Gains in Power from Structured Two-Sample Tests of Means on Graphs

We consider multivariate two-sample tests of means, where the location shift between the two populations is expected to be related to a known graph structure. An important application of such tests is the detection of differentially expressed genes between two patient populations, as shifts in expression levels are expected to be coherent with the structure of graphs reflecting gene properties such as biological process, molecular function, regulation, or metabolism. For a fixed graph of interest, we demonstrate that accounting for graph structure can yield more powerful tests under the assumption of smooth distribution shift on the graph. We also investigate the identification of non-homogeneous subgraphs of a given large graph, which poses both computational and multiple testing problems. The relevance and benefits of the proposed approach are illustrated on synthetic data and on breast cancer gene expression data analyzed in context of KEGG pathways

Realising context-sensitive mobile messaging

Mobile technologies aim to assist people as they move from place to place going about their daily work and social routines. Established and very popular mobile technologies include short-text messages and multimedia messages with newer growing technologies including Bluetooth mobile data transfer protocols and mobile web access.Here we present new work which combines all of the above technologies to fulfil some of the predictions for future context aware messaging. We present a context sensitive mobile messaging system which derives context in the form of physical locations through location sensing and the co-location of people through Bluetooth familiarity

FELIX A full acceptance detector at the LHC

The FELIX collaboration has proposed the construction of a full acceptance detector for the LHC, to be located at Intersection Region 4, and to be commissioned concurrently with the LHC. The primary mission of FELIX is QCD: to provide comprehensive and definitive observations of a very broad range of strong-interaction processes. This paper reviews the detector concept and performance characteristics, the physics menu, and plans for integration of FELIX into the collider lattice and physical environment. The current status of the FELIX Letter of Intent is discussed.Comment: 11 pages, 7 figures. To be published in "Proceedings of the XXVII International Symposium on Multiparticle Dynamics, Frascati (Rome), Italy 8-12 Sept. 1997 (Nuclear Physics B, Proceedings Supplement)

The Solar Orbiter mission and its prospects for helioseismology

Solar Orbiter is intended to become ESA's next solar mission in heritage of the successful SOHO project. The scientific objectives of the mission, its design, and its scientific payload are reviewed. Specific emphasis is given to the perspectives of Solar Orbiter with respect to helioseismology.Comment: 6 pages, 4 figure

Fast MCMC sampling for Markov jump processes and extensions

Markov jump processes (or continuous-time Markov chains) are a simple and important class of continuous-time dynamical systems. In this paper, we tackle the problem of simulating from the posterior distribution over paths in these models, given partial and noisy observations. Our approach is an auxiliary variable Gibbs sampler, and is based on the idea of uniformization. This sets up a Markov chain over paths by alternately sampling a finite set of virtual jump times given the current path and then sampling a new path given the set of extant and virtual jump times using a standard hidden Markov model forward filtering-backward sampling algorithm. Our method is exact and does not involve approximations like time-discretization. We demonstrate how our sampler extends naturally to MJP-based models like Markov-modulated Poisson processes and continuous-time Bayesian networks and show significant computational benefits over state-of-the-art MCMC samplers for these models.Comment: Accepted at the Journal of Machine Learning Research (JMLR

A comprehensive overview of genomic imprinting in breast and its deregulation in cancer

Genomic imprinting plays an important role in growth and development. Loss of imprinting (LOI) has been found in cancer, yet systematic studies are impeded by data-analytical challenges. We developed a methodology to detect monoallelically expressed loci without requiring genotyping data, and applied it on The Cancer Genome Atlas (TCGA, discovery) and Genotype-Tissue expression project (GTEx, validation) breast tissue RNA-seq data. Here, we report the identification of 30 putatively imprinted genes in breast. In breast cancer (TCGA), HM13 is featured by LOI and expression upregulation, which is linked to DNA demethylation. Other imprinted genes typically demonstrate lower expression in cancer, often associated with copy number variation and aberrant DNA methylation. Downregulation in cancer frequently leads to higher relative expression of the (imperfectly) silenced allele, yet this is not considered canonical LOI given the lack of (absolute) re-expression. In summary, our novel methodology highlights the massive deregulation of imprinting in breast cancer