Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes

<b>Method:</b> Dynamic Bayesian networks (DBNs) have been applied widely to reconstruct the structure of regulatory processes from time series data, and they have established themselves as a standard modelling tool in computational systems biology. The conventional approach is based on the assumption of a homogeneous Markov chain, and many recent research efforts have focused on relaxing this restriction. An approach that enjoys particular popularity is based on a combination of a DBN with a multiple changepoint process, and the application of a Bayesian inference scheme via reversible jump Markov chain Monte Carlo (RJMCMC). In the present article, we expand this approach in two ways. First, we show that a dynamic programming scheme allows the changepoints to be sampled from the correct conditional distribution, which results in improved convergence over RJMCMC. Second, we introduce a novel Bayesian clustering and information sharing scheme among nodes, which provides a mechanism for automatic model complexity tuning. <b>Results:</b> We evaluate the dynamic programming scheme on expression time series for Arabidopsis thaliana genes involved in circadian regulation. In a simulation study we demonstrate that the regularization scheme improves the network reconstruction accuracy over that obtained with recently proposed inhomogeneous DBNs. For gene expression profiles from a synthetically designed Saccharomyces cerevisiae strain under switching carbon metabolism we show that the combination of both: dynamic programming and regularization yields an inference procedure that outperforms two alternative established network reconstruction methods from the biology literature

Stability analysis of the Witten black hole (cigar soliton) under world-sheet RG flow

We analyze the stability of the Euclidean Witten black hole (the cigar soliton in mathematics literature) under first-order RG (Ricci) flow of the world-sheet sigma model. This analysis is from the target space point of view. We find that the Witten black hole has no unstable normalizable perturbative modes in a linearized mode analysis in which we consider circularly symmetric perturbations. Finally, we discuss a result from mathematics that implies the existence of a non-normalizable mode of the Witten black hole under which the geometry flows to the sausage solution studied by Fateev, Onofri and Zamolodchikov.Comment: 17 pages, version to appear in Physical Review D, and now has complete proof of stability for circularly symmetric perturbations, in response to referee comment

Tripartite Graph Clustering for Dynamic Sentiment Analysis on Social Media

The growing popularity of social media (e.g, Twitter) allows users to easily share information with each other and influence others by expressing their own sentiments on various subjects. In this work, we propose an unsupervised \emph{tri-clustering} framework, which analyzes both user-level and tweet-level sentiments through co-clustering of a tripartite graph. A compelling feature of the proposed framework is that the quality of sentiment clustering of tweets, users, and features can be mutually improved by joint clustering. We further investigate the evolution of user-level sentiments and latent feature vectors in an online framework and devise an efficient online algorithm to sequentially update the clustering of tweets, users and features with newly arrived data. The online framework not only provides better quality of both dynamic user-level and tweet-level sentiment analysis, but also improves the computational and storage efficiency. We verified the effectiveness and efficiency of the proposed approaches on the November 2012 California ballot Twitter data.Comment: A short version is in Proceeding of the 2014 ACM SIGMOD International Conference on Management of dat

Competing Ground States in Triple-layered Sr4Ru3O10: Verging on Itinerant Ferromagnetism with Critical Fluctuations

Sr4Ru3O10 is characterized by a sharp metamagnetic transition and ferromagnetic behavior occurring within the basal plane and along the c-axis, respectively. Resistivity at magnetic field, B, exhibits low-frequency quantum oscillations when B||c-axis and large magnetoresistivity accompanied by critical fluctuations driven by the metamagnetism when B^c-axis. The complex behavior evidenced in resistivity, magnetization and specific heat presented is not characteristic of any obvious ground states, and points to an exotic state that shows a delicate balance between fluctuations and order.Comment: 18 pages, 4 figure

The Performance of CRTNT Fluorescence Light Detector for Sub-EeV Cosmic Ray Observation

Cosmic Ray Tau Neutrino Telescopes (CRTNT) using for sub-EeV cosmic ray measurement is discussed. Performances of a stereoscope configuration with a tower of those telescopes plus two side-triggers are studied. This is done by using a detailed detector simulation driven by Corsika. Detector aperture as a function of shower energy above 10^17 eV is calculated. Event rate of about 20k per year for the second knee measurement is estimated. Event rate for cross calibration with detectors working on higher energy range is also estimated. Different configurations of the detectors are tried for optimization.Comment: 5 pages, 4 figures, submitted to HEP & N

Generalized r-matrix structure and algebro-geometric solution for integrable systems

The purpose of this paper is to construct a generalized r-matrix structure of finite dimensional systems and an approach to obtain the algebro-geometric solutions of integrable nonlinear evolution equations (NLEEs). Our starting point is a generalized Lax matrix instead of usual Lax pair. The generalized r-matrix structure and Hamiltonian functions are presented on the basis of fundamental Poisson bracket. It can be clearly seen that various nonlinear constrained (c-) and restricted (r-) systems, such as the c-AKNS, c-MKdV, c-Toda, r-Toda, c-Levi, etc, are derived from the reduction of this structure. All these nonlinear systems have {\it r}-matrices, and are completely integrable in Liouville's sense. Furthermore, our generalized structure is developed to become an approach to obtain the algebro-geometric solutions of integrable NLEEs. Finally, the two typical examples are considered to illustrate this approach: the infinite or periodic Toda lattice equation and the AKNS equation with the condition of decay at infinity or periodic boundary.Comment: 41 pages, 0 figure