BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Jiang Du, Joel S. Rozowsky, Jan O. Korbel, Zhengdong D. Zhang, Thomas E. Royce, ...
doi:10.1093/bioinformatics/btl515 A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating...
Jiang Du, Joel S. Rozowsky, Jan O. Korbel, Zhengdong D. Zhang, Thomas E. Royce, Martin H. Schultz, ...
Motivation: Large-scale tiling array experiments are becoming increasingly common in genomics. In particular, the ENCODE project requires the consistent segmentation of many different tiling array...
Craig C. Douglas, Sachit Malhotra, Martin H. Schultz
Alternating Direction Implicit (ADI) methods are very good smoothers for multigrid. Like multigrid itself, ADI propagates information very quickly across a grid. On parallel processors, ADI is very...
Optimal Block Diagonal Scaling of Block 2-Cyclic Matrices. (2005)
Eisenstat,Stanley C., Lewis,John W., Schultz,Martin H.
In this paper, we describe a class of optimal block diagonal scalings (preconditionings) of a symmetric positive definite block 2-cyclic matrix, generalizing a result of Forsythe and Strauss (1) for...
Alternating Direction Methods on Multiprocessors. (2002)
Johnsson,S. L., Saad,Youcef, Schultz,Martin H.
This document proposes a few implementation of the Alternating Direction Method for solving parabolic partial differential equations on multiprocessors. A careful complexity analysis of these...
Data Communication in Hypercubes. (2002)
Saad,Youcef, Schultz,Martin H.
In this paper we consider several algorithms for exchanging data among processors in a hypercube network. The data transfer problems considered are those arising from classical numerical algorithms...
Parallel Implementations of Preconditioned Conjugate Gradient Methods. (2002)
Saad,Youcef, Schultz,Martin H.
This document considers a few different implementations of classical iterative methods on parallel processors with the purpose of studying how multiprocessor architecture affects performance. The...
Data Communication in Parallel Architectures. (2002)
Saad, Youcef, Schultz, Martin H.
In this paper we consider different methods for exchanging data among processors in parallel computers. The most common data exchange operations in parallel numerical methods are examined and...
Solving Schroedinger's Equation on the Intel iPSC by the Alternating Direction Method. (2002)
Saied,Faisal, Ho,Ching-Tien, Johnsson,S. L., Schultz,Martin H.
Ths document considers the numerical solution of the time dependent, two dimensional Schrodinger's equation and investigate several different algorithms for implementing the Alternating Direction...
Solving Schroedinger's Equation on the Intel iPSC by the Alternating Direction Method, (2002)
Saied,Faisal, Ho,Ching-Tien, Johnson,S. L., Schultz,Martin H.
This document considers the numerical solution of the Schroedinger's equation and investigate several different algorithms for implementing the Alternating Direction Method on hypercubes. The author...
Variational Iterative Methods for Nonsymmetric Systems of Linear Equations. (1998)
Eisenstat,Stanley C., Elman,Howard C., Schultz,Martin H.
We consider a class of interative algorithms for solving systems of linear equations where the coefficient matrix is nonsymmetric with positive-definite symmetric part. The algorithms are modelled...
Algorithms and Data Structures for Sparse Symmetric Gaussian Elimination, (1998)
Eisenstat,Stanley C., Schultz,Martin H., Sherman,Andrew H.
Prepared in cooperation with Texas Univ. at Austin. Dept. of Computer Science.
An Efficient Method for Solving the Three-Dimensional Wide Angle Wave Equation, (1998)
Lee, Ding, Saad, Youcef, Schultz, Martin H.
The authors propose a new method for the solution of the wide angle wave equation in three dimensions. In contrast with standard techniques, our approach requires only solutions of successive...
Fast Algorithms for Parallel Architectures. (1998)
Our work on Fast Algorithms for Parallel Architectures led us to investigate methods for computing all eigenvalues and eigen vectors of a summetric tridiagonal matrix on a distributed-memory MIMD...
Parallel Multigrid with ADI-like Smoothers in Two Dimensions (1998)
Craig C. Douglas, Sachit Malhotra, Martin H. Schultz
. Alternating direction iterative (ADI) methods do not usually work well on parallel computers due to having to do parallel rather than serial tridiagonal solves in all but one dimension. An ADI-like...
Parallel Multigrid with ADI-like Smoothers in Two Dimensions (1998)
Craig Douglas, Sachit Malhotra, Martin H. Schultz
. Alternating direction iterative (ADI) methods do not usually work well on parallel computers due to having to do parallel rather than serial tridiagonal solves in all but one dimension. An ADI-like...
B. Gosh, Bhaskar Ghosh, S. Muthukrishnan, Martin H. Schultz
) Bhaskar Ghosh S. Muthukrishnan y Martin H. Schultz z Informix Software Inc. U. Warwick Yale U. Abstract We consider the following general problem modeling load balancing in a variety of distributed...
Parallel multigrid with ADIlike smoothers in two dimensions (1998)
Craig C. Douglas, Sachit Malhotra, Martin H. Schultz
Abstract. Alternating direction iterative (ADI) methods do not usually work well on parallel computers due to having to do parallel rather than serial tridiagonal solves in all but one dimension. An...
High Performance Computer Models in Computational Acoustics. (1997)
Resasco, Diana C., Schultz, Martin H.
The long term goals of this project is to develop accurate models and efficient algorithms for the numerical solution of wave propagation problems for Navy applications.
Craig C. Douglas, Sachit Malhotra, Martin H. Schultz
. Many problems based on unstructured grids provide a natural multigrid framework due to using an adaptive gridding procedure. When the grids are saved, even starting from just a fine grid problem...
Craig C. Douglas, Sachit Malhotra, Martin H. Schultz
Many problems based on unstructured grids provide a natural multigrid framework due to using an adaptive gridding procedure. When the grids are saved, even starting from just a ne grid problem poses...
Faster Schedules for Diffusive Load Balancing via Over-Relaxation (1995)
Bhaskar Ghosh, S. Muthukrishnan, Martin H. Schultz
Consider the following load balancing problem. We are given a graph with arbitrary topology and an arbitrary load distribution on the nodes. In each time step, a node can send any amount of load to...
Temporal Domain Parallelism: Does It Work? (1993)
Ashish Deshpande, Sachit Malhotra, Martin H. Schultz, Craig Douglas, Craig C. Douglas, Martin H
. Time dependent partial differential equations are often solved using algorithms which parallelize the solution process in the spatial domain. However, as the number of processors increases, the...
Parallel Programming Systems For Workstation Clusters (1993)
Craig C. Douglas, Timothy G. Mattson, MARTIN H. SCHULTZ
. In this paper, we describe experiments comparing the communication times for a number of different network programming environments on isolated 2 and 4 node workstation networks. In addition to...