Optimization and Parallelization of a Time Series Classification Algorithm

This technical report describes the steps taken to optimize and parallelize a time series classification algorithm as part of an Extended Collaborative Support Services (ECSS) project with XSEDE researcher Ramon Huerta at the University of California, San Diego. Switching from the GNU compiler to the Intel compiler and enabling Advanced Vector Extensions (AVX) resulted in a 2x speedup, while linking to the Intel Math Kernel Library (MKL) instead of the default LAPACK library further improved performance and provided an easy path to thread-level parallel execution. These changes resulted in a combined 46x speedup relative to a single core when running on all 16 cores of a dual-socket Intel Sandy Bridge node. Parallelization of several loops using OpenMP directives and the removal of an unnecessary duplicate call to a computationally demanding routine brought the total speedup to 86x. Optimization of linear algebra operations using time-space tradeoffs ultimately resulted in a total speedup of 168x relative to the original version and build of the code.National Science Foundation OCI-1053575Ope

Network cosmology

Prediction and control of the dynamics of complex networks is a central problem in network science. Structural and dynamical similarities of different real networks suggest that some universal laws might accurately describe the dynamics of these networks, albeit the nature and common origin of such laws remain elusive. Here we show that the causal network representing the large-scale structure of spacetime in our accelerating universe is a power-law graph with strong clustering, similar to many complex networks such as the Internet, social, or biological networks. We prove that this structural similarity is a consequence of the asymptotic equivalence between the large-scale growth dynamics of complex networks and causal networks. This equivalence suggests that unexpectedly similar laws govern the dynamics of complex networks and spacetime in the universe, with implications to network science and cosmology

Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation

BACKGROUND: Activation of naïve B lymphocytes by extracellular ligands, e.g. antigen, lipopolysaccharide (LPS) and CD40 ligand, induces a combination of common and ligand-specific phenotypic changes through complex signal transduction pathways. For example, although all three of these ligands induce proliferation, only stimulation through the B cell antigen receptor (BCR) induces apoptosis in resting splenic B cells. In order to define the common and unique biological responses to ligand stimulation, we compared the gene expression changes induced in normal primary B cells by a panel of ligands using cDNA microarrays and a statistical approach, CLASSIFI (Cluster Assignment for Biological Inference), which identifies significant co-clustering of genes with similar Gene Ontology™ annotation. RESULTS: CLASSIFI analysis revealed an overrepresentation of genes involved in ion and vesicle transport, including multiple components of the proton pump, in the BCR-specific gene cluster, suggesting that activation of antigen processing and presentation pathways is a major biological response to antigen receptor stimulation. Proton pump components that were not included in the initial microarray data set were also upregulated in response to BCR stimulation in follow up experiments. MHC Class II expression was found to be maintained specifically in response to BCR stimulation. Furthermore, ligand-specific internalization of the BCR, a first step in B cell antigen processing and presentation, was demonstrated. CONCLUSION: These observations provide experimental validation of the computational approach implemented in CLASSIFI, demonstrating that CLASSIFI-based gene expression cluster analysis is an effective data mining tool to identify biological processes that correlate with the experimental conditional variables. Furthermore, this analysis has identified at least thirty-eight candidate components of the B cell antigen processing and presentation pathway and sets the stage for future studies focused on a better understanding of the components involved in and unique to B cell antigen processing and presentation

A tale of two symmetrons: rules for construction of icosahedral capsids from trisymmetrons and pentasymmetrons.

The capsids of large, icosahedral dsDNA viruses are built from well-ordered aggregates of capsomers, known as trisymmetrons and pentasymmetrons, which are centered on the icosahedral 3-fold and 5-fold axes, respectively. We derive the complete set of rules for constructing an icosahedral structure from these symmetrons when the T lattice symmetry is odd and show that there are three classes of solutions, each of which follows from a different relationship between the size of the pentasymmetron and the values of the h and k icosahedral lattice parameters. Together, these three classes account for all possible ways of building an icosahedral structure solely from trisymmetrons and pentasymmetrons. Also, every icosahedral lattice with odd T number has solutions from exactly two of these three classes, with the set of allowed classes dependent on which of the two lattice parameters is odd. For symmetric lattices (if h=k or h=0), the two solutions yield the same symmetron sizes, but when the lattice parameters are equal (h=k) the solutions can be distinguished by the relative orientations of the symmetrons. We discuss these results in the context of known virus structures and explore the implications for viruses whose structures have not yet been solved

Computer Simulation of Random Sequential Adsorption of 2 Interacting Species on a Lattice

A computer-simulation model is introduced to study the variation in the coverage and porosity in a binary system by random sequential adsorption on a periodic square lattice. We study the effects of the range of the repulsive interaction between unlike species and of the probability of deposition of each particle type. For all choices of the interaction range there is a minimum in the total coverage of the lattice which occurs for equal deposition probability of the two species. The saturation coverage decreases on increasing the range of the interaction. For proper choices of the parameters of the model, regimes exist in which either pores or particles of one type form an infinite percolating network

A Real-Time 3D Reconstruction System for Screening Icosahedral Particles Under Different Conditions at the Microscope.

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013

A Real-Time 3D Reconstruction System for Screening Icosahedral Particles Under Different Conditions at the Microscope.

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013