# Siamese networks for Poincar'e embeddings and the reconstruction of evolutionary trees

arXiv: https://arxiv.org/abs/2410.07387 · HTML: https://mlsanity.com/paper/2410.07387/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 22 of its 52 references that are in the map.
- First posted on arXiv 9 Oct 2024.

## Builds on (most cited first, 22 of 22)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [Deep contextualized word representations](https://mlsanity.com/paper/1802.05365/) (2018)
- [Enriching Word Vectors with Subword Information](https://mlsanity.com/paper/1607.04606/) (2016)
- [Poincar'e Embeddings for Learning Hierarchical Representations](https://mlsanity.com/paper/1705.08039/) (2017)
- [Hyperbolic Graph Convolutional Neural Networks](https://mlsanity.com/paper/1910.12933/) (2019)
- [Hyperbolic Graph Neural Networks](https://mlsanity.com/paper/1910.12892/) (2019)
- [Hyperbolic Image Embeddings](https://mlsanity.com/paper/1904.02239/) (2019)
- [Representation Tradeoffs for Hyperbolic Embeddings](https://mlsanity.com/paper/1804.03329/) (2018)
- [Continuous Hierarchical Representations with Poincar'e Variational Auto-Encoders](https://mlsanity.com/paper/1901.06033/) (2019)
- [Hyperbolic Image Segmentation](https://mlsanity.com/paper/2203.05898/) (2022)
- [Mixed-curvature Variational Autoencoders](https://mlsanity.com/paper/1911.08411/) (2019)
- [Hyperbolic Contrastive Learning for Visual Representations beyond Objects](https://mlsanity.com/paper/2212.00653/) (2022)
- [Clipped Hyperbolic Classifiers Are Super-Hyperbolic Classifiers](https://mlsanity.com/paper/2107.11472/) (2021)
- [Hyperbolic Busemann Learning with Ideal Prototypes](https://mlsanity.com/paper/2106.14472/) (2021)
- [Contrastive Multi-view Hyperbolic Hierarchical Clustering](https://mlsanity.com/paper/2205.02618/) (2022)
- [Hyperbolic Contrastive Learning](https://mlsanity.com/paper/2302.01409/) (2023)
- [Hyperbolic vs Euclidean Embeddings in Few-Shot Learning: Two Sides of the Same Coin](https://mlsanity.com/paper/2309.10013/) (2023)

## Abstract (arXiv)

We present a method for reconstructing evolutionary trees from high-dimensional data, with a specific application to bird song spectrograms. We address the challenge of inferring phylogenetic relationships from phenotypic traits, like vocalizations, without predefined acoustic properties. Our approach combines two main components: Poincar'e embeddings for dimensionality reduction and distance computation, and the neighbor joining algorithm for tree reconstruction. Unlike previous work, we employ Siamese networks to learn embeddings from only leaf node samples of the latent tree. We demonstrate our method's effectiveness on both synthetic data and spectrograms from six species of finches.