FFAS server: novel features and applications.

The Fold and Function Assignment System (FFAS) server [Jaroszewski et al. (2005) FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Research, 33, W284-W288] implements the algorithm for protein profile-profile alignment introduced originally in [Rychlewski et al. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Science: a Publication of the Protein Society, 9, 232-241]. Here, we present updates, changes and novel functionality added to the server since 2005 and discuss its new applications. The sequence database used to calculate sequence profiles was enriched by adding sets of publicly available metagenomic sequences. The profile of a user's protein can now be compared with ∼20 additional profile databases, including several complete proteomes, human proteins involved in genetic diseases and a database of microbial virulence factors. A newly developed interface uses a system of tabs, allowing the user to navigate multiple results pages, and also includes novel functionality, such as a dotplot graph viewer, modeling tools, an improved 3D alignment viewer and links to the database of structural similarities. The FFAS server was also optimized for speed: running times were reduced by an order of magnitude. The FFAS server, http://ffas.godziklab.org, has no log-in requirement, albeit there is an option to register and store results in individual, password-protected directories. Source code and Linux executables for the FFAS program are available for download from the FFAS server

Maximizing the Sum Rate in Cellular Networks Using Multi-Convex Optimization

In this paper, we propose a novel algorithm to maximize the sum rate in interference-limited scenarios where each user decodes its own message with the presence of unknown interferences and noise considering the signal-to-interference-plus-noise-ratio. It is known that the problem of adapting the transmit and receive filters of the users to maximize the sum rate with a sum transmit power constraint is non-convex. Our novel approach is to formulate the sum rate maximization problem as an equivalent multi-convex optimization problem by adding two sets of auxiliary variables. An iterative algorithm which alternatingly adjusts the system variables and the auxiliary variables is proposed to solve the multi-convex optimization problem. The proposed algorithm is applied to a downlink cellular scenario consisting of several cells each of which contains a base station serving several mobile stations. We examine the two cases, with or without several half-duplex amplify-and-forward relays assisting the transmission. A sum power constraint at the base stations and a sum power constraint at the relays are assumed. Finally, we show that the proposed multi-convex formulation of the sum rate maximization problem is applicable to many other wireless systems in which the estimated data symbols are multi-affine functions of the system variables.Comment: 24 pages, 5 figure

Long-Term Measurements of Sunspot Magnetic Tilt Angles

Tilt angles of close to 30,600 sunspots are determined using Mount Wilson daily averaged magnetograms taken from 1974 to 2012, and MDI/SoHO magnetograms taken from 1996 to 2010. Within a cycle, more than 90% of sunspots have a normal polarity alignment along the east-west direction following Hale's law. The median tilts increase with increasing latitude (Joy's law) at a rate of ~0.5 degree per degree of latitude. Tilt angles of spots appear largely invariant with respect to time at a given latitude, but they decrease by ~0.9degree per year on average, a trend which largely reflects Joy's law following the butterfly diagram. We find an asymmetry between the hemispheres in the mean tilt angles. On average, the tilts are greater in the southern than in the northern hemisphere for all latitude zones, and the differences increase with increasing latitude.Comment: 29 pages, 13 figures, to appear on ApJ, October 20, 2012 website: http://www2.ess.ucla.edu/~jingli/ApJ201210

FLASH: Randomized Algorithms Accelerated over CPU-GPU for Ultra-High Dimensional Similarity Search

We present FLASH (\textbf{F}ast \textbf{L}SH \textbf{A}lgorithm for \textbf{S}imilarity search accelerated with \textbf{H}PC), a similarity search system for ultra-high dimensional datasets on a single machine, that does not require similarity computations and is tailored for high-performance computing platforms. By leveraging a LSH style randomized indexing procedure and combining it with several principled techniques, such as reservoir sampling, recent advances in one-pass minwise hashing, and count based estimations, we reduce the computational and parallelization costs of similarity search, while retaining sound theoretical guarantees. We evaluate FLASH on several real, high-dimensional datasets from different domains, including text, malicious URL, click-through prediction, social networks, etc. Our experiments shed new light on the difficulties associated with datasets having several million dimensions. Current state-of-the-art implementations either fail on the presented scale or are orders of magnitude slower than FLASH. FLASH is capable of computing an approximate k-NN graph, from scratch, over the full webspam dataset (1.3 billion nonzeros) in less than 10 seconds. Computing a full k-NN graph in less than 10 seconds on the webspam dataset, using brute-force ($n^2D$), will require at least 20 teraflops. We provide CPU and GPU implementations of FLASH for replicability of our results

Study of High Energy Heavy-Ion Collisions in a Relativistic BUU-Approach with Momentum-Dependent Mean-Fields

We introduce momentum-dependent scalar and vector fields into the Lorentz covariant relativistic BUU- (RBUU-) approach employing a polynomial ansatz for the relativistic nucleon-nucleon interaction. The momentum-dependent parametrizations are shown to be valid up to about 1 GeV/u for the empirical proton-nucleus optical potential. We perform numerical simulations for heavy-ion collisions within the RBUU-approach adopting momentum-dependent and momentum-independent mean-fields and calculate the transverse flow in and perpendicular to the reaction plane, the directivity distribution as well as subthreshold K+-production. By means of these observables we discuss the particular role of the momentum-dependent forces and their implications on the nuclear equation of state. We find that only a momentum-dependent parameter-set can explain the experimental data on the transverse flow in the reaction plane from 150 - 1000 MeV/u and the differential K+-production cross sections at 1 GeV/u at the same time.Comment: 27 pages, figures can be obtained from the authors, UGI-93-0