Application of new probabilistic graphical models in the genetic regulatory networks studies

This paper introduces two new probabilistic graphical models for reconstruction of genetic regulatory networks using DNA microarray data. One is an Independence Graph (IG) model with either a forward or a backward search algorithm and the other one is a Gaussian Network (GN) model with a novel greedy search method. The performances of both models were evaluated on four MAPK pathways in yeast and three simulated data sets. Generally, an IG model provides a sparse graph but a GN model produces a dense graph where more information about gene-gene interactions is preserved. Additionally, we found two key limitations in the prediction of genetic regulatory networks using DNA microarray data, the first is the sufficiency of sample size and the second is the complexity of network structures may not be captured without additional data at the protein level. Those limitations are present in all prediction methods which used only DNA microarray data.Comment: 38 pages, 3 figure

Joint QoS multicast routing and channel assignment in multiradio multichannel wireless mesh networks using intelligent computational methods

Copyright @ 2010 Elsevier B.V. All rights reserved.In this paper, the quality of service multicast routing and channel assignment (QoS-MRCA) problem is investigated. It is proved to be a NP-hard problem. Previous work separates the multicast tree construction from the channel assignment. Therefore they bear severe drawback, that is, channel assignment cannot work well with the determined multicast tree. In this paper, we integrate them together and solve it by intelligent computational methods. First, we develop a unified framework which consists of the problem formulation, the solution representation, the fitness function, and the channel assignment algorithm. Then, we propose three separate algorithms based on three representative intelligent computational methods (i.e., genetic algorithm, simulated annealing, and tabu search). These three algorithms aim to search minimum-interference multicast trees which also satisfy the end-to-end delay constraint and optimize the usage of the scarce radio network resource in wireless mesh networks. To achieve this goal, the optimization techniques based on state of the art genetic algorithm and the techniques to control the annealing process and the tabu search procedure are well developed separately. Simulation results show that the proposed three intelligent computational methods based multicast algorithms all achieve better performance in terms of both the total channel conflict and the tree cost than those comparative references.This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant EP/E060722/1

Evolutionary Approaches to Minimizing Network Coding Resources

We wish to minimize the resources used for network coding while achieving the desired throughput in a multicast scenario. We employ evolutionary approaches, based on a genetic algorithm, that avoid the computational complexity that makes the problem NP-hard. Our experiments show great improvements over the sub-optimal solutions of prior methods. Our new algorithms improve over our previously proposed algorithm in three ways. First, whereas the previous algorithm can be applied only to acyclic networks, our new method works also with networks with cycles. Second, we enrich the set of components used in the genetic algorithm, which improves the performance. Third, we develop a novel distributed framework. Combining distributed random network coding with our distributed optimization yields a network coding protocol where the resources used for coding are optimized in the setup phase by running our evolutionary algorithm at each node of the network. We demonstrate the effectiveness of our approach by carrying out simulations on a number of different sets of network topologies.Comment: 9 pages, 6 figures, accepted to the 26th Annual IEEE Conference on Computer Communications (INFOCOM 2007

Causal graphical models in systems genetics: A unified framework for joint inference of causal network and genetic architecture for correlated phenotypes

Causal inference approaches in systems genetics exploit quantitative trait loci (QTL) genotypes to infer causal relationships among phenotypes. The genetic architecture of each phenotype may be complex, and poorly estimated genetic architectures may compromise the inference of causal relationships among phenotypes. Existing methods assume QTLs are known or inferred without regard to the phenotype network structure. In this paper we develop a QTL-driven phenotype network method (QTLnet) to jointly infer a causal phenotype network and associated genetic architecture for sets of correlated phenotypes. Randomization of alleles during meiosis and the unidirectional influence of genotype on phenotype allow the inference of QTLs causal to phenotypes. Causal relationships among phenotypes can be inferred using these QTL nodes, enabling us to distinguish among phenotype networks that would otherwise be distribution equivalent. We jointly model phenotypes and QTLs using homogeneous conditional Gaussian regression models, and we derive a graphical criterion for distribution equivalence. We validate the QTLnet approach in a simulation study. Finally, we illustrate with simulated data and a real example how QTLnet can be used to infer both direct and indirect effects of QTLs and phenotypes that co-map to a genomic region.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS288 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org