Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation
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arXiv
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| Autori principali: | , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2024
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| _version_ | 1866908562328911872 |
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| author | Urata, Tsuyoshi Yokoyama, Manato Miyaji, Haruki Hayamizu, Momoko |
| author_facet | Urata, Tsuyoshi Yokoyama, Manato Miyaji, Haruki Hayamizu, Momoko |
| contents | The C-Orientation problem asks whether it is possible to orient an undirected graph to a directed phylogenetic network of a desired network class C. This problem arises, for example, when visualising evolutionary data, as popular methods such as Neighbor-Net are distance-based and inevitably produce undirected graphs. The complexity of C-Orientation remains open for many classes C, including binary tree-child networks, and practical methods are still lacking. In this paper, we propose an exact FPT algorithm for C-Orientation that is applicable to any class C and parameterised by the reticulation number and the maximum size of minimal basic cycles, and a very fast heuristic for Tree-Child Orientation. While the state-of-the-art for C-Orientation is a simple exponential time algorithm whose computational bottleneck lies in searching for appropriate reticulation vertex placements, our methods significantly reduce this search space. Experiments show that, although our FPT algorithm is still exponential, it significantly outperforms the existing method. The heuristic runs even faster but with increasing false negatives as the reticulation number grows. Given this trade-off, we also discuss theoretical directions for improvement and biological applicability of the heuristic approach. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2407_09776 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation Urata, Tsuyoshi Yokoyama, Manato Miyaji, Haruki Hayamizu, Momoko Data Structures and Algorithms 68R10 The C-Orientation problem asks whether it is possible to orient an undirected graph to a directed phylogenetic network of a desired network class C. This problem arises, for example, when visualising evolutionary data, as popular methods such as Neighbor-Net are distance-based and inevitably produce undirected graphs. The complexity of C-Orientation remains open for many classes C, including binary tree-child networks, and practical methods are still lacking. In this paper, we propose an exact FPT algorithm for C-Orientation that is applicable to any class C and parameterised by the reticulation number and the maximum size of minimal basic cycles, and a very fast heuristic for Tree-Child Orientation. While the state-of-the-art for C-Orientation is a simple exponential time algorithm whose computational bottleneck lies in searching for appropriate reticulation vertex placements, our methods significantly reduce this search space. Experiments show that, although our FPT algorithm is still exponential, it significantly outperforms the existing method. The heuristic runs even faster but with increasing false negatives as the reticulation number grows. Given this trade-off, we also discuss theoretical directions for improvement and biological applicability of the heuristic approach. |
| title | Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation |
| topic | Data Structures and Algorithms 68R10 |
| url | https://arxiv.org/abs/2407.09776 |