17965840
Novel Approaches to Biomolecular Sequence Indexing
In many biomolecular database applications involving string/sequence data, it is common to have similarity search in the form of near neighbor queries or nearest neighbor queries. The similarity between strings/sequences are typically measured in terms of the least costly set of allowed edit operations that transform one string/sequence to another. In this survey, we briefly describe some of the recent developments in biomolecular sequence indexing methods that allow efficient similarity search. Our focus here is on global similarity measures that compare sequences in full; such measures are important for comparing protein sequences and smaller biomolecules. Examples include character and block edit distances and their weighted variants. Two major approaches are summarized here: distance based indexing and embeddings of general sequence similarity measures to Hamming distance, for which efficient indexing methods are available.
2396831
Mining coherent patterns from heterogeneous microarray data
Microarray technology is a powerful tool for geneticists to monitor interactions among tens of thousands of genes simultaneously. There has been extensive research on coherent subspace clustering of gene expressions measured under consistent experimental settings. However, these methods assume that all experiments are run using the same batch of microarray chips with similar characteristics of noise. Algorithms developed under this assumption may not be applicable for analyzing data collected from heterogeneous settings, where the set of genes being monitored may be different and expression levels may be not directly comparable even for the same gene. In this paper, we propose a model, F-cluster, for mining subspace coherent patterns from heterogeneous gene expression data. We compare our model with previously proposed models. We analyze the search space of the problem and give a naïve solution for it.
3577423
Locating faulty code using failure-inducing chops
Software debugging is the process of locating and correcting faulty code. Prior techniques to locate faulty code either use program analysis techniques such as backward dynamic program slicing or exclusively use delta debugging to analyze the state changes during program execution. In this paper, we present a new approach that integrates the potential of delta debugging algorithm with the benefit of forward and backward dynamic program slicing to narrow down the search for faulty code. Our approach is to use delta debugging algorithm to identify a minimal failure-inducing input, use this input to compute a forward dynamic slice and then intersect the statements in this forward dynamic slice with the statements in the backward dynamic slice of the erroneous output to compute a failure-inducing chop. We implemented our technique and conducted experiments with faulty versions of several programs from the Siemens suite to evaluate our technique. Our experiments show that failure-inducing chops can greatly reduce the size of search space compared to the dynamic slices without significantly compromising the capability to locate the faulty code. We also applied our technique to several programs with known memory related bugs such as buffer overflow bugs. The failure-inducing chop in several of these cases contained only 2 to 4 statements which included the code causing memory corruption.
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.
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.
14579845
Texture image retrieval based on a Gaussian mixture model and similarity measure using a Kullback divergence
In a content-based image retrieval (CBIR) system, indexing feature vectors and the similarity measure between feature vectors are two key factors for retrieval performance. We present a new CBIR system with statistical-model based image feature extraction in the wavelet domain and a Kullback divergence based similarity measure. A two component Gaussian mixture model (GMM) in the wavelet domain is employed and the model parameters are used to form features for image indexing. A new Kullback divergence based similarity measure is then presented for image retrieval. The experimental results demonstrate that the similarity measure based on the Kullback divergence is more effective than conventional similarity measures, such as the city-block distance and the Euclidean distance. It is shown that the new CBIR system, with the combination of the GMM and the new Kullback divergence based similarity measure, outperforms most other methods in retrieval performance for texture images, while keeping a comparable level of computational complexity.
8448018
Efficient Frequent Pattern Mining on Web Logs
Mining frequent patterns from Web logs is an important data mining task. Candidate-generation-and-test and pattern-growth are two representative frequent pattern mining approaches. We have conducted extensive experiments on real world Web log data to analyse the characteristics of Web logs and the behaviours of these two approaches on Web logs. To improve the performance of current algorithms on mining Web logs, we propose a new algorithm – Combined Frequent Pattern Mining (CFPM) to cater for Web log data specifically. We use heuristics to prune search space and reduce costs in mining so that better efficiency is achieved. Experimental results show that CFPM significantly improves the performance of the pattern-growth approach by 1.2–7.8 times on mining frequent patterns from Web logs.