An Efficient O(n log n) Algorithm for Sorting Signed Permutations by Reversals

Grunnleggende konsepter

This article presents the first algorithm that runs in O(n log n) time in the worst case for the Signed Sorting by Reversals problem, which transforms a signed permutation into the identity permutation using a minimum-length sequence of reversals.

Sammendrag

The article presents an efficient algorithm for the Signed Sorting by Reversals problem, which involves transforming a signed permutation into the identity permutation using a minimum-length sequence of reversals.

The key highlights and insights are:

1. The algorithm runs in O(n log n) time in the worst case, improving upon the previous best algorithm with a running time of O(n log^2 n/ log log n).
2. The algorithm is relatively simple to implement and has low hidden constants.
3. The algorithm is based on a binary search tree data structure that efficiently maintains the state of the permutation and its components through each reversal.
4. The algorithm uses a recovery scheme to handle cases where no good reversal is available, by backtracking and inserting new good reversals at appropriate points.
5. The article provides a thorough theoretical analysis of the algorithm's correctness and efficiency, building upon previous work by Tannier et al.

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A Simple and Efficient Algorithm for Sorting Signed Permutations by Reversals

by Krister M. S... klokken arxiv.org 04-01-2024

https://arxiv.org/pdf/2403.20165.pdf

Dypere Spørsmål

What are the potential applications of this efficient Signed Sorting by Reversals algorithm beyond genome rearrangement problems

The efficient Signed Sorting by Reversals algorithm has potential applications beyond genome rearrangement problems. One possible application is in the field of data compression. By representing data as permutations and using the algorithm to find the minimum sequence of reversals to sort them, data can be compressed efficiently. This can be particularly useful in scenarios where data needs to be stored or transmitted in a compressed format, such as in large-scale data storage systems or network communication protocols.

How could the algorithm be further optimized or adapted to handle additional constraints or variations of the problem

To further optimize or adapt the algorithm to handle additional constraints or variations of the problem, several approaches can be considered. One option is to incorporate parallel processing techniques to speed up the computation of the reversal sequences. By dividing the task into smaller subproblems and processing them simultaneously on multiple processors or cores, the overall runtime of the algorithm can be reduced significantly. Additionally, exploring different data structures or algorithms for maintaining the extremal values and subsets of eligible elements could lead to further improvements in efficiency and scalability.

What are the implications of the O(n log n) running time for the likely lower bound of the problem, and how does this relate to the computational complexity of genome rearrangement problems in general

The O(n log n) running time of the algorithm has important implications for the likely lower bound of the problem. The fact that the algorithm achieves a runtime of O(n log n) suggests that it is close to the optimal efficiency for solving the Signed Sorting by Reversals problem. This is significant in the context of genome rearrangement problems, as it indicates that the algorithm is highly efficient and capable of handling large-scale genomic data with minimal computational overhead. The computational complexity of genome rearrangement problems in general is a critical factor in understanding the evolutionary processes and genetic variations within species, making the efficient algorithm a valuable tool for genomic research and analysis.