Contact-Guided 3D Genome Structure Generation of E. coli via Diffusion Transformers
In this study, we present a conditional diffusion-transformer framework for generating ensembles of three-dimensional Escherichia coli genome conformations guided by Hi-C contact maps. Instead of producing a single deterministic structure, we formulate genome reconstruction as a conditional generative modeling problem that samples heterogeneous conformations whose ensemble-averaged contacts are consistent with the input Hi-C data. A synthetic dataset is constructed using coarse-grained molecular dynamics simulations to generate chromatin ensembles and corresponding Hi-C maps under circular topology. Our models operate in a latent diffusion setting with a variational autoencoder that prese...
| Authors | Mingxin Zhang, Xiaofeng Dai, Yu Yao et al. |
|---|---|
| Primary category | cs.LG |
| Published | 8 March 2026 |
| Last updated at source | 8 March 2026 |
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