Combinatorial Scientific Computing:

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Combinatorial Scientific Computing

• The Role of Discrete Algorithms in
• Computational Science Engineering
• Bruce Hendrickson
• Sandia National Labs

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CS and CSE

• Whats in the intersection?

• Compilers, system software, computer
  architecture, etc.

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CS and CSE

• Combinatorial Scientific Computing

• Whats in the intersection?

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Combinatorial Scientific Computing

• Development, application and analysis of
  combinatorial algorithms to enable scientific and
  engineering computations

Theory
Practice
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Worlds Apart

• Computer Science
• Graph algorithms, set theory, complexity theory,
  etc.
• Computational Science Engineering
• Numerical analysis, PDEs, linear algebra, etc.
• Differ in many ways
• Vocabulary, concepts and abstractions
• Culture mathematics versus engineering
• Definition of success
• Aesthetics
• Not an easy divide to span!

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Sparse Direct Methods

• Reorderings for sparse factorizations
• Powerfully phrased as graph problems
• Fill reducing orderings
• Minimum degree (greedy)
• Nested dissection (divide conquer)
• Bandwidth reducing orderings
• graph traversals, graph eigenvectors
• Heavy diagonal to reduce pivoting (matching)
• Efficient exploitation of sparsity
• Factorization, triangular solves, etc.

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Graphs and sparse Gaussian elimination (1961-)
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Sparse Direct Methods

• Reorderings for sparse factorizations
• Powerfully phrased as graph problems
• Fill reducing orderings
• Minimum degree (greedy)
• Nested dissection (divide conquer)
• Bandwidth reducing orderings
• graph traversals, graph eigenvectors
• Heavy diagonal to reduce pivoting (matching)
• Efficient exploitation of sparsity
• Factorization, triangular solves, etc.

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Preconditioning

• Incomplete Factorizations
• Exploiting sparsity patterns, e.g. level-of-fill
• Orderings
• Partitioning for domain decomposition
• Graph techniques in algebraic multigrid
• Independent sets, matchings, etc.
• Support Theory
• Spanning trees graph embedding techniques

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Numerical Optimization

• Sparse Jacobian Evaluation
• Exploit sparsity to minimize function calls
• Graph coloring on column intersection graph
• Sparse basis construction
• Matroids, graph colorings, spanning trees, etc.
• Hybrid of combinatorics and numerics

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ParallelizingScientific Computations

• Graph Algorithms
• Partitioning
• Coloring
• Independent sets, etc.
• Geometric algorithms
• Space-filling curves octrees for particles
• Geometric partitioning
• Reordering for memory locality

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Parallelization Strategies

• Observation Parallelization is usually
  orthogonal to numerics
• Issues are non-numerical
• Load balancing
• Communication minimization
• Scheduling, etc.
• Almost invariably combinatorial in spirit

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Mesh Generation

• Geometric algorithms
• data structures
• Delaunay/Voronoi decompositions
• Convex hulls
• Intersection checking, etc.
• Topology of unstructured meshes
• graph algorithms

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More Mesh Generation

• Rich amalgam of mathematical ideas
• Differential geometry
• Harmonic mappings numerical PDEs
• Optimization to improve mesh quality

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Computational Biology

• Genomics
• Fragment assembly
• Sequence analysis, etc.
• Lots of string algorithms
• Proteomics
• Structural comparisons
• NMR and Mass Spec analysis
• Phylogenics
• Literature mining
• Microarray clustering analysis
• Etc, etc.

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Statistical Physics

• Ising spin models and percolation theory
• Pfaffians, permanents matching
• Very rich graph theory
• Several Nobel prizes awarded
• Other percolation models
• External fields, Connectivity, Rigidity, etc.
• Network flow and other graph algorithms

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Graphs in Chemisty

• Categorizing molecules by graph properties
• Various topological invariants, graph properties
• Used to screen molecules for desired properties
• Combinatorics of polymers
• Geometric and graph properties
• Statistically correct ensembles
• Graph enumeration and sampling

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CSE Techniques in Computer Science

• Continuous methods in discrete optimization
• Using matrix eigenvectors to understand graphs
• Approximation algorithms via linear or quadratic
  programming
• Linear algebra in information analysis
• Latent semantic indexing (SVD for info retrieval)
• Googles page ranking (eigenvector
  Perron-Frobenius)
• Kleinbergs hubs and authorities (SVD)
• Multilevel combinatorial algorithms
• Dominant paradigm for practical graph
  partitioning
• Being applied to range of combinatorial problems
• Origins in algebraic multigrid

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The Future

• Its tough to make predictions,
• especially about the future
• Yogi
  Berra
• Prediction All of the aforementioned and more.

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Info Organization, Analysis Mining

• Graph algorithms and linear algebra
• Importance ranking of documents/pages
• Information retrieval
• Publication mining is key tool in biology
• Text analysis inference
• Simulation output already overwhelming
• Learning theory
• Advanced visualization

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More Biology

• Gene promotion and inhibition
• Strings and learning theory
• Multi-atom interactions
• Protein complexes
• Regulatory networks
• Geometry, topology and graphs
• Biological systems
• Whole cell modeling
• Ecological models
• Topology and graph analysis

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Fast Algorithms for Huge Problems

• For computer science theorists, key distinction
  is between polynomial exponential time
• For scientific computing, key is often linear
  versus quadratic time

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Examples

• Approximate max-weight matching
• Monien, Preis, Diekmann, Drake, Hougardy
• Useful for partitioning
• Exact algorithm O(mn) time
• 2-approximation in O(m) time

• Extreme Case
• Can we understand anything interesting about our
  data when we do not even have time to read all of
  it? - Ronitt Rubinfeld

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Sublinear Time Algorithms

• Fast Monte Carlo algorithms for finding low-rank
  approximations to a matrix
• Frieze, Kannan, Vempala
• Find B0 such that A B0F ? minB A -
  BF e AF
• Run-time independent of size of matrix!
• Approximating weight of MST in sublinear time
• Chazelle, Rubinfeld, Trevisani
• Key idea estimate number of connected components
  in time independent of size of graph

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Elsewhere at CSE-03

• MS23/47 Combinatorial Algorithms in Scientific
  Computing
• CP8/32 Discrete Algorithms
• IP4 Computational Proteomics (Mark Gerstein)
• MS25 Computational Proteomics
• CP20 Methods for Particle Simulations
• CP26 Geometric Algorithms
• MS81 Locality in Scientific Applications
• Discrete algorithms play a role in numerous
  individual talks!

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Hard Questions

• How will combinatorial methods be used by people
  who dont understand them in detail?
• What are the implications
• for teaching?
• for software development?
• for journals?
• for professional societies?

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Morals

• Things are clearer if you look at them from
  multiple perspectives
• Combinatorial algorithms are pervasive in
  scientific computing and will become more so
• Lots of exciting opportunities
• High impact for discrete algorithms work
• Enabling for scientific computing

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Thanks

• Yogi Berra, Erik Boman, Edmond Chow, Karen
  Devine, Jean-Loup Faulon, John Gilbert, Mike
  Heath, Pat Knupp, Esmond Ng, Ali Pinar, Steve
  Plimpton, Cindy Phillips, Alex Pothen, Robert
  Preis, Padma Raghavan, Jonathan Shewchuk,
  Shang-Hua Teng, Sivan Toledo, etc.

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For More Information

• www.cs.sandia.gov/bahendr
• lists.odu.edu/listinfo/csc
• Sandia is a multiprogram laboratory operated by
  Sandia Corporation, a Lockheed-Martin Company,
  for the US DOE under contract DE-AC-94AL85000