HiCP2GAN: A Plug and Play Foundation Model-based GAN for Hi-C Enhancement

Abstract

The three-dimensional organization of chromatin shapes gene regulation and cellular function. Hi-C has emerged as the primary technique for mapping chromatin interactions genome-wide, yet high-resolution data remain costly and scarce, leaving many studies with sparse contact maps that limit downstream analysis. Deep learning methods, especially generative adversarial networks (GANs), have shown promise for enhancing low-resolution Hi-C data. Most existing GAN-based approaches, however, rely on custom discriminators trained from scratch, which can yield unstable training and limited generalization. Hi-C foundation models pretrained on large-scale data capture rich, transferable representations of chromatin structure; their use as discriminators within adversarial enhancement frameworks has not been explored. In this work, we introduce HiCP2GAN, a plug-and-play GAN that employs a pretrained Vision Transformer-based Hi-C foundation model as its discriminator. The discriminator was pretrained on 118 million Hi-C patches across diverse species and cell types, providing biologically meaningful gradients for adversarial supervision. The HiCP2GAN framework is generator-agnostic: any compatible Hi-C resolution enhancement architecture can serve as the generator, enabling fair comparison across methods. The encoder phase of the foundation model was adapted as a discriminator backbone and experimented with finetuning different numbers of layers from the input while freezing the deeper transformer layers. Finetuning the first few layers while freezing the rest preserved pretrained knowledge while allowing task-specific adaptation. Experiments on human cell lines show that HiCP2GAN consistently improves resolution over standalone generators and conventional GAN-based models, while serving as a plug-and-play framework for most non-GAN generator models. HiCP2GAN is publicly available at https://github.com/OluwadareLab/HiCP2GAN.