# HyCoSeq: Contextual Hyperbolic Representation Learning for Genomic Sequences

arXiv: https://arxiv.org/abs/2609.16925 · HTML: https://mlsanity.com/paper/2609.16925/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 9 of its 24 references that are in the map.
- First posted on arXiv 15 Sep 2026.

## Builds on (most cited first, 9 of 9)

- [Poincar'e Embeddings for Learning Hierarchical Representations](https://mlsanity.com/paper/1705.08039/) (2017)
- [Learning Continuous Hierarchies in the Lorentz Model of Hyperbolic Geometry](https://mlsanity.com/paper/1806.03417/) (2018)
- [Representation Tradeoffs for Hyperbolic Embeddings](https://mlsanity.com/paper/1804.03329/) (2018)
- [Riemannian Adaptive Optimization Methods](https://mlsanity.com/paper/1810.00760/) (2018)
- [Geoopt: Riemannian Optimization in PyTorch](https://mlsanity.com/paper/2005.02819/) (2020)
- [Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling](https://mlsanity.com/paper/2403.03234/) (2024)
- [Fully Hyperbolic Convolutional Neural Networks for Computer Vision](https://mlsanity.com/paper/2303.15919/) (2023)
- [Lorentzian Residual Neural Networks](https://mlsanity.com/paper/2412.14695/) (2024)
- [Hyperbolic Genome Embeddings](https://mlsanity.com/paper/2507.21648/) (2025)

## Abstract (arXiv)

Hyperbolic geometry provides a natural inductive bias for genomic representation learning, but existing hyperbolic genomic models primarily use Lorentz convolutions to learn local sequence representations, while their residual pathways do not directly aggregate full Lorentz representations. We propose HyCoSeq, a contextual hyperbolic representation learning framework for genomic sequences. HyCoSeq incorporates weighted Lorentzian residual aggregation into multi-curvature Lorentz encoding, allowing full Lorentz representations to participate directly in geometry-consistent local aggregation. It further introduces a bidirectional long short-term memory network that integrates information from both sequence directions to learn contextual relationships among local representations at different positions within a genomic sequence, thereby extending local hyperbolic convolutional encoding to sequence-level contextualized representations. Extensive experiments across diverse genomic tasks show that HyCoSeq outperforms existing hyperbolic baselines and, without large-scale genomic pretraining, achieves competitive performance against substantially larger pretrained DNA language models.