David Eppstein - Publications
- Speeding up dynamic programming.
29th IEEE Symp. Foundations of
Comp. Sci., White Plains, New York, 1988, pp. 488–496.
Worksh. Algorithms for Molecular Genetics, Bethesda, Maryland, 1988.
Tech. Rep. CUCS-379-88, Computer Science Dept., Columbia University, 1988.
Appeared as "Efficient algorithms with applications to molecular biology" in
Int. Advanced Workshop on Sequences, Positano, Italy, 1988.
Sequences: Combinatorics, Compression, Security, Transmission,
R. M. Capocelli, ed., Springer, 1990, pp. 59–74.
The FOCS and Positano versions of this paper merged my results
on a dynamic program used for RNA secondary structure prediction,
with Raffaele's on sequence comparison.
The Bethesda talk and the TR version both used the longer title
"Speeding up dynamic programming
with application to the computation of RNA structure", and included only
the RNA result, which
used a mild convexity assumption on certain costs
to save two orders of magnitude in total time.
This work incited a boom in computational biology within the theory
community that is still going strong.
But the RNA results were quickly improved by a log factor
[Aggarwal et al. at the same FOCS] and never made it into a journal paper.
Citations of "Efficient algorithms..." –
MIT hypertext bibliography –
- Sparse dynamic programming.
and G.F. Italiano.
1st ACM-SIAM Symp. Discrete Algorithms,
San Francisco, 1990, pp. 513–522.
"Sparse dynamic programming I: linear cost functions", J. ACM
39: 519–545, 1992.
"Sparse dynamic programming II: convex and concave cost functions", J. ACM 39: 546–567, 1992.
Considers sequence alignment and RNA structure problems
in which the solution is constructed by piecing together
some initial set of fragments (e.g. short sequences that match exactly).
The method is to consider a planar point set formed by
the fragment positions in the two input sequences,
and use plane sweep to construct a cellular decomposition of the plane
similar to the rectilinear Voronoi diagram.
Citations to conference version –
Citations to SDP I –
Citations to SDP II)
- Efficient algorithms for sequence analysis.
and G.F. Italiano.
International Advanced Workshop on
Sequences, Positano, Italy, 1991.
Sequences II: Methods in Communication, Security, and Computer Science,
R.M. Capocelli, A. De Santis, and U. Vaccaro, eds.,
Springer, 1993, pp. 225–244.
Surveys results on speeding up certain dynamic programs
used for sequence comparison and RNA structure prediction.
David Eppstein –
Theory Group –
Inf. & Comp. Sci. –
from a common source file.