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.
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.
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 .
5219400
Timer Interaction in Route Flap Damping
Route Flap Damping is a mechanism generally used in network routing protocols. Its goal is to limit the global impact of unstable routes by temporarily suppressing routes with rapid changes over short time periods. Although route damping is a clearly defined and simple procedure at each router, its effect in a large network setting is not well understood. We show that the current damping design leads to the intended behavior only under persistent route flapping. When the number of flaps is small, the global routing dynamics deviates significantly from the expected behavior with a longer convergence delay. Previous work observed that a single route flap can falsely trigger route suppression due to path exploration. However our simulations show that this false suppression only accounts for 30% of the convergence delay after a single route flap. Our study reveals previously unknown interactions between reuse timers at different routers. Route suppression and reuse at different routers are triggered at different times and thus affect the number of updates received by other routers. In turn, this impacts other routers' damping behavior. We propose to use Root Cause Notification to eliminate both false suppression and undesirable timer interaction
2500417
Evolutionary Induction of Sparse Neural Trees
This paper is concerned with the automatic induction of parsimonious neural networks. In contrast to other program induction situations, network induction entails parametric learning as well as structural adaptation. We present a novel representation scheme called neural trees that allows efficient learning of both network architectures and parameters by genetic search. A hybrid evolutionary method is developed for neural tree induction that combines genetic programming and the breeder genetic algorithm under the unified framework of the minimum description length principle. The method is successfully applied to the induction of higher order neural trees while still keeping the resulting structures sparse to ensure good generalization performance. Empirical results are provided on two chaotic time series prediction problems of practical interest.
8056566
Bayesian Evolutionary Optimization Using Helmholtz Machines
Recently, several evolutionary algorithms have been proposed that build and use an explicit distribution model of the population to perform optimization. One of the main issues in this class of algorithms is how to estimate the distribution of selected samples. In this paper, we present a Bayesian evolutionary algorithm (BEA) that learns the sample distribution by a probabilistic graphical model known as Helmholtz machines. Due to the generative nature and availability of the wake-sleep learning algorithm, the Helmholtz machines provide an effective tool for modeling and sampling from the distribution of selected individuals. The proposed method has been applied to a suite of GA-deceptive functions. Experimental results show that the BEA with the Helmholtz machine outperforms the simple genetic algorithm.
15099164
A scalable supervised algorithm for dimensionality reduction on streaming data
Algorithms on streaming data have attracted increasing attention in the past decade. Among them, dimensionality reduction algorithms are greatly interesting due to the desirability of real tasks. Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) are two of the most widely used dimensionality reduction approaches. However, PCA is not optimal for general classification problems because it is unsupervised and ignores valuable label information for classification. On the other hand, the performance of LDA is degraded when encountering limited available low-dimensional spaces and singularity problem. Recently, Maximum Margin Criterion (MMC) was proposed to overcome the shortcomings of PCA and LDA. Nevertheless, the original MMC algorithm could not satisfy the streaming data model to handle large-scale high-dimensional data set. Thus an effective, efficient and scalable approach is needed. In this paper, we propose a supervised incremental dimensionality reduction algorithm and its extension to infer adaptive low-dimensional spaces by optimizing the maximum margin criterion. Experimental results on a synthetic dataset and real datasets demonstrate the superior performance of our proposed algorithm on streaming data.
41094552
The Statistical Inference Method in Heuristic Search Techniques
In this paper we present a new heuristic searching algorithm by introducing statistical inference method on the basic of algorithm A*. It's called algorithm SA*. The following results have been proved. (1) Algorithm SA* in superior to algorithm A*. (2) The mean complexity of SA* is CN2, but in some case A* exhibits exponential complexity (eN). (3) In a (N,d,F)- game tree, the mean complexity of SA* is CN2, but the complexity of other known game-searching algoritham (α-β , SSS* etc.) is at least dN. (4) The maximal storage-space required by SA* is C,N. 
 
This shows that under a given significance level SA* is superior to other known algorithm (e.g. A*, B*, α-β, SSS* etc.).