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Hyperpath Heuristic Enumeration Algorithm Results Availability

Shortest hyperpath heuristic

Spencer Krieger and John Kececioglu
January, 2021

Overview

Our fast heuristic is the first available method for the shortest source-sink hyperpath problem in general directed hypergraphs (which is NP-complete), where hyperedges have arbitrary tail and head sets, and the length of a hyperpath is the sum of the weights of its hyperedges. Our heuristic always finds an s,t-hyperpath if one exists and appropriately handles cycles. While the heuristic is not guaranteed to find a shortest s,t-hyperpath in general, our results show it quickly finds a hyperpath that is optimal on over 99% of real-world instances.

The heuristic proceeds similarly to Dijkstra's algorithm for finding shortest paths in ordinary graphs, but with several key differences. Our heap is composed of hyperedges e, which are prioritized by the length of the shortest known hyperpath from s to e. Computing the length of this shortest s,e-hyperpath is also NP-complete, so we use a greedy heuristic to compute approximate shortest s,e-hyperpaths.


Source code

The hyperpath heuristic source code is available on GitHub.


Videos

The following video was presented at WABI 2020 and gives more detailed information on the heuristic:
A shorter version was presented at SCS 2021:
Terms of Use
The hyperpaths source code is free for noncommercial use, and comes with neither warranty nor guarantee. The hyperpaths source code cannot be redistributed in any form without consent of the authors. If you wish to use the hyperpaths source code for commercial purpose, you must first obtain the permission from all authors. All noteworthy uses of the hyperpaths source code should cite the related paper.

Citation
Noteworthy uses of the hyperpath heuristic or hyperpath enumeration algorithm source code should cite the following publication: Spencer Krieger and John Kececioglu, “Heuristic shortest hyperpaths in cell signaling hypergraphs,” Algorithms for Molecular Biology, vol. 17, no. 1, p. 12, 2022. link

Funding
Research supported by the US National Science Foundation through grants IIS-2041613 and CCF-1617192.

Other hypergraph algorithms
Check out our other research on hypergraph algorithms for pathway inference here.

Contact
Spencer Krieger
skrieger@arizona.edu

Department of Computer Science
University of Arizona
754 Gould-Simpson
1040 E. 4th Street
Tucson, AZ 85721, USA

Last Updated: 2022-01-16 15:28:31 -0700