Stochastic dynamic modeling of short gene expression time-series data

Copyright [2008] IEEE. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Brunel University's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to [email protected]. By choosing to view this document, you agree to all provisions of the copyright laws protecting it.In this paper, the expectation maximization (EM) algorithm is applied for modeling the gene regulatory network from gene time-series data. The gene regulatory network is viewed as a stochastic dynamic model, which consists of the noisy gene measurement from microarray and the gene regulation first-order autoregressive (AR) stochastic dynamic process. By using the EM algorithm, both the model parameters and the actual values of the gene expression levels can be identified simultaneously. Moreover, the algorithm can deal with the sparse parameter identification and the noisy data in an efficient way. It is also shown that the EM algorithm can handle the microarray gene expression data with large number of variables but a small number of observations. The gene expression stochastic dynamic models for four real-world gene expression data sets are constructed to demonstrate the advantages of the introduced algorithm. Several indices are proposed to evaluate the models of inferred gene regulatory networks, and the relevant biological properties are discussed

Microwave Remote Sensing of Ocean Surface Wind Speed and Rain Rates over Tropical Storms

The value of using narrowly spaced frequencies within a microwave band to measure wind speeds and rain rates over tropical storms with radiometers is reviewed. The technique focuses on results obtained in the overflights of Hurricane Allen during 5 and 8 of August, 1980

Multi-membership gene regulation in pathway based microarray analysis

This article is available through the Brunel Open Access Publishing Fund. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowledge in a holistic analytical approach. We propose a methodology that can be facilitated for pathway based microarray data analysis, based on the observation that a substantial proportion of genes present in biochemical pathway databases are members of a number of distinct pathways. Our methodology aims towards establishing the state of individual pathways, by identifying those truly affected by the experimental conditions based on the behaviour of such genes. For that purpose it considers all the pathways in which a gene participates and the general census of gene expression per pathway. Results: We utilise hill climbing, simulated annealing and a genetic algorithm to analyse the consistency of the produced results, through the application of fuzzy adjusted rand indexes and hamming distance. All algorithms produce highly consistent genes to pathways allocations, revealing the contribution of genes to pathway functionality, in agreement with current pathway state visualisation techniques, with the simulated annealing search proving slightly superior in terms of efficiency. Conclusions: We show that the expression values of genes, which are members of a number of biochemical pathways or modules, are the net effect of the contribution of each gene to these biochemical processes. We show that by manipulating the pathway and module contribution of such genes to follow underlying trends we can interpret microarray results centred on the behaviour of these genes.The work was sponsored by the studentship scheme of the School of Information Systems, Computing and Mathematics, Brunel Universit

DFM synthesis approach based on product-process interface modelling. Application to the peen forming process.

Engineering design approach are curently CAD-centred design process. Manufacturing information is selected and assessed very late in the design process and above all as a reactive task instead of being proactive to lead the design choices. DFM appraoches are therefore assesment methods that compare several design alternatives and not real design approaches at all. Main added value of this research work concerns the use of a product-process interface model to jointly manage both the product and the manufacturing data in a proactive DFM way. The DFM synthesis approach and the interface model are presented via the description of the DFM software platform

Spatial Persistence of Fluctuating Interfaces

We show that the probability, P_0(l), that the height of a fluctuating (d+1)-dimensional interface in its steady state stays above its initial value up to a distance l, along any linear cut in the d-dimensional space, decays as P_0(l) \sim l^(-\theta). Here \theta is a `spatial' persistence exponent, and takes different values, \theta_s or \theta_0, depending on how the point from which l is measured is specified. While \theta_s is related to fractional Brownian motion, and can be determined exactly, \theta_0 is non-trivial even for Gaussian interfaces.Comment: 5 pages, new material adde

Ground state numerical study of the three-dimensional random field Ising model

The random field Ising model in three dimensions with Gaussian random fields is studied at zero temperature for system sizes up to 60^3. For each realization of the normalized random fields, the strength of the random field, Delta and a uniform external, H is adjusted to find the finite-size critical point. The finite-size critical point is identified as the point in the H-Delta plane where three degenerate ground states have the largest discontinuities in the magnetization. The discontinuities in the magnetization and bond energy between these ground states are used to calculate the magnetization and specific heat critical exponents and both exponents are found to be near zero.Comment: 10 pages, 6 figures; new references and small changes to tex

RICE Limits on the Diffuse Ultra-High Energy Neutrino Flux

We present new limits on ultra-high energy neutrino fluxes above 100 PeV based on data collected by the Radio Ice Cherenkov Experiment (RICE) at the South Pole from 1999-2005. We discuss estimation of backgrounds, calibration and data analysis algorithms (both on-line and off-line), procedures used for the dedicated neutrino search, and refinements in our Monte Carlo (MC) simulation, including recent in situ measurements of the complex ice dielectric constant. An enlarged data set and a more detailed study of hadronic showers results in a sensitivity improvement of more than one order of magnitude compared to our previously published results. Examination of the full RICE data set yields zero acceptable neutrino candidates, resulting in 95% confidence-level model dependent limits on the flux (E_\nu)^2(d\phi/dE_\nu)<10^{-6} GeV/(cm^2s~sr}) in the energy range 10^{17}< E_\nu< 10^{20} eV. The new RICE results rule out the most intense flux model projections at 95% confidence level.Comment: Submitted to Astropart. Phy

DBR-free semiconductor disc laser on SiC heatspreader emitting 10.1 W at 1007 nm

We report a distributed Bragg reflector-free semiconductor disc laser which emits 10 W continuous wave output power at a wavelength of 1007 nm when pumped with 40 W at 808 nm, focused into a 230 μm diameter spot on the gain chip. By introducing a birefringent filter plate in the laser cavity the wavelength could be tuned from 995 to 1020 nm. The laser consisted of a gain chip located at the beam waist of a linear concentric resonator with an output coupling of 2.15%. The gain chip consists of a 1.574-μm-thick resonant periodic gain structure, with ten In0.13Ga0.87As quantum wells embedded in strain-compensating GaAs0.94P0.06 barrier layers, van der Waals bonded to a silicon carbide intra-cavity heat spreader.</p

Understanding Collateral Evolution in Linux Device Drivers

In a modern operating system (OS), device drivers can make up over 70% of the source code. Driver code is also heavily dependent on the rest of the OS, for functions and data structure defined in the kernel and driver support libraries. These two properties together pose a significant problem for OS evolution, as any changes in the interfaces exported by the kernel and driver support libraries can trigger a large number of adjustments in dependent drivers. These adjustments, which we refer to as collateral evolutions, may be complex, entailing substantial code reorganizations. Collateral evolution of device drivers is thus time consuming and error prone. In this paper, we present a qualitative and quantitative assessment of the collateral evolution problem in Linux device driver code. We provide a taxonomy of evolutions and collateral evolutions, and show that from one version of Linux to the next, collateral evolutions can account for up to 35% of the lines modified in such code. We then identify some of the challenges that must be met in the future to automate the collateral evolution process

Exploiting Term Hiding to Reduce Run-time Checking Overhead

One of the most attractive features of untyped languages is the flexibility in term creation and manipulation. However, with such power comes the responsibility of ensuring the correctness of these operations. A solution is adding run-time checks to the program via assertions, but this can introduce overheads that are in many cases impractical. While static analysis can greatly reduce such overheads, the gains depend strongly on the quality of the information inferred. Reusable libraries, i.e., library modules that are pre-compiled independently of the client, pose special challenges in this context. We propose a technique which takes advantage of module systems which can hide a selected set of functor symbols to significantly enrich the shape information that can be inferred for reusable libraries, as well as an improved run-time checking approach that leverages the proposed mechanisms to achieve large reductions in overhead, closer to those of static languages, even in the reusable-library context. While the approach is general and system-independent, we present it for concreteness in the context of the Ciao assertion language and combined static/dynamic checking framework. Our method maintains the full expressiveness of the assertion language in this context. In contrast to other approaches it does not introduce the need to switch the language to a (static) type system, which is known to change the semantics in languages like Prolog. We also study the approach experimentally and evaluate the overhead reduction achieved in the run-time checks.Comment: 26 pages, 10 figures, 2 tables; an extension of the paper version accepted to PADL'18 (includes proofs, extra figures and examples omitted due to space reasons