$\textit{BlockFormer}$ : Transformer-based inference from genomic contact maps
Locating genomic features from genomic contact maps, such as centromere identification from genome-wide chromosome conformation capture techniques, notably Hi-C, can be formulated as an inverse problem: infer one parameter per entity given a map summarizing pairwise interactions through blocks of variable numbers and sizes. In this work, we introduce a data-driven approach that leverages shared structure between these contact maps, such as global alignment between localized patterns, while handling the variability in number and size of chromosomes arising in real-world data. Our approach relies on a transformer architecture capable of handling such variability and a custom simulator to ge...
| Authors | Eloïse Touron, Pedro L. C. Rodrigues, Julyan Arbel et al. |
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| Primary category | cs.LG |
| Published | 20 May 2026 |
| Last updated at source | 30 September 2026 |
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