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ItemVirus Quasispecies Assembly using Network Flows(Georgia Institute of Technology, 2009-09-25) Zelikovsky, AlexanderUnderstanding how the genomes of viruses mutate and evolve within infected individuals is critically important in epidemiology. In this talk I focus on optimization problems in sequence assembly for viruses based on 454 Lifesciences system. Several formulations of the quasispecies assembly problem and a measure of the assembly quality will be given. I will describe a scalable assembling method for quasispecies based on network flow and maximum likelihood formulations and then give details of existing and novel methods for reliably assembling quasipsecies that have very long common segments. Finally, I report the results of assembling 44 quasispecies from the 1700 bp long E1E2 region of Hepatitis C Virus.
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ItemMulti-Scale Protein Modeling and Cellular Automata : Two Opportunities for Collaboration(Georgia Institute of Technology, 2009-09-18) Leamy, Michael J.This talk will discuss two M&S research directions being pursued by the speaker in the GWW School of Mechanical Engineering. Both approaches are explicit and time-marching in nature, and should therefore be amenable to parallelization strategies (and thus collaboration). The first part of the talk will detail a multi-scale physics-based modeling approach for simulating protein dynamics. The multi-scale continuum formulation to be described uses an intrinsic continuum formulation, and subsequent finite element discretization, informed by interatomic potentials (commonly found in molecular dynamics simulations). In the current context, intrinsic refers to a description of the protein's configuration using curvatures and strains vice displacements and rotations. The advantage of doing so is that highly-curved and twisted geometries associated with proteins in their native conformation can be accurately modeled with a sparse discretization. This positively impacts the degrees of freedom required, and more importantly, the time step required for stability. The second part of the talk will discuss a Cellular Automata (CA)-based approach for simulating elastic wave propagation in structures. By generalizing the cell shape to triangles, it will be shown that the approach has the same utility as the structural finite element method, with a number of advantages. First, code development is greatly simplified and fits naturally with modern, object-oriented languages. Second, all interactions are local and thus the method avoids the need for a central authority, easing parallelization. Third, the discontinuous nature of the state representation appears to be responsible for more-accurate wavefront modeling than traditional finite element approaches. Similar treatments are expected to perform as well with electromagnetic wave propagation, and could potentially be event-driven.
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ItemAn analytical GPU performance model and a dynamic compilation system for CPU/GPU systems(Georgia Institute of Technology, 2009-09-11) Kim, Hyesoon
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ItemOpen challenges in shape and animation processing(Georgia Institute of Technology, 2009-08-28) Rossignac, JarekJarek Rossignac (IC, http://www.gvu.gatech.edu/~jarek/) will present an overview of his recent research activities (with collaborators and students) and open challenges in shape and animation processing. These include: - SOT: Compact representation of tetrahedral meshes - J-splines: C^4 subdivision curves, surfaces, and animation - SAM: Steady interpolating affine motion - OCTOR: Exceptions in steady patterns - Pearling: Realtime segmentation of tubular structures in images and 3D medical scans - Surgem: Heart surgery planning and optimization based on blood flow simulation - APL: Aquatic Propulsion Lab, tools for designing and simulating swimming strategies - Ball map: Tangent-ball correspondence and compatibility between pairs of shapes - Ball-morph: Interpolation and applications to entertainment and medical surface reconstruction.
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ItemBlocked Plane Rotations for Band Reduction and Sparse SVD(Georgia Institute of Technology, 2009-08-26) Rajamanickam, SivaWith the success of Basic Linear Algebra Subroutines (BLAS) in using the memory efficiently, the algorithms with vector operations (BLAS2) have given way to algorithms with matrix operations (BLAS3). In some cases, BLAS3 based algorithms are successful even with the cost of doing additional floating point operations and using additional memory. In this talk, I will talk about two problems where algorithms with vector operations when combined with blocking can perform better than BLAS3 based algorithms. Band reduction methods are mainly used in computing the eigen value decomposition and singular value decomposition of band matrices. In the first part of this talk, I will outline a blocking scheme for plane rotations. The blocked plane rotations when coupled with a pipelining scheme leads to fewer floating point operations and memory usage than the BLAS3 based band reduction methods. The blocked method is also able to extract the same performance benefits from the cache as the BLAS3 based methods leading to a faster band reduction method. I will also show how we can exploit the zeros while finding the eigen and singular vectors. In the second part of the talk, I will introduce a method for computing the bidiagonalization of a sparse upper triangular matrix R. In this method, we exploit the sparsity of R and use plane rotations to reduce it to the bidiagonal form. We choose the rotations to minimize the fill generated in R itself. I will show how to extend this method to use dynamic blocking and the pipelining scheme to arrive at an efficient R-bidiagonalization method for computing the sparse SVD.
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ItemDependable direct solutions for linear systems using a little extra precision(Georgia Institute of Technology, 2009-08-21) Riedy, E. JasonSolving a square linear system Ax=b often is considered a black box. It's supposed to "just work," and failures often are blamed on the original data or subtleties of floating-point. Now that we have an abundance of cheap computations, however, we can do much better. A little extra precision in just the right places produces accurate solutions cheaply or demonstrates when problems are too hard to solve without significant cost. This talk will outline the method, iterative refinement with a new twist; the benefits, small backward and forward errors; and the trade-offs and unexpected benefits.
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ItemMatrix algorithms for data clustering and nonlinear dimension reduction(Georgia Institute of Technology, 2008-10-03) Zha, Hongyuan ; Zhang, Ming
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ItemWhat Can We Do with a Multitude of Genome Sequences?(Georgia Institute of Technology, 2008-02-06) Tompa, MartinThere are currently 575 bacterial species and 28 vertebrate species, ranging from primates to fishes, for which we know (nearly) their entire DNA sequences. These number will continue to increase rapidly over the next few years. Comparing these genome sequences has emerged as one of the most important areas of computational biology. For example, one way to predict functional portions of the human genome is to search among related genomes for sequences that appear to be remarkably similar due to selective pressure. I will discuss and demonstrate some of the methods and tools for such an approach, as well as some of the challenges and unsolved problems. This talk will be self-contained: no knowledge of biology beyond what you have heard in the news will be assumed.
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Item100 Years of Digital Data(Georgia Institute of Technology, 2008-01-23) Berman, FrancineThe Information Age has brought with it a deluge of digital data. Current estimates are that in 2006, 161 exabytes (10¹⁸ bytes) of digital data were created from cell phones, computers, iPods, DVDs, sensors, satellites, scientific instruments, and other sources, providing a foundation for our digital world. Migrating digital content through new generations of storage media, making sense of its content, and ensuring that needed information is accessible now and for the foreseeable future constitute some of the most critical challenges of the Information Age. The San Diego Supercomputer Center (SDSC) is leading the development and deployment of a comprehensive infrastructure for managing, storing, preserving, and using digital data. In this talk, Berman discusses SDSC's approach to building and deploying data-oriented computational and data cyberinfrastructure, and describes the next generation of challenges and opportunities for the data that drives the Information Age.
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ItemWorkshop on Future Direction in Numerical Algorithms and Optimization(Georgia Institute of Technology, 2008-01-15) Park, Haesun ; Golub, Gene ; Wu, Weili ; Du, Ding-Zhu