The multiple sequence alignment problem in biology
SIAM Journal on Applied Mathematics
Speeding up dynamic programming algorithms for finding optimal lattice paths
SIAM Journal on Applied Mathematics
Complexity analysis admissible heuristic search
AAAI '98/IAAI '98 Proceedings of the fifteenth national/tenth conference on Artificial intelligence/Innovative applications of artificial intelligence
A linear space algorithm for computing maximal common subsequences
Communications of the ACM
Sokoban: enhancing general single-agent search methods using domain knowledge
Artificial Intelligence - Special issue on heuristic search in artificial intelligence
A Divide and Conquer Bidirectional Search: First Results
IJCAI '99 Proceedings of the Sixteenth International Joint Conference on Artificial Intelligence
Recent Progress in the Design and Analysis of Admissible Heuristic Functions
Proceedings of the Seventeenth National Conference on Artificial Intelligence and Twelfth Conference on Innovative Applications of Artificial Intelligence
A* with Partial Expansion for Large Branching Factor Problems
Proceedings of the Seventeenth National Conference on Artificial Intelligence and Twelfth Conference on Innovative Applications of Artificial Intelligence
Divide-and-Conquer Frontier Search Applied to Optimal Sequence Alignment
Proceedings of the Seventeenth National Conference on Artificial Intelligence and Twelfth Conference on Innovative Applications of Artificial Intelligence
Hierarchical A *: searching abstraction hierarchies efficiently
AAAI'96 Proceedings of the thirteenth national conference on Artificial intelligence - Volume 1
Duality in permutation state spaces and the dual search algorithm
Artificial Intelligence
Space-efficient memory-based heuristics
AAAI'04 Proceedings of the 19th national conference on Artifical intelligence
Sequential and parallel algorithms for frontier A* with delayed duplicate detection
AAAI'06 proceedings of the 21st national conference on Artificial intelligence - Volume 2
External-memory pattern databases using structured duplicate detection
AAAI'05 Proceedings of the 20th national conference on Artificial intelligence - Volume 3
An improved search algorithm for optimal multiple-sequence alignment
Journal of Artificial Intelligence Research
Journal of Artificial Intelligence Research
Comparing best-first search and dynamic programming for optimal multiple sequence alignment
IJCAI'03 Proceedings of the 18th international joint conference on Artificial intelligence
IJCAI'03 Proceedings of the 18th international joint conference on Artificial intelligence
FAHR: focused A* heuristic recomputation
IROS'09 Proceedings of the 2009 IEEE/RSJ international conference on Intelligent robots and systems
Predicting the performance of IDA* using conditional distributions
Journal of Artificial Intelligence Research
Inconsistent heuristics in theory and practice
Artificial Intelligence
Solving the 24 puzzle with instance dependent pattern databases
SARA'05 Proceedings of the 6th international conference on Abstraction, Reformulation and Approximation
Vectorized algorithms for quadtree construction and descent
ICA3PP'12 Proceedings of the 12th international conference on Algorithms and Architectures for Parallel Processing - Volume Part I
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The time and space needs of an A* search are strongly influenced by the quality of the heuristic evaluation function. Usually there is a trade-off since better heuristics may require more time and/or space to evaluate. Multiple sequence alignment is an important application for single-agent search. The traditional heuristic uses multiple pairwise alignments that require relatively little space. Three-way alignments produce better heuristics, but they are not used in practice due to the large space requirements. This paper presents a memory-efficient way to represent three-way heuristics as an octree. The required portions of the octree are computed on demand. The octree-supported three-way heuristics result in such a substantial reduction to the size of the A* open list that they offset the additional space and time requirements for the three-way alignments. The resulting multiple sequence alignments are both faster and use less memory than using A* with traditional pairwise heuristics.