45,524 research outputs found
Fast matrix multiplication techniques based on the Adleman-Lipton model
On distributed memory electronic computers, the implementation and
association of fast parallel matrix multiplication algorithms has yielded
astounding results and insights. In this discourse, we use the tools of
molecular biology to demonstrate the theoretical encoding of Strassen's fast
matrix multiplication algorithm with DNA based on an -moduli set in the
residue number system, thereby demonstrating the viability of computational
mathematics with DNA. As a result, a general scalable implementation of this
model in the DNA computing paradigm is presented and can be generalized to the
application of \emph{all} fast matrix multiplication algorithms on a DNA
computer. We also discuss the practical capabilities and issues of this
scalable implementation. Fast methods of matrix computations with DNA are
important because they also allow for the efficient implementation of other
algorithms (i.e. inversion, computing determinants, and graph theory) with DNA.Comment: To appear in the International Journal of Computer Engineering
Research. Minor changes made to make the preprint as similar as possible to
the published versio
Scalable Task-Based Algorithm for Multiplication of Block-Rank-Sparse Matrices
A task-based formulation of Scalable Universal Matrix Multiplication
Algorithm (SUMMA), a popular algorithm for matrix multiplication (MM), is
applied to the multiplication of hierarchy-free, rank-structured matrices that
appear in the domain of quantum chemistry (QC). The novel features of our
formulation are: (1) concurrent scheduling of multiple SUMMA iterations, and
(2) fine-grained task-based composition. These features make it tolerant of the
load imbalance due to the irregular matrix structure and eliminate all
artifactual sources of global synchronization.Scalability of iterative
computation of square-root inverse of block-rank-sparse QC matrices is
demonstrated; for full-rank (dense) matrices the performance of our SUMMA
formulation usually exceeds that of the state-of-the-art dense MM
implementations (ScaLAPACK and Cyclops Tensor Framework).Comment: 8 pages, 6 figures, accepted to IA3 2015. arXiv admin note: text
overlap with arXiv:1504.0504
Improving the numerical stability of fast matrix multiplication
Fast algorithms for matrix multiplication, namely those that perform
asymptotically fewer scalar operations than the classical algorithm, have been
considered primarily of theoretical interest. Apart from Strassen's original
algorithm, few fast algorithms have been efficiently implemented or used in
practical applications. However, there exist many practical alternatives to
Strassen's algorithm with varying performance and numerical properties. Fast
algorithms are known to be numerically stable, but because their error bounds
are slightly weaker than the classical algorithm, they are not used even in
cases where they provide a performance benefit.
We argue in this paper that the numerical sacrifice of fast algorithms,
particularly for the typical use cases of practical algorithms, is not
prohibitive, and we explore ways to improve the accuracy both theoretically and
empirically. The numerical accuracy of fast matrix multiplication depends on
properties of the algorithm and of the input matrices, and we consider both
contributions independently. We generalize and tighten previous error analyses
of fast algorithms and compare their properties. We discuss algorithmic
techniques for improving the error guarantees from two perspectives:
manipulating the algorithms, and reducing input anomalies by various forms of
diagonal scaling. Finally, we benchmark performance and demonstrate our
improved numerical accuracy
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