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.
620811
Using data mining techniques to learn layouts of flat-file biological datasets
One of the major problems in biological data integration is that many data sources are stored as atlasses, with a variety of different layouts. Integrating data from such sources can be an extremely time-consuming task. We have been developing data mining techniques to help learn the layout of a dataset in a semi-automatic way. In this paper, we focus on the problem of identifying delimiters for optional fields. Since these fields do not occur in every record, frequency based methods are not able to identify the corresponding delimiters. We present a method which uses contrast analysis on the frequency of sequences to identify such delimiters and help complete the layout descriptions. We demonstrate the effectiveness of this technique using three atlasses biological datasets.
18526893
Scaling and parallelizing a scientific feature mining application using a cluster middleware
Summary form only given. As scientific simulations are generating large amounts of data, analyzing this data to gain insights into scientific phenomenon is increasingly becoming a challenge. We present a case study on the use of a cluster middleware for rapidly creating a scalable and parallel implementation of a scientific data analysis application. Using FREERIDE (framework for rapid implementation of data mining engines), we parallelize as well as scale to disk-resident datasets a feature extraction algorithm. We have developed a parallel algorithm for this problem which matches the communication and computation structure supported by the FREERIDE system. The main observations from our experimental results are as follows: 1) the overhead of using the middleware is quite small in most cases, 2) there is an overhead associated with breaking the datasets into more partitions or chunks, and 3) if the dataset is partitioned into the same number of chunks, the execution time stays proportional to the size of the dataset and inversely proportional to the number of nodes, i.e. the overhead of communication or reading disk-resident datasets is very small.
17630030
Prediction of Protein Complexes Based on Protein Interaction Data and Functional Annotation Data Using Kernel Methods
Prediction of protein complexes is a crucial problem in computational biology. The increasing amount of available genomic data can enhance the identification of protein complexes. Here we describe an approach for predicting protein complexes based on integration of protein-protein interaction (PPI) data and protein functional annotation data. The basic idea is that proteins in protein complexes often interact with each other and protein complexes exhibit high functional consistency/even multiple functional consistency. We create a protein-protein relationship network (PPRN) via a kernel-based integration of these two genomic data. Then we apply the MCODE algorithm on PPRN to detect network clusters as numerically determined protein complexes. We present the results of the approach to yeast Sacchromyces cerevisiae. Comparison with well-known experimentally derived complexes and results of other methods verifies the effectiveness of our approach.
5632028
On the Laplacian Spectra of Graphs
We first establish the relationship between the largest eigenvalue of the Laplacian matrix of a graph and its bipartite density. Then we present lower and upper bounds for the largest Laplacian eigenvalue of a graph in terms of its largest degree and diameter.
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.
10102756
Semi-Empirical Multiprocessor Performance Predictions
This paper presents a multiprocessor performance prediction methodology supported by experimental measurements, which predicts the execution time of large application programs on large parallel architectures based on a small set of sample data. We propose a graph model to describe application program behavior. In order to precisely abstract an architecture model for the prediction, important and implicit architecture parameters are obtained by experiments. We focus on performance predictions of application programs in shared-memory and data-parallel architectures. Real world applications are implemented using the shared-memory model on the KSR-1 and using the data-parallel model on the CM-5 for performance measurements and prediction validation. We show that experimental measurements provide strong support for performance predictions on multiprocessors with implicit communications and complex memory systems, such as shared-memory and data-parallel systems, while analytical techniques partially applied in the prediction significantly reduce computer simulation and measurement time.
17528755
Significance of Gene Ranking for Classification of Microarray Samples
Many methods for classification and gene selection with microarray data have been developed. These methods usually give a ranking of genes. Evaluating the statistical significance of the gene ranking is important for understanding the results and for further biological investigations, but this question has not been well addressed for machine learning methods in existing works. Here, we address this problem by formulating it in the framework of hypothesis testing and propose a solution based on resampling. The proposed r-test methods convert gene ranking results into position p-values to evaluate the significance of genes. The methods are tested on three real microarray data sets and three simulation data sets with support vector machines as the method of classification and gene selection. The obtained position p-values help to determine the number of genes to be selected and enable scientists to analyze selection results by sophisticated multivariate methods under the same statistical inference paradigm as for simple hypothesis testing methods