TFBSTools: an R/bioconductor package for transcription factor binding site analysis.

Summary: The ability to efficiently investigate transcription factor binding sites (TFBSs) genome-wide is central to computational studies of gene regulation. TFBSTools is an R/Bioconductor package for the analysis and manipulation of TFBSs and their associated transcription factor profile matrices. TFBStools provides a toolkit for handling TFBS profile matrices, scanning sequences and alignments including whole genomes, and querying the JASPAR database. The functionality of the package can be easily extended to include advanced statistical analysis, data visualization and data integration. Availability and implementation: The package is implemented in R and available under GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/TFBSTools/). Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Stochastic L-BFGS: Improved Convergence Rates and Practical Acceleration Strategies

We revisit the stochastic limited-memory BFGS (L-BFGS) algorithm. By proposing a new framework for the convergence analysis, we prove improved convergence rates and computational complexities of the stochastic L-BFGS algorithms compared to previous works. In addition, we propose several practical acceleration strategies to speed up the empirical performance of such algorithms. We also provide theoretical analyses for most of the strategies. Experiments on large-scale logistic and ridge regression problems demonstrate that our proposed strategies yield significant improvements vis-\`a-vis competing state-of-the-art algorithms

Non-equilibrium spatial distribution of Rashba spin torque in ferromagnetic metal layer

We study the spatial distribution of spin torque induced by a strong Rashba spin-orbit coupling (RSOC) in a ferromagnetic (FM) metal layer, using the Keldysh non-equilibrium Green's function method. In the presence of the s-d interaction between the non-equilibrium conduction electrons and the local magnetic moments, the RSOC effect induces a torque on the moments, which we term as the Rashba spin torque. A correlation between the Rashba spin torque and the spatial spin current is presented in this work, clearly mapping the spatial distribution of Rashba Spin torque in a nano-sized ferromagnetic device. When local magnetism is turned on, the out-of-plane (Sz) Spin Hall effect (SHE) is disrupted, but rather unexpectedly an in-plane (Sy) SHE is detected. We also study the effect of Rashba strength (\alpha_R) and splitting exchange (\Delta) on the non-equilibrium Rashba spin torque averaged over the device. Rashba spin torque allows an efficient transfer of spin momentum such that a typical switching field of 20 mT can be attained with a low current density of less than 10^6 A/cm^2