinct statements in a pruned dynamic slice are 1.79 to 190.57 times less than the full dynamic slice. Confidence values also prioritize the statements in the dynamic slice according to the likelihood of them being faulty. We show that examining the statements in the order of increasing confidence values is an effective strategy for reducing the effort of fault location.
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.