Vector encoding of phylogenetic trees by ordered leaf attachment
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arXiv
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| Auteurs principaux: | , , |
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| Format: | Preprint |
| Publié: |
2025
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| _version_ | 1866915212844597248 |
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| author | Richman, Harry Zhang, Cheng Matsen IV, Frederick A. |
| author_facet | Richman, Harry Zhang, Cheng Matsen IV, Frederick A. |
| contents | As part of work to connect phylogenetics with machine learning, there has been considerable recent interest in vector encodings of phylogenetic trees. We present a simple new "ordered leaf attachment" (OLA) method for uniquely encoding a binary, rooted phylogenetic tree topology as an integer vector. OLA encoding and decoding take linear time in the number of leaf nodes, and the set of vectors corresponding to trees is a simply-described subset of integer sequences. The OLA encoding is unique compared to other existing encodings in having these properties. The integer vector encoding induces a distance on the set of trees, and we investigate this distance in relation to the NNI and SPR distances. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2503_10169 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Vector encoding of phylogenetic trees by ordered leaf attachment Richman, Harry Zhang, Cheng Matsen IV, Frederick A. Populations and Evolution Combinatorics 92B10, 05C05, 05C85, 68W40 As part of work to connect phylogenetics with machine learning, there has been considerable recent interest in vector encodings of phylogenetic trees. We present a simple new "ordered leaf attachment" (OLA) method for uniquely encoding a binary, rooted phylogenetic tree topology as an integer vector. OLA encoding and decoding take linear time in the number of leaf nodes, and the set of vectors corresponding to trees is a simply-described subset of integer sequences. The OLA encoding is unique compared to other existing encodings in having these properties. The integer vector encoding induces a distance on the set of trees, and we investigate this distance in relation to the NNI and SPR distances. |
| title | Vector encoding of phylogenetic trees by ordered leaf attachment |
| topic | Populations and Evolution Combinatorics 92B10, 05C05, 05C85, 68W40 |
| url | https://arxiv.org/abs/2503.10169 |