2642244
CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays
SUMMARY
To increase compatibility between different generations of Affymetrix GeneChip arrays, we propose a method of filtering probes based on their sequences. Our method is implemented as a web-based service for downloading necessary materials for converting the raw data files (*.CEL) for comparative analysis. The user can specify the appropriate level of filtering by setting the criteria for the minimum overlap length between probe sequences and the minimum number of usable probe pairs per probe set. Our website supports a within-species comparison for human and mouse GeneChip arrays.


AVAILABILITY
http://www.crosschip.org
9400771
Identification of biochemical networks by S-tree based genetic programming
MOTIVATION
Most previous approaches to model biochemical networks have focused either on the characterization of a network structure with a number of components or on the estimation of kinetic parameters of a network with a relatively small number of components. For system-level understanding, however, we should examine both the interactions among the components and the dynamic behaviors of the components. A key obstacle to this simultaneous identification of the structure and parameters is the lack of data compared with the relatively large number of parameters to be estimated. Hence, there are many plausible networks for the given data, but most of them are not likely to exist in the real system.


RESULTS
We propose a new representation named S-trees for both the structural and dynamical modeling of a biochemical network within a unified scheme. We further present S-tree based genetic programming to identify the structure of a biochemical network and to estimate the corresponding parameter values at the same time. While other evolutionary algorithms require additional techniques for sparse structure identification, our approach can automatically assemble the sparse primitives of a biochemical network in an efficient way. We evaluate our algorithm on the dynamic profiles of an artificial genetic network. In 20 trials for four settings, we obtain the true structure and their relative squared errors are <5% regardless of releasing constraints about structural sparseness. In addition, we confirm that the proposed algorithm is robust within +/-10% noise ratio. Furthermore, the proposed approach ensures a reasonable estimate of a real yeast fermentation pathway. The comparatively less important connections with non-zero parameters can be detected even though their orders are below 10(-2). To demonstrate the usefulness of the proposed algorithm for real experimental biological data, we provide an additional example on the transcriptional network of SOS response to DNA damage in Escherichia coli. We confirm that the proposed algorithm can successfully identify the true structure except only one relation.
7763980
Bayesian Network Learning with Feature Abstraction for Gene-drug Dependency Analysis
Combined analysis of the microarray and drug-activity datasets has the potential of revealing valuable knowledge about various relations among gene expressions and drug activities in the malignant cell. In this paper, we apply Bayesian networks, a tool for compact representation of the joint probability distribution, to such analysis. For the alleviation of data dimensionality problem, the huge datasets were condensed using a feature abstraction technique. The proposed analysis method was applied to the NCI60 dataset (http://discover.nci.nih.gov) consisting of gene expression profiles and drug activity patterns on human cancer cell lines. The Bayesian networks, learned from the condensed dataset, identified most of the salient pairwise correlations and some known relationships among several features in the original dataset, confirming the effectiveness of the proposed feature abstraction method. Also, a survey of the recent literature confirms the several relationships appearing in the learned Bayesian network to be biologically meaningful.
10593169
ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs
ProMiR is a web-based service for the prediction of potential microRNAs (miRNAs) in a query sequence of 60–150 nt, using a probabilistic colearning model. Identification of miRNAs requires a computational method to predict clustered and nonclustered, conserved and nonconserved miRNAs in various species. Here we present an improved version of ProMiR for identifying new clusters near known or unknown miRNAs. This new version, ProMiR II, integrates additional evidence, such as free energy data, G/C ratio, conservation score and entropy of candidate sequences, for more controllable prediction of miRNAs in mouse and human genomes. It also provides a wider range of services, e.g. the prediction of miRNA genes in long nonrelated sequences such as viral genomes. Importantly, we have validated this method using several case studies. All data used in ProMiR II are structured in the MySQL database for efficient analysis. The ProMiR II web server is available at .
15657776
Link fusion: a unified link analysis framework for multi-type interrelated data objects
Web link analysis has proven to be a significant enhancement for quality based web search. Most existing links can be classified into two categories: intra-type links (e.g., web hyperlinks), which represent the relationship of data objects within a homogeneous data type (web pages), and inter-type links (e.g., user browsing log) which represent the relationship of data objects across different data types (users and web pages). Unfortunately, most link analysis research only considers one type of link. In this paper, we propose a unified link analysis framework, called "link fusion", which considers both the inter- and intra- type link structure among multiple-type inter-related data objects and brings order to objects in each data type at the same time. The PageRank and HITS algorithms are shown to be special cases of our unified link analysis framework. Experiments on an instantiation of the framework that makes use of the user data and web pages extracted from a proxy log show that our proposed algorithm could improve the search effectiveness over the HITS and DirectHit algorithms by 24.6% and 38.2% respectively.
2491447
Unsupervised image segmentation using local homogeneity analysis
In this paper, a novel method is presented for unsupervised image segmentation based on local homogeneity analysis. First, a criterion for homogeneity of a certain pattern is proposed. Applying the criterion to local windows in the original image results in the "H-image". The high and low values of the H-image correspond to possible region boundaries and region interiors respectively. Then, a region growing method is used to segment the image based on the H-image. Finally, visually similar regions are merged together to avoid over-segmentation. Experimental results on real images show the effectiveness and robustness of the method.
8791084
Collecting the internet AS-level topology
At the inter-domain level, the Internet topology can be represented by a graph with Autonomous Systems (ASes) as nodes and AS peerings as links. This AS-level topology graph has been widely used in a variety of research efforts. Conventionally this topology graph is derived from routing tables collected by Route Views or RIPE RIS. In this work, we assemble the most complete AS-level topology by extending the conventional method along two dimensions. First, in addition to using data from RouteViews and RIPE RIS, we also collect data from many other sources, including route servers, looking glasses, and routing registries. Second, in addition to using routing tables, we also accumulate topological information from routing updates over time. The resulting topology graph on a recent day contains 44% more links and 3% more nodes than that from using RouteViews routing tables alone. Our data collection and topology generation process have been automated, and we publish the latest topology on the web on a daily basis.
36699108
New Results for Global Exponential Stability of Delayed Cohen-Grossberg Neural Networks
The exponential stability is discussed for Cohen-Grossberg neural networks with discrete delays. Without assuming the boundedness, differentiability and monotonicity of the activation functions, the nonlinear measure approach is employed to analyze the existence and uniqueness of an equilibrium, and a novel Lyapunov functional is constructed to investigate the exponential stability of the networks. New general sufficient conditions, which are independent of the delays, are derived for the global exponential stability of the delayed neural networks.
1876424
A Similarity Reinforcement Algorithm for Heterogeneous Web Pages
Many machine learning and data mining algorithms crucially rely on the similarity metrics. However, most early research works such as Vector Space Model or Latent Semantic Index only used single relationship to measure the similarity of data objects. In this paper, we first use an Intra- and Inter- Type Relationship Matrix (IITRM) to represent a set of heterogeneous data objects and their inter-relationships. Then, we propose a novel similarity-calculating algorithm over the Inter- and Intra- Type Relationship Matrix. It tries to integrate information from heterogeneous sources to serve their purposes by iteratively computing. This algorithm can help detect latent relationships among heterogeneous data objects. Our new algorithm is based on the intuition that the intra-relationship should affect the inter-relationship, and vice versa. Experimental results on the MSN logs dataset show that our algorithm outperforms the traditional Cosine similarity.