17413518
Enhancing the Effectiveness of Clustering with Spectra Analysis
For many clustering algorithms, such as K-Means, EM, and CLOPE, there is usually a requirement to set some parameters. Often, these parameters directly or indirectly control the number of clusters, that is, k, to return. In the presence of different data characteristics and analysis contexts, it is often difficult for the user to estimate the number of clusters in the data set. This is especially true in text collections such as Web documents, images, or biological data. In an effort to improve the effectiveness of clustering, we seek the answer to a fundamental question: How can we effectively estimate the number of clusters in a given data set? We propose an efficient method based on spectra analysis of eigenvalues (not eigenvectors) of the data set as the solution to the above. We first present the relationship between a data set and its underlying spectra with theoretical and experimental results. We then show how our method is capable of suggesting a range of k that is well suited to different analysis contexts. Finally, we conclude with further empirical results to show how the answer to this fundamental question enhances the clustering process for large text collections.
41398857
BIRD: Biomedical Information Integration and Discovery with Semantic Web Services
Biomedical research is now information intensive; the volume and diversity of new data sources challenges current database technologies. The development and tuning of database technologies for biology and medicine will maintain and accelerate the current pace for innovation and discovery. New promising application fields such as the Semantic Web and Semantic Web Services can leverage the potential of biomedical information integration and discovery, facing the problem of semantic heterogeneity of biomedical information sources in a variety of storage and data formats widely distributed both across the Internet and within individual organizations. In this paper, we present BIRD, a fully-fledged biomedical information integration solution that combines natural language analysis and semantically-empowered techniques to ascertain how the user needs can be best fit. Our approach is backed with a proof-of-concept implementation where the breakthrough and efficiency of integrating the biomedical publications database PubMed, the Database of Interacting Proteins (DIP) and the Munich Information Center for Protein Sequences (MIPS) has been tested.
15077137
Modeling nonlinearity in dilution design microarray data
MOTIVATION
Dilution design (Mixed tissue RNA) has been utilized by some researchers to evaluate and assess the performance of multiple microarray platforms. Current microarray data analysis approaches assume that the quantified signal intensities are linearly related to the expression of the corresponding genes in the sample. However, there are sources of nonlinearity in microarray expression measurements. Such nonlinearity study in the expressions of the RNA mixtures provides a new way to analyze gene expression data, and we argue that the nonlinearity can reveal novel information for microarray data analysis. Therefore, we proposed a statistical model, called proportion model, which is based on the linear regression analysis. To approximately quantify the nonlinearity in the dilution design, a new calibration, beta ratio (BR) was derived from the proportion model. Furthermore, a new adjusted fold change (adj-FC) was proposed to predict the true FC without nonlinearity, in particular for large FC.


RESULTS
We applied our method to one microarray dilution dataset. The experimental results indicated that, to some extent, there are global biases comparing with the linear assumption for the significant genes. Further analysis of those highly expressed genes with significant nonlinearity revealed some promising results, e.g. 'poison' effect was discovered for some genes in RNA mixtures. The adj-FCs of those genes with 'poison' effect, indicate that the nonlinearity can be also caused by the inherent feature of the genes besides signal noise and technical variation. Moreover, when percentage of overlapping genes (POG) was used as a cross-platform consistency measure, adj-FC outperformed simple fold change to show that Affymetrix and Illumina platforms are consistent.


AVAILABILITY
The R codes which implements all described methods, and some Supplementary material, are freely available from http://www.utdallas.edu/~ying.liu/BetaRatio.htm
5940493
Efficient schema design for a pharmaceutical data repository
Large scientific databases often consist of heterogeneous components that differ in the number of attributes and the number of tuples. In this paper, we show that increased performance is achieved when a complex schema is used to represent different components of a data repository. The driving application used in this study is a pharmaceutical drug repository. The types of access patterns associated with this repository consist of the retrieval of a selected set of attribute values for a consecutive or a random set of tuples. These consecutive and random access patterns, which are typical of a drug discovery experiment, are used to measure the data retrieval throughput for different schemas.
14379760
Protein Quaternary Fold Recognition Using Conditional Graphical Models
Protein fold recognition is a crucial step in inferring biological structure and function. This paper focuses on machine learning methods for predicting quaternary structural folds, which consist of multiple protein chains that form chemical bonds among side chains to reach a structurally stable domain. The complexity associated with modeling the quaternary fold poses major theoretical and computational challenges to current machine learning methods. We propose methods to address these challenges and show how (1) domain knowledge is encoded and utilized to characterize structural properties using segmentation conditional graphical models; and (2) model complexity is handled through efficient inference algorithms. Our model follows a discriminative approach so that any informative features, such as those representative of overlapping or long-range interactions, can be used conveniently. The model is applied to predict two important quaternary folds, the triple β-spirals and double-barrel trimers. Cross-family validation shows that our method outperforms other state-of-the art algorithms.
8217950
Evolutionary ensembles with negative correlation learning
Based on negative correlation learning and evolutionary learning, this paper presents evolutionary ensembles with negative correlation learning (EENCL) to address the issues of automatic determination of the number of individual neural networks (NNs) in an ensemble and the exploitation of the interaction between individual NN design and combination. The idea of EENCL is to encourage different individual NNs in the ensemble to learn different parts or aspects of the training data so that the ensemble can learn better the entire training data. The cooperation and specialization among different individual NNs are considered during the individual NN design. This provides an opportunity for different NNs to interact with each other and to specialize. Experiments on two real-world problems demonstrate that EENCL can produce NN ensembles with good generalization ability.
11535936
Efficient implementation of tuple pattern based retrieval
Tuple pattern based retrieval is a language construct that matches a tuple pattern against a set of tuples to retrieve components of those tuples. This high-level abstraction allows programs to be written more easily and clearly than otherwise. This paper describes a clean and automatic method for transforming tuple pattern based retrievals into efficient implementations. The paper also presents two systems that implement the method, and describes successful experience and experiments in generating efficient implementations for graph algorithms, program analysis, security, and other applications.
15838270
Eliminating Dead Code on Recursive Data
This paper describes a general and powerful method for dead code analysis and elimination in the presence of recursive data constructions. We represent partially dead recursive data using liveness patterns based on general regular tree grammars extended with the notion of live and dead, and we formulate the analysis as computing liveness patterns at all program points based on program semantics. This analysis yields a most precise liveness pattern for the data at each program point, which is significantly more precise than results from previous methods. The analysis algorithm takes cubic time in terms of the size of the program in the worst case but is very efficient in practice, as shown by our prototype implementation. The analysis results are used to identify and eliminate dead code. The general framework for representing and analyzing properties of recursive data structures using general regular tree grammars applies to other analyses as well.