ADPfusion
generalized Algebraic Dynamic Programming Homepage
Ideas implemented here are described in a couple of papers:
 Christian Hoener zu Siederdissen
Sneaking Around ConcatMap: Efficient Combinators for Dynamic Programming
2012, Proceedings of the 17th ACM SIGPLAN international conference on Functional programming
paper preprint  Andrew Farmer, Christian Höner zu Siederdissen, and Andy Gill.
The HERMIT in the stream: fusing stream fusion’s concatMap
2014, Proceedings of the ACM SIGPLAN 2014 workshop on Partial evaluation and program manipulation.
paper  Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler.
Product Grammars for Alignment and Folding
2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics. 99
paper  Christian Höner zu Siederdissen, Sonja J. Prohaska, and Peter F. Stadler
Algebraic Dynamic Programming over General Data Structures
2015, BMC Bioinformatics
preprint  Maik Riechert, Christian Höner zu Siederdissen, and Peter F. Stadler
Algebraic dynamic programming for multiple contextfree languages
2015, submitted
preprint
Introduction
ADPfusion combines streamfusion (using the stream interface provided by the vector library) and typelevel programming to provide highly efficient dynamic programming combinators.
From the programmers' viewpoint, ADPfusion behaves very much like the original ADP implementation http://bibiserv.techfak.unibielefeld.de/adp/ developed by Robert Giegerich and colleagues, though both combinator semantics and backtracking are different.
The library internals, however, are designed not only to speed up ADP by a large margin (which this library does), but also to provide further runtime improvements by allowing the programmer to switch over to other kinds of data structures with better time and space behaviour. Most importantly, dynamic programming tables can be strict, removing indirections present in lazy, boxed tables.
As an example, even rather complex ADP code tends to be completely optimized to loops that use only unboxed variables (Int# and others, indexIntArray# and others).
Completely novel (compared to ADP), is the idea of allowing efficient monadic combinators. This facilitates writing code that performs backtracking, or samples structures stochastically, among others things.
Installation
Follow the gADP examples.
Implementors Notes (if you want to extend ADPfusion)

The general inlining scheme is: (i) mkStream is {# INLINE mkStream #}, inner functions like mk, step, worker functions, and indexmodifying functions get an {# INLINE [0] funName #}. Where there is no function to annotate, use delay_inline.

If you implement a new kind of memoizing table, like the dense Table.Array ones, you will have to implement mkStream code. When you hand to the left, the (i,j) indices and modify their extend (by, say, having NonEmpty table constaints), you have to delay_inline this (until inliner phase 0). Otherwise you will break fusion for mkStream.

Terminals that capture both, say indexing functions, and data should have no strictness annotations for the indexing function. This allows the code to be duplicated, then inlined. This improves performance a lot, because otherwise a function is created that performs these lookups, which has serious (50% slower or so) performance implications.
Contact
Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany
choener@bioinf.unileipzig.de
http://www.bioinf.unileipzig.de/~choener/