Fitting trees to $\ell_1$-hyperbolic distances
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arXiv
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| Formato: | Preprint |
| Publicado: |
2024
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| _version_ | 1866914932214202368 |
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| author | Yim, Joon-Hyeok Gilbert, Anna C. |
| author_facet | Yim, Joon-Hyeok Gilbert, Anna C. |
| contents | Building trees to represent or to fit distances is a critical component of phylogenetic analysis, metric embeddings, approximation algorithms, geometric graph neural nets, and the analysis of hierarchical data. Much of the previous algorithmic work, however, has focused on generic metric spaces (i.e., those with no a priori constraints). Leveraging several ideas from the mathematical analysis of hyperbolic geometry and geometric group theory, we study the tree fitting problem as finding the relation between the hyperbolicity (ultrametricity) vector and the error of tree (ultrametric) embedding. That is, we define a vector of hyperbolicity (ultrametric) values over all triples of points and compare the $\ell_p$ norms of this vector with the $\ell_q$ norm of the distortion of the best tree fit to the distances. This formulation allows us to define the average hyperbolicity (ultrametricity) in terms of a normalized $\ell_1$ norm of the hyperbolicity vector. Furthermore, we can interpret the classical tree fitting result of Gromov as a $p = q = \infty$ result. We present an algorithm HCCRootedTreeFit such that the $\ell_1$ error of the output embedding is analytically bounded in terms of the $\ell_1$ norm of the hyperbolicity vector (i.e., $p = q = 1$) and that this result is tight. Furthermore, this algorithm has significantly different theoretical and empirical performance as compared to Gromov's result and related algorithms. Finally, we show using HCCRootedTreeFit and related tree fitting algorithms, that supposedly standard data sets for hierarchical data analysis and geometric graph neural networks have radically different tree fits than those of synthetic, truly tree-like data sets, suggesting that a much more refined analysis of these standard data sets is called for. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2409_01010 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Fitting trees to $\ell_1$-hyperbolic distances Yim, Joon-Hyeok Gilbert, Anna C. Data Structures and Algorithms Machine Learning Metric Geometry Building trees to represent or to fit distances is a critical component of phylogenetic analysis, metric embeddings, approximation algorithms, geometric graph neural nets, and the analysis of hierarchical data. Much of the previous algorithmic work, however, has focused on generic metric spaces (i.e., those with no a priori constraints). Leveraging several ideas from the mathematical analysis of hyperbolic geometry and geometric group theory, we study the tree fitting problem as finding the relation between the hyperbolicity (ultrametricity) vector and the error of tree (ultrametric) embedding. That is, we define a vector of hyperbolicity (ultrametric) values over all triples of points and compare the $\ell_p$ norms of this vector with the $\ell_q$ norm of the distortion of the best tree fit to the distances. This formulation allows us to define the average hyperbolicity (ultrametricity) in terms of a normalized $\ell_1$ norm of the hyperbolicity vector. Furthermore, we can interpret the classical tree fitting result of Gromov as a $p = q = \infty$ result. We present an algorithm HCCRootedTreeFit such that the $\ell_1$ error of the output embedding is analytically bounded in terms of the $\ell_1$ norm of the hyperbolicity vector (i.e., $p = q = 1$) and that this result is tight. Furthermore, this algorithm has significantly different theoretical and empirical performance as compared to Gromov's result and related algorithms. Finally, we show using HCCRootedTreeFit and related tree fitting algorithms, that supposedly standard data sets for hierarchical data analysis and geometric graph neural networks have radically different tree fits than those of synthetic, truly tree-like data sets, suggesting that a much more refined analysis of these standard data sets is called for. |
| title | Fitting trees to $\ell_1$-hyperbolic distances |
| topic | Data Structures and Algorithms Machine Learning Metric Geometry |
| url | https://arxiv.org/abs/2409.01010 |